Error regarding cnv_somatic_pair_workflow
Hi,
I'm trying to use this workflow on Terra for somatic CNV call using generated PON from normal bams: github.com/broadinstitute/gatk/cnv_somatic_pair_workflow:4.1.7.0
In the config, here are the arguments I used:
common_sites: hg38_v0_exome_calling_regions.v1.interval_list
gatk_docker: "broadinstitute/gatk:4.1.0.0"
intervals: hg38_v0_exome_calling_regions.v1.interval_list
And I think I gave the sample_ID, tumor and control pairs correctly in the config.
The job ran for 90 mins before hitting an error on CollectAllelicCountsTumor step.
And here is the whole log file for the failed CollectAllelicCountsTumor:
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.fac741a4 22:35:07.484 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 22:35:08.291 INFO CollectAllelicCounts - ------------------------------------------------------------ 22:35:08.292 INFO CollectAllelicCounts - The Genome Analysis Toolkit (GATK) v4.1.0.0 22:35:08.292 INFO CollectAllelicCounts - For support and documentation go to https://software.broadinstitute.org/gatk/ 22:35:08.293 INFO CollectAllelicCounts - Executing as root@4b630cf95fa9 on Linux v5.4.89+ amd64 22:35:08.294 INFO CollectAllelicCounts - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_191-8u191-b12-0ubuntu0.16.04.1-b12 22:35:08.294 INFO CollectAllelicCounts - Start Date/Time: March 22, 2021 10:35:07 PM UTC 22:35:08.294 INFO CollectAllelicCounts - ------------------------------------------------------------ 22:35:08.295 INFO CollectAllelicCounts - ------------------------------------------------------------ 22:35:08.296 INFO CollectAllelicCounts - HTSJDK Version: 2.18.2 22:35:08.296 INFO CollectAllelicCounts - Picard Version: 2.18.25 22:35:08.296 INFO CollectAllelicCounts - HTSJDK Defaults.COMPRESSION_LEVEL : 2 22:35:08.297 INFO CollectAllelicCounts - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 22:35:08.297 INFO CollectAllelicCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 22:35:08.298 INFO CollectAllelicCounts - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 22:35:08.298 INFO CollectAllelicCounts - Deflater: IntelDeflater 22:35:08.298 INFO CollectAllelicCounts - Inflater: IntelInflater 22:35:08.299 INFO CollectAllelicCounts - GCS max retries/reopens: 20 22:35:08.299 INFO CollectAllelicCounts - Requester pays: disabled 22:35:08.299 INFO CollectAllelicCounts - Initializing engine 22:35:09.865 INFO IntervalArgumentCollection - Processing 220960836 bp from intervals 22:35:09.933 INFO CollectAllelicCounts - Done initializing engine 22:35:09.942 INFO CollectAllelicCounts - Collecting allelic counts... 22:35:09.942 INFO ProgressMeter - Starting traversal 22:35:09.942 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minute 22:35:14.603 WARN AllelicCountCollector - The reference position at chr1:347832-347832 has an unknown base call (value: N). Skipping... 22:35:14.604 WARN AllelicCountCollector - The reference position at chr1:347833-347833 has an unknown base call (value: N). Skipping... 22:35:14.605 WARN AllelicCountCollector - The reference position at chr1:347834-347834 has an unknown base call (value: N). Skipping... 22:35:14.605 WARN AllelicCountCollector - The reference position at chr1:347835-347835 has an unknown base call (value: N). Skipping... 22:35:14.606 WARN AllelicCountCollector - The reference position at chr1:347836-347836 has an unknown base call (value: N). Skipping... 22:35:14.606 WARN AllelicCountCollector - The reference position at chr1:347837-347837 has an unknown base call (value: N). Skipping... 22:35:14.607 WARN AllelicCountCollector - The reference position at chr1:347838-347838 has an unknown base call (value: N). Skipping... 22:35:14.607 WARN AllelicCountCollector - The reference position at chr1:347839-347839 has an unknown base call (value: N). Skipping... 22:35:14.608 WARN AllelicCountCollector - The reference position at chr1:347840-347840 has an unknown base call (value: N). Skipping... 22:35:14.608 WARN AllelicCountCollector - The reference position at chr1:347841-347841 has an unknown base call (value: N). Skipping... 22:35:14.609 WARN AllelicCountCollector - The reference position at chr1:347842-347842 has an unknown base call (value: N). Skipping... 22:35:14.609 WARN AllelicCountCollector - The reference position at chr1:347843-347843 has an unknown base call (value: N). Skipping... 22:35:14.610 WARN AllelicCountCollector - The reference position at chr1:347844-347844 has an unknown base call (value: N). Skipping... 22:35:14.610 WARN AllelicCountCollector - The reference position at chr1:347845-347845 has an unknown base call (value: N). Skipping... 22:35:14.611 WARN AllelicCountCollector - The reference position at chr1:347846-347846 has an unknown base call (value: N). Skipping... 22:35:14.611 WARN AllelicCountCollector - The reference position at chr1:347847-347847 has an unknown base call (value: N). Skipping... 22:35:14.612 WARN AllelicCountCollector - The reference position at chr1:347848-347848 has an unknown base call (value: N). Skipping... 22:35:14.612 WARN AllelicCountCollector - The reference position at chr1:347849-347849 has an unknown base call (value: N). Skipping... 22:35:14.613 WARN AllelicCountCollector - The reference position at chr1:347850-347850 has an unknown base call (value: N). Skipping... 22:35:14.613 WARN AllelicCountCollector - The reference position at chr1:347851-347851 has an unknown base call (value: N). Skipping... 22:35:14.614 WARN AllelicCountCollector - The reference position at chr1:347852-347852 has an unknown base call (value: N). Skipping... 22:35:14.614 WARN AllelicCountCollector - The reference position at chr1:347853-347853 has an unknown base call (value: N). Skipping... 22:35:14.615 WARN AllelicCountCollector - The reference position at chr1:347854-347854 has an unknown base call (value: N). Skipping... 22:35:14.615 WARN AllelicCountCollector - The reference position at chr1:347855-347855 has an unknown base call (value: N). Skipping... 22:35:14.616 WARN AllelicCountCollector - The reference position at chr1:347856-347856 has an unknown base call (value: N). Skipping... 22:35:14.616 WARN AllelicCountCollector - The reference position at chr1:347857-347857 has an unknown base call (value: N). Skipping... 22:35:14.617 WARN AllelicCountCollector - The reference position at chr1:347858-347858 has an unknown base call (value: N). Skipping... 22:35:14.617 WARN AllelicCountCollector - The reference position at chr1:347859-347859 has an unknown base call (value: N). Skipping... 22:35:14.618 WARN AllelicCountCollector - The reference position at chr1:347860-347860 has an unknown base call (value: N). Skipping... 22:35:14.618 WARN AllelicCountCollector - The reference position at chr1:347861-347861 has an unknown base call (value: N). Skipping... 22:35:14.618 WARN AllelicCountCollector - The reference position at chr1:347862-347862 has an unknown base call (value: N). Skipping... 22:35:14.619 WARN AllelicCountCollector - The reference position at chr1:347863-347863 has an unknown base call (value: N). Skipping... 22:35:14.619 WARN AllelicCountCollector - The reference position at chr1:347864-347864 has an unknown base call (value: N). Skipping... 22:35:14.620 WARN AllelicCountCollector - The reference position at chr1:347865-347865 has an unknown base call (value: N). Skipping... 22:35:14.620 WARN AllelicCountCollector - The reference position at chr1:347866-347866 has an unknown base call (value: N). Skipping... 22:35:14.621 WARN AllelicCountCollector - The reference position at chr1:347867-347867 has an unknown base call (value: N). Skipping... 22:35:14.621 WARN AllelicCountCollector - The reference position at chr1:347868-347868 has an unknown base call (value: N). Skipping... 22:35:14.622 WARN AllelicCountCollector - The reference position at chr1:347869-347869 has an unknown base call (value: N). Skipping... 22:35:14.622 WARN AllelicCountCollector - The reference position at chr1:347870-347870 has an unknown base call (value: N). Skipping... 22:35:14.623 WARN AllelicCountCollector - The reference position at chr1:347871-347871 has an unknown base call (value: N). Skipping... 22:35:14.623 WARN AllelicCountCollector - The reference position at chr1:347872-347872 has an unknown base call (value: N). Skipping... 22:35:14.624 WARN AllelicCountCollector - The reference position at chr1:347873-347873 has an unknown base call (value: N). Skipping... 22:35:14.624 WARN AllelicCountCollector - The reference position at chr1:347874-347874 has an unknown base call (value: N). Skipping... 22:35:14.625 WARN AllelicCountCollector - The reference position at chr1:347875-347875 has an unknown base call (value: N). Skipping... 22:35:14.625 WARN AllelicCountCollector - The reference position at chr1:347876-347876 has an unknown base call (value: N). Skipping... 22:35:14.626 WARN AllelicCountCollector - The reference position at chr1:347877-347877 has an unknown base call (value: N). Skipping... 22:35:14.626 WARN AllelicCountCollector - The reference position at chr1:347878-347878 has an unknown base call (value: N). Skipping... 22:35:14.627 WARN AllelicCountCollector - The reference position at chr1:347879-347879 has an unknown base call (value: N). Skipping... 22:35:14.627 WARN AllelicCountCollector - The reference position at chr1:347880-347880 has an unknown base call (value: N). Skipping... 22:35:14.628 WARN AllelicCountCollector - The reference position at chr1:347881-347881 has an unknown base call (value: N). Skipping... 22:35:14.628 WARN AllelicCountCollector - The reference position at chr1:347882-347882 has an unknown base call (value: N). Skipping... 22:35:14.629 WARN AllelicCountCollector - The reference position at chr1:347883-347883 has an unknown base call (value: N). Skipping... 22:35:14.629 WARN AllelicCountCollector - The reference position at chr1:347884-347884 has an unknown base call (value: N). Skipping... 22:35:14.629 WARN AllelicCountCollector - The reference position at chr1:347885-347885 has an unknown base call (value: N). Skipping... 22:35:14.630 WARN AllelicCountCollector - The reference position at chr1:347886-347886 has an unknown base call (value: N). Skipping... 22:35:14.630 WARN AllelicCountCollector - The reference position at chr1:347887-347887 has an unknown base call (value: N). Skipping... 22:35:14.631 WARN AllelicCountCollector - The reference position at chr1:347888-347888 has an unknown base call (value: N). Skipping... 22:35:14.631 WARN AllelicCountCollector - The reference position at chr1:347889-347889 has an unknown base call (value: N). Skipping... 22:35:14.632 WARN AllelicCountCollector - The reference position at chr1:347890-347890 has an unknown base call (value: N). Skipping... 22:35:14.632 WARN AllelicCountCollector - The reference position at chr1:347891-347891 has an unknown base call (value: N). Skipping... 22:35:14.633 WARN AllelicCountCollector - The reference position at chr1:347892-347892 has an unknown base call (value: N). Skipping... 22:35:14.633 WARN AllelicCountCollector - The reference position at chr1:347893-347893 has an unknown base call (value: N). Skipping... 22:35:14.634 WARN AllelicCountCollector - The reference position at chr1:347894-347894 has an unknown base call (value: N). Skipping... 22:35:14.634 WARN AllelicCountCollector - The reference position at chr1:347895-347895 has an unknown base call (value: N). Skipping... 22:35:14.635 WARN AllelicCountCollector - The reference position at chr1:347896-347896 has an unknown base call (value: N). Skipping... 22:35:14.635 WARN AllelicCountCollector - The reference position at chr1:347897-347897 has an unknown base call (value: N). Skipping... 22:35:14.636 WARN AllelicCountCollector - The reference position at chr1:347898-347898 has an unknown base call (value: N). Skipping... 22:35:14.636 WARN AllelicCountCollector - The reference position at chr1:347899-347899 has an unknown base call (value: N). Skipping... 22:35:14.637 WARN AllelicCountCollector - The reference position at chr1:347900-347900 has an unknown base call (value: N). Skipping... 22:35:14.637 WARN AllelicCountCollector - The reference position at chr1:347901-347901 has an unknown base call (value: N). Skipping... 22:35:14.637 WARN AllelicCountCollector - The reference position at chr1:347902-347902 has an unknown base call (value: N). Skipping... 22:35:14.638 WARN AllelicCountCollector - The reference position at chr1:347903-347903 has an unknown base call (value: N). Skipping... 22:35:14.638 WARN AllelicCountCollector - The reference position at chr1:347904-347904 has an unknown base call (value: N). Skipping... 22:35:14.639 WARN AllelicCountCollector - The reference position at chr1:347905-347905 has an unknown base call (value: N). Skipping... 22:35:14.639 WARN AllelicCountCollector - The reference position at chr1:347906-347906 has an unknown base call (value: N). Skipping... 22:35:14.640 WARN AllelicCountCollector - The reference position at chr1:347907-347907 has an unknown base call (value: N). Skipping... 22:35:14.640 WARN AllelicCountCollector - The reference position at chr1:347908-347908 has an unknown base call (value: N). Skipping... 22:35:14.641 WARN AllelicCountCollector - The reference position at chr1:347909-347909 has an unknown base call (value: N). Skipping... 22:35:14.641 WARN AllelicCountCollector - The reference position at chr1:347910-347910 has an unknown base call (value: N). Skipping... 22:35:14.641 WARN AllelicCountCollector - The reference position at chr1:347911-347911 has an unknown base call (value: N). Skipping... 22:35:14.642 WARN AllelicCountCollector - The reference position at chr1:347912-347912 has an unknown base call (value: N). Skipping... 22:35:14.642 WARN AllelicCountCollector - The reference position at chr1:347913-347913 has an unknown base call (value: N). Skipping... 22:35:14.643 WARN AllelicCountCollector - The reference position at chr1:347914-347914 has an unknown base call (value: N). Skipping... 22:35:14.643 WARN AllelicCountCollector - The reference position at chr1:347915-347915 has an unknown base call (value: N). Skipping... 22:35:14.644 WARN AllelicCountCollector - The reference position at chr1:347916-347916 has an unknown base call (value: N). Skipping... 22:35:14.644 WARN AllelicCountCollector - The reference position at chr1:347917-347917 has an unknown base call (value: N). Skipping... 22:35:14.645 WARN AllelicCountCollector - The reference position at chr1:347918-347918 has an unknown base call (value: N). Skipping... 22:35:14.645 WARN AllelicCountCollector - The reference position at chr1:347919-347919 has an unknown base call (value: N). Skipping... 22:35:14.646 WARN AllelicCountCollector - The reference position at chr1:347920-347920 has an unknown base call (value: N). Skipping... 22:35:14.646 WARN AllelicCountCollector - The reference position at chr1:347921-347921 has an unknown base call (value: N). Skipping... 22:35:14.647 WARN AllelicCountCollector - The reference position at chr1:347922-347922 has an unknown base call (value: N). Skipping... 22:35:14.647 WARN AllelicCountCollector - The reference position at chr1:347923-347923 has an unknown base call (value: N). Skipping... 22:35:14.648 WARN AllelicCountCollector - The reference position at chr1:347924-347924 has an unknown base call (value: N). Skipping... 22:35:14.648 WARN AllelicCountCollector - The reference position at chr1:347925-347925 has an unknown base call (value: N). Skipping... 22:35:14.649 WARN AllelicCountCollector - The reference position at chr1:347926-347926 has an unknown base call (value: N). Skipping... 22:35:14.649 WARN AllelicCountCollector - The reference position at chr1:347927-347927 has an unknown base call (value: N). Skipping... 22:35:14.650 WARN AllelicCountCollector - The reference position at chr1:347928-347928 has an unknown base call (value: N). Skipping... 22:35:14.650 WARN AllelicCountCollector - The reference position at chr1:347929-347929 has an unknown base call (value: N). Skipping... 22:35:14.651 WARN AllelicCountCollector - The reference position at chr1:347930-347930 has an unknown base call (value: N). Skipping... 22:35:14.651 WARN AllelicCountCollector - The reference position at chr1:347931-347931 has an unknown base call (value: N). Skipping... 22:35:14.652 WARN AllelicCountCollector - The reference position at chr1:347932-347932 has an unknown base call (value: N). Skipping... 22:35:14.652 WARN AllelicCountCollector - The reference position at chr1:347933-347933 has an unknown base call (value: N). Skipping... 22:35:14.652 WARN AllelicCountCollector - The reference position at chr1:347934-347934 has an unknown base call (value: N). Skipping... 22:35:14.653 WARN AllelicCountCollector - The reference position at chr1:347935-347935 has an unknown base call (value: N). Skipping... 22:35:14.653 WARN AllelicCountCollector - The reference position at chr1:347936-347936 has an unknown base call (value: N). Skipping... 22:35:14.654 WARN AllelicCountCollector - The reference position at chr1:347937-347937 has an unknown base call (value: N). Skipping... 22:35:14.654 WARN AllelicCountCollector - The reference position at chr1:347938-347938 has an unknown base call (value: N). Skipping... 22:35:14.655 WARN AllelicCountCollector - The reference position at chr1:347939-347939 has an unknown base call (value: N). Skipping... 22:35:14.655 WARN AllelicCountCollector - The reference position at chr1:347940-347940 has an unknown base call (value: N). Skipping... 22:35:14.656 WARN AllelicCountCollector - The reference position at chr1:347941-347941 has an unknown base call (value: N). Skipping... 22:35:14.656 WARN AllelicCountCollector - The reference position at chr1:347942-347942 has an unknown base call (value: N). Skipping... 22:35:14.656 WARN AllelicCountCollector - The reference position at chr1:347943-347943 has an unknown base call (value: N). Skipping... 22:35:14.657 WARN AllelicCountCollector - The reference position at chr1:347944-347944 has an unknown base call (value: N). Skipping... 22:35:14.657 WARN AllelicCountCollector - The reference position at chr1:347945-347945 has an unknown base call (value: N). Skipping... 22:35:14.658 WARN AllelicCountCollector - The reference position at chr1:347946-347946 has an unknown base call (value: N). Skipping... 22:35:14.658 WARN AllelicCountCollector - The reference position at chr1:347947-347947 has an unknown base call (value: N). Skipping... 22:35:14.659 WARN AllelicCountCollector - The reference position at chr1:347948-347948 has an unknown base call (value: N). Skipping... 22:35:14.660 WARN AllelicCountCollector - The reference position at chr1:347949-347949 has an unknown base call (value: N). Skipping... 22:35:14.660 WARN AllelicCountCollector - The reference position at chr1:347950-347950 has an unknown base call (value: N). Skipping... 22:35:14.661 WARN AllelicCountCollector - The reference position at chr1:347951-347951 has an unknown base call (value: N). Skipping... 22:35:14.661 WARN AllelicCountCollector - The reference position at chr1:347952-347952 has an unknown base call (value: N). Skipping... 22:35:14.662 WARN AllelicCountCollector - The reference position at chr1:347953-347953 has an unknown base call (value: N). Skipping... 22:35:14.662 WARN AllelicCountCollector - The reference position at chr1:347954-347954 has an unknown base call (value: N). Skipping... 22:35:14.662 WARN AllelicCountCollector - The reference position at chr1:347955-347955 has an unknown base call (value: N). Skipping... 22:35:14.663 WARN AllelicCountCollector - The reference position at chr1:347956-347956 has an unknown base call (value: N). Skipping... 22:35:14.663 WARN AllelicCountCollector - The reference position at chr1:347957-347957 has an unknown base call (value: N). Skipping... 22:35:14.664 WARN AllelicCountCollector - The reference position at chr1:347958-347958 has an unknown base call (value: N). Skipping... 22:35:14.664 WARN AllelicCountCollector - The reference position at chr1:347959-347959 has an unknown base call (value: N). Skipping... 22:35:14.665 WARN AllelicCountCollector - The reference position at chr1:347960-347960 has an unknown base call (value: N). Skipping... 22:35:14.665 WARN AllelicCountCollector - The reference position at chr1:347961-347961 has an unknown base call (value: N). Skipping... 22:35:14.666 WARN AllelicCountCollector - The reference position at chr1:347962-347962 has an unknown base call (value: N). Skipping... 22:35:14.666 WARN AllelicCountCollector - The reference position at chr1:347963-347963 has an unknown base call (value: N). Skipping... 22:35:14.667 WARN AllelicCountCollector - The reference position at chr1:347964-347964 has an unknown base call (value: N). Skipping... 22:35:14.667 WARN AllelicCountCollector - The reference position at chr1:347965-347965 has an unknown base call (value: N). Skipping... 22:35:14.668 WARN AllelicCountCollector - The reference position at chr1:347966-347966 has an unknown base call (value: N). Skipping... 22:35:14.668 WARN AllelicCountCollector - The reference position at chr1:347967-347967 has an unknown base call (value: N). Skipping... 22:35:14.669 WARN AllelicCountCollector - The reference position at chr1:347968-347968 has an unknown base call (value: N). Skipping... 22:35:14.759 WARN AllelicCountCollector - The reference position at chr1:585921-585921 has an unknown base call (value: N). Skipping... 22:35:14.760 WARN AllelicCountCollector - The reference position at chr1:585922-585922 has an unknown base call (value: N). Skipping... 22:35:14.760 WARN AllelicCountCollector - The reference position at chr1:585923-585923 has an unknown base call (value: N). Skipping... 22:35:14.761 WARN AllelicCountCollector - The reference position at chr1:585924-585924 has an unknown base call (value: N). Skipping... 22:35:14.761 WARN AllelicCountCollector - The reference position at chr1:585925-585925 has an unknown base call (value: N). Skipping... 22:35:14.762 WARN AllelicCountCollector - The reference position at chr1:585926-585926 has an unknown base call (value: N). Skipping... 22:35:14.762 WARN AllelicCountCollector - The reference position at chr1:585927-585927 has an unknown base call (value: N). Skipping... 22:35:14.763 WARN AllelicCountCollector - The reference position at chr1:585928-585928 has an unknown base call (value: N). Skipping... 22:35:14.763 WARN AllelicCountCollector - The reference position at chr1:585929-585929 has an unknown base call (value: N). Skipping... 22:35:14.764 WARN AllelicCountCollector - The reference position at chr1:585930-585930 has an unknown base call (value: N). Skipping... 22:35:14.764 WARN AllelicCountCollector - The reference position at chr1:585931-585931 has an unknown base call (value: N). Skipping... 22:35:14.765 WARN AllelicCountCollector - The reference position at chr1:585932-585932 has an unknown base call (value: N). Skipping... 22:35:14.765 WARN AllelicCountCollector - The reference position at chr1:585933-585933 has an unknown base call (value: N). Skipping... 22:35:14.766 WARN AllelicCountCollector - The reference position at chr1:585934-585934 has an unknown base call (value: N). Skipping... 22:35:14.766 WARN AllelicCountCollector - The reference position at chr1:585935-585935 has an unknown base call (value: N). Skipping... 22:35:14.767 WARN AllelicCountCollector - The reference position at chr1:585936-585936 has an unknown base call (value: N). Skipping... 22:35:14.767 WARN AllelicCountCollector - The reference position at chr1:585937-585937 has an unknown base call (value: N). Skipping... 22:35:14.768 WARN AllelicCountCollector - The reference position at chr1:585938-585938 has an unknown base call (value: N). Skipping... 22:35:14.768 WARN AllelicCountCollector - The reference position at chr1:585939-585939 has an unknown base call (value: N). Skipping... 22:35:14.769 WARN AllelicCountCollector - The reference position at chr1:585940-585940 has an unknown base call (value: N). Skipping... 22:35:14.769 WARN AllelicCountCollector - The reference position at chr1:585941-585941 has an unknown base call (value: N). Skipping... 22:35:14.769 WARN AllelicCountCollector - The reference position at chr1:585942-585942 has an unknown base call (value: N). Skipping... 22:35:14.770 WARN AllelicCountCollector - The reference position at chr1:585943-585943 has an unknown base call (value: N). Skipping... 22:35:14.770 WARN AllelicCountCollector - The reference position at chr1:585944-585944 has an unknown base call (value: N). Skipping... 22:35:14.771 WARN AllelicCountCollector - The reference position at chr1:585945-585945 has an unknown base call (value: N). Skipping... 22:35:14.771 WARN AllelicCountCollector - The reference position at chr1:585946-585946 has an unknown base call (value: N). Skipping... 22:35:14.772 WARN AllelicCountCollector - The reference position at chr1:585947-585947 has an unknown base call (value: N). Skipping... 22:35:14.772 WARN AllelicCountCollector - The reference position at chr1:585948-585948 has an unknown base call (value: N). Skipping... 22:35:14.773 WARN AllelicCountCollector - The reference position at chr1:585949-585949 has an unknown base call (value: N). Skipping... 22:35:14.773 WARN AllelicCountCollector - The reference position at chr1:585950-585950 has an unknown base call (value: N). Skipping... 22:35:14.774 WARN AllelicCountCollector - The reference position at chr1:585951-585951 has an unknown base call (value: N). Skipping... 22:35:14.774 WARN AllelicCountCollector - The reference position at chr1:585952-585952 has an unknown base call (value: N). Skipping... 22:35:14.775 WARN AllelicCountCollector - The reference position at chr1:585953-585953 has an unknown base call (value: N). Skipping... 22:35:14.775 WARN AllelicCountCollector - The reference position at chr1:585954-585954 has an unknown base call (value: N). Skipping... 22:35:14.776 WARN AllelicCountCollector - The reference position at chr1:585955-585955 has an unknown base call (value: N). Skipping... 22:35:14.776 WARN AllelicCountCollector - The reference position at chr1:585956-585956 has an unknown base call (value: N). Skipping... 22:35:14.776 WARN AllelicCountCollector - The reference position at chr1:585957-585957 has an unknown base call (value: N). Skipping... 22:35:14.777 WARN AllelicCountCollector - The reference position at chr1:585958-585958 has an unknown base call (value: N). Skipping... 22:35:14.777 WARN AllelicCountCollector - The reference position at chr1:585959-585959 has an unknown base call (value: N). Skipping... 22:35:14.778 WARN AllelicCountCollector - The reference position at chr1:585960-585960 has an unknown base call (value: N). Skipping... 22:35:14.778 WARN AllelicCountCollector - The reference position at chr1:585961-585961 has an unknown base call (value: N). Skipping... 22:35:14.779 WARN AllelicCountCollector - The reference position at chr1:585962-585962 has an unknown base call (value: N). Skipping... 22:35:14.779 WARN AllelicCountCollector - The reference position at chr1:585963-585963 has an unknown base call (value: N). Skipping... 22:35:14.780 WARN AllelicCountCollector - The reference position at chr1:585964-585964 has an unknown base call (value: N). Skipping... 22:35:14.780 WARN AllelicCountCollector - The reference position at chr1:585965-585965 has an unknown base call (value: N). Skipping... 22:35:14.781 WARN AllelicCountCollector - The reference position at chr1:585966-585966 has an unknown base call (value: N). Skipping... 22:35:14.781 WARN AllelicCountCollector - The reference position at chr1:585967-585967 has an unknown base call (value: N). Skipping... 22:35:14.782 WARN AllelicCountCollector - The reference position at chr1:585968-585968 has an unknown base call (value: N). Skipping... 22:35:14.782 WARN AllelicCountCollector - The reference position at chr1:585969-585969 has an unknown base call (value: N). Skipping... 22:35:14.782 WARN AllelicCountCollector - The reference position at chr1:585970-585970 has an unknown base call (value: N). Skipping... 22:35:14.783 WARN AllelicCountCollector - The reference position at chr1:585971-585971 has an unknown base call (value: N). Skipping... 22:35:14.784 WARN AllelicCountCollector - The reference position at chr1:585972-585972 has an unknown base call (value: N). Skipping... 22:35:14.784 WARN AllelicCountCollector - The reference position at chr1:585973-585973 has an unknown base call (value: N). Skipping... 22:35:14.785 WARN AllelicCountCollector - The reference position at chr1:585974-585974 has an unknown base call (value: N). Skipping... 22:35:14.785 WARN AllelicCountCollector - The reference position at chr1:585975-585975 has an unknown base call (value: N). Skipping... 22:35:14.786 WARN AllelicCountCollector - The reference position at chr1:585976-585976 has an unknown base call (value: N). Skipping... 22:35:14.786 WARN AllelicCountCollector - The reference position at chr1:585977-585977 has an unknown base call (value: N). Skipping... 22:35:14.787 WARN AllelicCountCollector - The reference position at chr1:585978-585978 has an unknown base call (value: N). Skipping... 22:35:14.787 WARN AllelicCountCollector - The reference position at chr1:585979-585979 has an unknown base call (value: N). Skipping... 22:35:14.788 WARN AllelicCountCollector - The reference position at chr1:585980-585980 has an unknown base call (value: N). Skipping... 22:35:14.788 WARN AllelicCountCollector - The reference position at chr1:585981-585981 has an unknown base call (value: N). Skipping... 22:35:14.788 WARN AllelicCountCollector - The reference position at chr1:585982-585982 has an unknown base call (value: N). Skipping... 22:35:14.789 WARN AllelicCountCollector - The reference position at chr1:585983-585983 has an unknown base call (value: N). Skipping... 22:35:14.789 WARN AllelicCountCollector - The reference position at chr1:585984-585984 has an unknown base call (value: N). Skipping... 22:35:14.790 WARN AllelicCountCollector - The reference position at chr1:585985-585985 has an unknown base call (value: N). Skipping... 22:35:14.790 WARN AllelicCountCollector - The reference position at chr1:585986-585986 has an unknown base call (value: N). Skipping... 22:35:14.791 WARN AllelicCountCollector - The reference position at chr1:585987-585987 has an unknown base call (value: N). Skipping... 22:35:14.791 WARN AllelicCountCollector - The reference position at chr1:585988-585988 has an unknown base call (value: N). Skipping... 22:35:19.960 INFO ProgressMeter - chr1:1312610 0.2 296000 1775112.4 22:35:29.953 INFO ProgressMeter - chr1:8364242 0.3 1201000 3601199.4 22:35:39.962 INFO ProgressMeter - chr1:16027406 0.5 2356000 4709017.6 22:35:49.991 INFO ProgressMeter - chr1:22586386 0.7 3201000 4795745.1 22:35:59.995 INFO ProgressMeter - chr1:29325083 0.8 4181000 5011987.5 22:36:09.999 INFO ProgressMeter - chr1:40541479 1.0 5485000 5479885.4 22:36:19.999 INFO ProgressMeter - chr1:47333967 1.2 6408000 5488180.9 22:36:30.001 INFO ProgressMeter - chr1:63325237 1.3 7609000 5702686.8 22:36:40.057 INFO ProgressMeter - chr1:109251161 1.5 10195000 6788143.8 22:36:50.056 INFO ProgressMeter - chr1:121388143 1.7 11540000 6916184.7 22:37:00.059 INFO ProgressMeter - chr1:148541008 1.8 12224000 6660612.4 22:37:10.417 INFO ProgressMeter - chr1:152215695 2.0 12954000 6451516.5 22:37:20.468 INFO ProgressMeter - chr1:153777302 2.2 13157000 6048036.8 22:37:30.474 INFO ProgressMeter - chr1:156585665 2.3 13843000 5910339.4 22:37:40.476 INFO ProgressMeter - chr1:168088192 2.5 15173000 6047710.5 22:37:50.484 INFO ProgressMeter - chr1:189777112 2.7 16758000 6263073.0 22:38:00.498 INFO ProgressMeter - chr1:206484856 2.8 18099000 6367095.7 22:38:10.500 INFO ProgressMeter - chr1:217737874 3.0 18941000 6294189.6 22:38:17.531 WARN AllelicCountCollector - The reference position at chr1:228558365-228558365 has an unknown base call (value: N). Skipping... 22:38:17.531 WARN AllelicCountCollector - The reference position at chr1:228558366-228558366 has an unknown base call (value: N). Skipping... 22:38:17.531 WARN AllelicCountCollector - The reference position at chr1:228558367-228558367 has an unknown base call (value: N). Skipping... 22:38:17.532 WARN AllelicCountCollector - The reference position at chr1:228558368-228558368 has an unknown base call (value: N). Skipping... 22:38:17.532 WARN AllelicCountCollector - The reference position at chr1:228558369-228558369 has an unknown base call (value: N). Skipping... 22:38:17.533 WARN AllelicCountCollector - The reference position at chr1:228558370-228558370 has an unknown base call (value: N). Skipping... 22:38:17.533 WARN AllelicCountCollector - The reference position at chr1:228558371-228558371 has an unknown base call (value: N). Skipping... 22:38:17.534 WARN AllelicCountCollector - The reference position at chr1:228558372-228558372 has an unknown base call (value: N). Skipping... 22:38:17.534 WARN AllelicCountCollector - The reference position at chr1:228558373-228558373 has an unknown base call (value: N). Skipping... 22:38:17.534 WARN AllelicCountCollector - The reference position at chr1:228558374-228558374 has an unknown base call (value: N). Skipping... 22:38:17.535 WARN AllelicCountCollector - The reference position at chr1:228558375-228558375 has an unknown base call (value: N). Skipping... 22:38:17.535 WARN AllelicCountCollector - The reference position at chr1:228558376-228558376 has an unknown base call (value: N). Skipping... 22:38:17.535 WARN AllelicCountCollector - The reference position at chr1:228558377-228558377 has an unknown base call (value: N). Skipping... 22:38:17.536 WARN AllelicCountCollector - The reference position at chr1:228558378-228558378 has an unknown base call (value: N). Skipping... 22:38:17.536 WARN AllelicCountCollector - The reference position at chr1:228558379-228558379 has an unknown base call (value: N). Skipping... 22:38:17.536 WARN AllelicCountCollector - The reference position at chr1:228558380-228558380 has an unknown base call (value: N). Skipping... 22:38:17.536 WARN AllelicCountCollector - The reference position at chr1:228558381-228558381 has an unknown base call (value: N). Skipping... 22:38:17.537 WARN AllelicCountCollector - The reference position at chr1:228558382-228558382 has an unknown base call (value: N). Skipping... 22:38:17.537 WARN AllelicCountCollector - The reference position at chr1:228558383-228558383 has an unknown base call (value: N). Skipping... 22:38:17.537 WARN AllelicCountCollector - The reference position at chr1:228558384-228558384 has an unknown base call (value: N). Skipping... 22:38:17.537 WARN AllelicCountCollector - The reference position at chr1:228558385-228558385 has an unknown base call (value: N). Skipping... 22:38:17.537 WARN AllelicCountCollector - The reference position at chr1:228558386-228558386 has an unknown base call (value: N). Skipping... 22:38:17.537 WARN AllelicCountCollector - The reference position at chr1:228558387-228558387 has an unknown base call (value: N). Skipping... 22:38:17.537 WARN AllelicCountCollector - The reference position at chr1:228558388-228558388 has an unknown base call (value: N). Skipping... 22:38:17.537 WARN AllelicCountCollector - The reference position at chr1:228558389-228558389 has an unknown base call (value: N). Skipping... 22:38:17.538 WARN AllelicCountCollector - The reference position at chr1:228558390-228558390 has an unknown base call (value: N). Skipping... 22:38:17.538 WARN AllelicCountCollector - The reference position at chr1:228558391-228558391 has an unknown base call (value: N). Skipping... 22:38:17.538 WARN AllelicCountCollector - The reference position at chr1:228558392-228558392 has an unknown base call (value: N). Skipping... 22:38:17.538 WARN AllelicCountCollector - The reference position at chr1:228558393-228558393 has an unknown base call (value: N). Skipping... 22:38:17.538 WARN AllelicCountCollector - The reference position at chr1:228558394-228558394 has an unknown base call (value: N). Skipping... 22:38:17.538 WARN AllelicCountCollector - The reference position at chr1:228558395-228558395 has an unknown base call (value: N). Skipping... 22:38:17.538 WARN AllelicCountCollector - The reference position at chr1:228558396-228558396 has an unknown base call (value: N). Skipping... 22:38:17.538 WARN AllelicCountCollector - The reference position at chr1:228558397-228558397 has an unknown base call (value: N). Skipping... 22:38:17.539 WARN AllelicCountCollector - The reference position at chr1:228558398-228558398 has an unknown base call (value: N). Skipping... 22:38:17.539 WARN AllelicCountCollector - The reference position at chr1:228558399-228558399 has an unknown base call (value: N). Skipping... 22:38:17.539 WARN AllelicCountCollector - The reference position at chr1:228558400-228558400 has an unknown base call (value: N). Skipping... 22:38:17.539 WARN AllelicCountCollector - The reference position at chr1:228558401-228558401 has an unknown base call (value: N). Skipping... 22:38:17.539 WARN AllelicCountCollector - The reference position at chr1:228558402-228558402 has an unknown base call (value: N). Skipping... 22:38:17.539 WARN AllelicCountCollector - The reference position at chr1:228558403-228558403 has an unknown base call (value: N). Skipping... 22:38:17.539 WARN AllelicCountCollector - The reference position at chr1:228558404-228558404 has an unknown base call (value: N). Skipping... 22:38:17.539 WARN AllelicCountCollector - The reference position at chr1:228558405-228558405 has an unknown base call (value: N). Skipping... 22:38:17.540 WARN AllelicCountCollector - The reference position at chr1:228558406-228558406 has an unknown base call (value: N). Skipping... 22:38:17.540 WARN AllelicCountCollector - The reference position at chr1:228558407-228558407 has an unknown base call (value: N). Skipping... 22:38:17.540 WARN AllelicCountCollector - The reference position at chr1:228558408-228558408 has an unknown base call (value: N). Skipping... 22:38:17.540 WARN AllelicCountCollector - The reference position at chr1:228558409-228558409 has an unknown base call (value: N). Skipping... 22:38:17.540 WARN AllelicCountCollector - The reference position at chr1:228558410-228558410 has an unknown base call (value: N). Skipping... 22:38:17.540 WARN AllelicCountCollector - The reference position at chr1:228558411-228558411 has an unknown base call (value: N). Skipping... 22:38:17.540 WARN AllelicCountCollector - The reference position at chr1:228558412-228558412 has an unknown base call (value: N). Skipping... 22:38:17.541 WARN AllelicCountCollector - The reference position at chr1:228558413-228558413 has an unknown base call (value: N). Skipping... 22:38:17.541 WARN AllelicCountCollector - The reference position at chr1:228558414-228558414 has an unknown base call (value: N). Skipping... 22:38:17.541 WARN AllelicCountCollector - The reference position at chr1:228558415-228558415 has an unknown base call (value: N). Skipping... 22:38:17.541 WARN AllelicCountCollector - The reference position at chr1:228558416-228558416 has an unknown base call (value: N). Skipping... 22:38:17.541 WARN AllelicCountCollector - The reference position at chr1:228558417-228558417 has an unknown base call (value: N). Skipping... 22:38:17.541 WARN AllelicCountCollector - The reference position at chr1:228558418-228558418 has an unknown base call (value: N). Skipping... 22:38:17.541 WARN AllelicCountCollector - The reference position at chr1:228558419-228558419 has an unknown base call (value: N). Skipping... 22:38:17.541 WARN AllelicCountCollector - The reference position at chr1:228558420-228558420 has an unknown base call (value: N). Skipping... 22:38:17.541 WARN AllelicCountCollector - The reference position at chr1:228558421-228558421 has an unknown base call (value: N). Skipping... 22:38:17.541 WARN AllelicCountCollector - The reference position at chr1:228558422-228558422 has an unknown base call (value: N). Skipping... 22:38:17.541 WARN AllelicCountCollector - The reference position at chr1:228558423-228558423 has an unknown base call (value: N). Skipping... 22:38:17.541 WARN AllelicCountCollector - The reference position at chr1:228558424-228558424 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558425-228558425 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558426-228558426 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558427-228558427 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558428-228558428 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558429-228558429 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558430-228558430 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558431-228558431 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558432-228558432 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558433-228558433 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558434-228558434 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558435-228558435 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558436-228558436 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558437-228558437 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558438-228558438 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558439-228558439 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558440-228558440 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558441-228558441 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558442-228558442 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558443-228558443 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558444-228558444 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558445-228558445 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558446-228558446 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558447-228558447 has an unknown base call (value: N). Skipping... 22:38:17.542 WARN AllelicCountCollector - The reference position at chr1:228558448-228558448 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558449-228558449 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558450-228558450 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558451-228558451 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558452-228558452 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558453-228558453 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558454-228558454 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558455-228558455 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558456-228558456 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558457-228558457 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558458-228558458 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558459-228558459 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558460-228558460 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558461-228558461 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558462-228558462 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558463-228558463 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558464-228558464 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558465-228558465 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558466-228558466 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558467-228558467 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558468-228558468 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558469-228558469 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558470-228558470 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558471-228558471 has an unknown base call (value: N). Skipping... 22:38:17.543 WARN AllelicCountCollector - The reference position at chr1:228558472-228558472 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558473-228558473 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558474-228558474 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558475-228558475 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558476-228558476 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558477-228558477 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558478-228558478 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558479-228558479 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558480-228558480 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558481-228558481 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558482-228558482 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558483-228558483 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558484-228558484 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558485-228558485 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558486-228558486 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558487-228558487 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558488-228558488 has an unknown base call (value: N). Skipping... 22:38:17.544 WARN AllelicCountCollector - The reference position at chr1:228558489-228558489 has an unknown base call (value: N). Skipping... 22:38:20.501 INFO ProgressMeter - chr1:235551634 3.2 20375000 6415369.6 22:38:26.880 WARN AllelicCountCollector - The reference position at chr1:248755122-248755122 has an unknown base call (value: N). Skipping... 22:38:30.502 INFO ProgressMeter - chr2:9318475 3.3 21832000 6531344.9 22:38:40.510 INFO ProgressMeter - chr2:27311367 3.5 23062000 6571431.3 22:38:50.545 INFO ProgressMeter - chr2:42763794 3.7 24192000 6579813.4 22:39:00.558 INFO ProgressMeter - chr2:68129982 3.8 25662000 6676582.2 22:39:10.559 INFO ProgressMeter - chr2:85540074 4.0 26791000 6680603.1 22:39:25.295 INFO ProgressMeter - chr2:96278079 4.3 27564000 6476732.0 22:39:35.296 INFO ProgressMeter - chr2:109915813 4.4 28662000 6480900.8 22:39:45.302 INFO ProgressMeter - chr2:130743535 4.6 29998000 6536485.1 22:39:55.303 INFO ProgressMeter - chr2:160100345 4.8 31399000 6601976.5 22:40:05.307 INFO ProgressMeter - chr2:178678927 4.9 32874000 6677997.3 22:40:15.319 INFO ProgressMeter - chr2:206756818 5.1 34763000 6830225.1 22:40:28.935 INFO ProgressMeter - chr2:218262969 5.3 35462000 6670135.9 22:40:38.935 INFO ProgressMeter - chr2:227815487 5.5 36240000 6609279.3 22:40:48.939 INFO ProgressMeter - chr2:240042802 5.6 37249000 6592821.2 22:40:58.951 INFO ProgressMeter - chr3:9835197 5.8 38105000 6550852.7 22:41:09.037 INFO ProgressMeter - chr3:31182073 6.0 39322000 6570220.0 22:41:19.040 INFO ProgressMeter - chr3:44658728 6.2 40430000 6572256.1 22:41:29.550 INFO ProgressMeter - chr3:49076718 6.3 41154000 6504727.3 22:41:39.552 INFO ProgressMeter - chr3:51962123 6.5 41683000 6419221.4 22:41:49.554 INFO ProgressMeter - chr3:64607076 6.7 42696000 6410634.3 22:41:59.815 INFO ProgressMeter - chr3:108399261 6.8 44041000 6447037.1 22:42:09.820 INFO ProgressMeter - chr3:125756095 7.0 45357000 6481469.6 22:42:19.820 INFO ProgressMeter - chr3:139124845 7.2 46543000 6496230.3 22:42:39.522 INFO ProgressMeter - chr3:158298061 7.5 47676000 6362752.7 22:42:49.522 INFO ProgressMeter - chr3:185193041 7.7 49189000 6421833.9 22:42:59.922 INFO ProgressMeter - chr3:195784952 7.8 49980000 6380710.6 22:43:14.358 INFO ProgressMeter - chr3:196218044 8.1 50057000 6200109.8 22:43:24.362 INFO ProgressMeter - chr4:2829815 8.2 50833000 6168816.3 22:43:34.314 WARN AllelicCountCollector - The reference position at chr4:9272917-9272917 has an unknown base call (value: N). Skipping... 22:43:34.314 WARN AllelicCountCollector - The reference position at chr4:9272918-9272918 has an unknown base call (value: N). Skipping... 22:43:34.314 WARN AllelicCountCollector - The reference position at chr4:9272919-9272919 has an unknown base call (value: N). Skipping... 22:43:34.314 WARN AllelicCountCollector - The reference position at chr4:9272920-9272920 has an unknown base call (value: N). Skipping... 22:43:34.314 WARN AllelicCountCollector - The reference position at chr4:9272921-9272921 has an unknown base call (value: N). Skipping... 22:43:34.314 WARN AllelicCountCollector - The reference position at chr4:9272922-9272922 has an unknown base call (value: N). Skipping... 22:43:34.314 WARN AllelicCountCollector - The reference position at chr4:9272923-9272923 has an unknown base call (value: N). Skipping... 22:43:34.315 WARN AllelicCountCollector - The reference position at chr4:9272924-9272924 has an unknown base call (value: N). Skipping... 22:43:34.315 WARN AllelicCountCollector - The reference position at chr4:9272925-9272925 has an unknown base call (value: N). Skipping... 22:43:34.315 WARN AllelicCountCollector - The reference position at chr4:9272926-9272926 has an unknown base call (value: N). Skipping... 22:43:34.315 WARN AllelicCountCollector - The reference position at chr4:9272927-9272927 has an unknown base call (value: N). Skipping... 22:43:34.315 WARN AllelicCountCollector - The reference position at chr4:9272928-9272928 has an unknown base call (value: N). Skipping... 22:43:34.316 WARN AllelicCountCollector - The reference position at chr4:9272929-9272929 has an unknown base call (value: N). Skipping... 22:43:34.316 WARN AllelicCountCollector - The reference position at chr4:9272930-9272930 has an unknown base call (value: N). Skipping... 22:43:34.316 WARN AllelicCountCollector - The reference position at chr4:9272931-9272931 has an unknown base call (value: N). Skipping... 22:43:34.316 WARN AllelicCountCollector - The reference position at chr4:9272932-9272932 has an unknown base call (value: N). Skipping... 22:43:34.316 WARN AllelicCountCollector - The reference position at chr4:9272933-9272933 has an unknown base call (value: N). Skipping... 22:43:34.317 WARN AllelicCountCollector - The reference position at chr4:9272934-9272934 has an unknown base call (value: N). Skipping... 22:43:34.317 WARN AllelicCountCollector - The reference position at chr4:9272935-9272935 has an unknown base call (value: N). Skipping... 22:43:34.317 WARN AllelicCountCollector - The reference position at chr4:9272936-9272936 has an unknown base call (value: N). Skipping... 22:43:34.317 WARN AllelicCountCollector - The reference position at chr4:9272937-9272937 has an unknown base call (value: N). Skipping... 22:43:34.317 WARN AllelicCountCollector - The reference position at chr4:9272938-9272938 has an unknown base call (value: N). Skipping... 22:43:34.317 WARN AllelicCountCollector - The reference position at chr4:9272939-9272939 has an unknown base call (value: N). Skipping... 22:43:34.317 WARN AllelicCountCollector - The reference position at chr4:9272940-9272940 has an unknown base call (value: N). Skipping... 22:43:34.317 WARN AllelicCountCollector - The reference position at chr4:9272941-9272941 has an unknown base call (value: N). Skipping... 22:43:34.318 WARN AllelicCountCollector - The reference position at chr4:9272942-9272942 has an unknown base call (value: N). Skipping... 22:43:34.318 WARN AllelicCountCollector - The reference position at chr4:9272943-9272943 has an unknown base call (value: N). Skipping... 22:43:34.318 WARN AllelicCountCollector - The reference position at chr4:9272944-9272944 has an unknown base call (value: N). Skipping... 22:43:34.318 WARN AllelicCountCollector - The reference position at chr4:9272945-9272945 has an unknown base call (value: N). Skipping... 22:43:34.318 WARN AllelicCountCollector - The reference position at chr4:9272946-9272946 has an unknown base call (value: N). Skipping... 22:43:34.318 WARN AllelicCountCollector - The reference position at chr4:9272947-9272947 has an unknown base call (value: N). Skipping... 22:43:34.318 WARN AllelicCountCollector - The reference position at chr4:9272948-9272948 has an unknown base call (value: N). Skipping... 22:43:34.318 WARN AllelicCountCollector - The reference position at chr4:9272949-9272949 has an unknown base call (value: N). Skipping... 22:43:34.318 WARN AllelicCountCollector - The reference position at chr4:9272950-9272950 has an unknown base call (value: N). Skipping... 22:43:34.318 WARN AllelicCountCollector - The reference position at chr4:9272951-9272951 has an unknown base call (value: N). Skipping... 22:43:34.319 WARN AllelicCountCollector - The reference position at chr4:9272952-9272952 has an unknown base call (value: N). Skipping... 22:43:34.319 WARN AllelicCountCollector - The reference position at chr4:9272953-9272953 has an unknown base call (value: N). Skipping... 22:43:34.319 WARN AllelicCountCollector - The reference position at chr4:9272954-9272954 has an unknown base call (value: N). Skipping... 22:43:34.319 WARN AllelicCountCollector - The reference position at chr4:9272955-9272955 has an unknown base call (value: N). Skipping... 22:43:34.319 WARN AllelicCountCollector - The reference position at chr4:9272956-9272956 has an unknown base call (value: N). Skipping... 22:43:34.319 WARN AllelicCountCollector - The reference position at chr4:9272957-9272957 has an unknown base call (value: N). Skipping... 22:43:34.319 WARN AllelicCountCollector - The reference position at chr4:9272958-9272958 has an unknown base call (value: N). Skipping... 22:43:34.319 WARN AllelicCountCollector - The reference position at chr4:9272959-9272959 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272960-9272960 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272961-9272961 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272962-9272962 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272963-9272963 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272964-9272964 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272965-9272965 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272966-9272966 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272967-9272967 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272968-9272968 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272969-9272969 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272970-9272970 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272971-9272971 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272972-9272972 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272973-9272973 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272974-9272974 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272975-9272975 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272976-9272976 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272977-9272977 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272978-9272978 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272979-9272979 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272980-9272980 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272981-9272981 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272982-9272982 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272983-9272983 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272984-9272984 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272985-9272985 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272986-9272986 has an unknown base call (value: N). Skipping... 22:43:34.320 WARN AllelicCountCollector - The reference position at chr4:9272987-9272987 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9272988-9272988 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9272989-9272989 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9272990-9272990 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9272991-9272991 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9272992-9272992 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9272993-9272993 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9272994-9272994 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9272995-9272995 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9272996-9272996 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9272997-9272997 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9272998-9272998 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9272999-9272999 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273000-9273000 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273001-9273001 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273002-9273002 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273003-9273003 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273004-9273004 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273005-9273005 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273006-9273006 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273007-9273007 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273008-9273008 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273009-9273009 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273010-9273010 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273011-9273011 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273012-9273012 has an unknown base call (value: N). Skipping... 22:43:34.321 WARN AllelicCountCollector - The reference position at chr4:9273013-9273013 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273014-9273014 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273015-9273015 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273016-9273016 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273017-9273017 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273018-9273018 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273019-9273019 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273020-9273020 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273021-9273021 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273022-9273022 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273023-9273023 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273024-9273024 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273025-9273025 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273026-9273026 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273027-9273027 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273028-9273028 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273029-9273029 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273030-9273030 has an unknown base call (value: N). Skipping... 22:43:34.322 WARN AllelicCountCollector - The reference position at chr4:9273031-9273031 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273032-9273032 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273033-9273033 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273034-9273034 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273035-9273035 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273036-9273036 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273037-9273037 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273038-9273038 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273039-9273039 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273040-9273040 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273041-9273041 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273042-9273042 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273043-9273043 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273044-9273044 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273045-9273045 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273046-9273046 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273047-9273047 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273048-9273048 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273049-9273049 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273050-9273050 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273051-9273051 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273052-9273052 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273053-9273053 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273054-9273054 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273055-9273055 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273056-9273056 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273057-9273057 has an unknown base call (value: N). Skipping... 22:43:34.323 WARN AllelicCountCollector - The reference position at chr4:9273058-9273058 has an unknown base call (value: N). Skipping... 22:43:34.324 WARN AllelicCountCollector - The reference position at chr4:9273059-9273059 has an unknown base call (value: N). Skipping... 22:43:34.324 WARN AllelicCountCollector - The reference position at chr4:9273060-9273060 has an unknown base call (value: N). Skipping... 22:43:34.324 WARN AllelicCountCollector - The reference position at chr4:9273061-9273061 has an unknown base call (value: N). Skipping... 22:43:34.324 WARN AllelicCountCollector - The reference position at chr4:9273062-9273062 has an unknown base call (value: N). Skipping... 22:43:34.324 WARN AllelicCountCollector - The reference position at chr4:9273063-9273063 has an unknown base call (value: N). Skipping... 22:43:34.324 WARN AllelicCountCollector - The reference position at chr4:9273064-9273064 has an unknown base call (value: N). Skipping... 22:43:34.603 INFO ProgressMeter - chr4:9384090 8.4 51497000 6122577.6 22:43:44.605 INFO ProgressMeter - chr4:48170322 8.6 53054000 6185107.9 22:43:45.191 WARN AllelicCountCollector - The reference position at chr4:49486776-49486776 has an unknown base call (value: N). Skipping... 22:43:45.191 WARN AllelicCountCollector - The reference position at chr4:49486777-49486777 has an unknown base call (value: N). Skipping... 22:43:45.192 WARN AllelicCountCollector - The reference position at chr4:49486778-49486778 has an unknown base call (value: N). Skipping... 22:43:45.192 WARN AllelicCountCollector - The reference position at chr4:49486779-49486779 has an unknown base call (value: N). Skipping... 22:43:45.192 WARN AllelicCountCollector - The reference position at chr4:49486780-49486780 has an unknown base call (value: N). Skipping... 22:43:45.192 WARN AllelicCountCollector - The reference position at chr4:49486781-49486781 has an unknown base call (value: N). Skipping... 22:43:45.193 WARN AllelicCountCollector - The reference position at chr4:49486782-49486782 has an unknown base call (value: N). Skipping... 22:43:45.193 WARN AllelicCountCollector - The reference position at chr4:49486783-49486783 has an unknown base call (value: N). Skipping... 22:43:45.193 WARN AllelicCountCollector - The reference position at chr4:49486784-49486784 has an unknown base call (value: N). Skipping... 22:43:45.193 WARN AllelicCountCollector - The reference position at chr4:49486785-49486785 has an unknown base call (value: N). Skipping... 22:43:45.193 WARN AllelicCountCollector - The reference position at chr4:49486786-49486786 has an unknown base call (value: N). Skipping... 22:43:45.193 WARN AllelicCountCollector - The reference position at chr4:49486787-49486787 has an unknown base call (value: N). Skipping... 22:43:45.193 WARN AllelicCountCollector - The reference position at chr4:49486788-49486788 has an unknown base call (value: N). Skipping... 22:43:45.193 WARN AllelicCountCollector - The reference position at chr4:49486789-49486789 has an unknown base call (value: N). Skipping... 22:43:45.193 WARN AllelicCountCollector - The reference position at chr4:49486790-49486790 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486791-49486791 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486792-49486792 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486793-49486793 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486794-49486794 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486795-49486795 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486796-49486796 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486797-49486797 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486798-49486798 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486799-49486799 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486800-49486800 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486801-49486801 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486802-49486802 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486803-49486803 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486804-49486804 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486805-49486805 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486806-49486806 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486807-49486807 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486808-49486808 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486809-49486809 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486810-49486810 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486811-49486811 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486812-49486812 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486813-49486813 has an unknown base call (value: N). Skipping... 22:43:45.194 WARN AllelicCountCollector - The reference position at chr4:49486814-49486814 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486815-49486815 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486816-49486816 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486817-49486817 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486818-49486818 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486819-49486819 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486820-49486820 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486821-49486821 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486822-49486822 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486823-49486823 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486824-49486824 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486825-49486825 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486826-49486826 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486827-49486827 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486828-49486828 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486829-49486829 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486830-49486830 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486831-49486831 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486832-49486832 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486833-49486833 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486834-49486834 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486835-49486835 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486836-49486836 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486837-49486837 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486838-49486838 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486839-49486839 has an unknown base call (value: N). Skipping... 22:43:45.195 WARN AllelicCountCollector - The reference position at chr4:49486840-49486840 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486841-49486841 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486842-49486842 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486843-49486843 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486844-49486844 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486845-49486845 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486846-49486846 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486847-49486847 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486848-49486848 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486849-49486849 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486850-49486850 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486851-49486851 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486852-49486852 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486853-49486853 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486854-49486854 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486855-49486855 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486856-49486856 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486857-49486857 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486858-49486858 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486859-49486859 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486860-49486860 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486861-49486861 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486862-49486862 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486863-49486863 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486864-49486864 has an unknown base call (value: N). Skipping... 22:43:45.196 WARN AllelicCountCollector - The reference position at chr4:49486865-49486865 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486866-49486866 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486867-49486867 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486868-49486868 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486869-49486869 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486870-49486870 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486871-49486871 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486872-49486872 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486873-49486873 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486874-49486874 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486875-49486875 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486876-49486876 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486877-49486877 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486878-49486878 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486879-49486879 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486880-49486880 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486881-49486881 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486882-49486882 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486883-49486883 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486884-49486884 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486885-49486885 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486886-49486886 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486887-49486887 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486888-49486888 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486889-49486889 has an unknown base call (value: N). Skipping... 22:43:45.197 WARN AllelicCountCollector - The reference position at chr4:49486890-49486890 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486891-49486891 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486892-49486892 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486893-49486893 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486894-49486894 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486895-49486895 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486896-49486896 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486897-49486897 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486898-49486898 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486899-49486899 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486900-49486900 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486901-49486901 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486902-49486902 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486903-49486903 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486904-49486904 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486905-49486905 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486906-49486906 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486907-49486907 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486908-49486908 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486909-49486909 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486910-49486910 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486911-49486911 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486912-49486912 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486913-49486913 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486914-49486914 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486915-49486915 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486916-49486916 has an unknown base call (value: N). Skipping... 22:43:45.198 WARN AllelicCountCollector - The reference position at chr4:49486917-49486917 has an unknown base call (value: N). Skipping... 22:43:45.199 WARN AllelicCountCollector - The reference position at chr4:49486918-49486918 has an unknown base call (value: N). Skipping... 22:43:45.199 WARN AllelicCountCollector - The reference position at chr4:49486919-49486919 has an unknown base call (value: N). Skipping... 22:43:45.199 WARN AllelicCountCollector - The reference position at chr4:49486920-49486920 has an unknown base call (value: N). Skipping... 22:43:45.199 WARN AllelicCountCollector - The reference position at chr4:49486921-49486921 has an unknown base call (value: N). Skipping... 22:43:45.199 WARN AllelicCountCollector - The reference position at chr4:49486922-49486922 has an unknown base call (value: N). Skipping... 22:43:45.199 WARN AllelicCountCollector - The reference position at chr4:49486923-49486923 has an unknown base call (value: N). Skipping... 22:43:45.199 WARN AllelicCountCollector - The reference position at chr4:49486924-49486924 has an unknown base call (value: N). Skipping... 22:43:54.605 INFO ProgressMeter - chr4:78768708 8.7 54629000 6247336.4 22:44:04.635 INFO ProgressMeter - chr4:109472932 8.9 56232000 6310025.2 22:44:14.642 INFO ProgressMeter - chr4:145139908 9.1 57791000 6365827.7 22:44:25.441 INFO ProgressMeter - chr4:185169145 9.3 59498000 6426449.8 22:44:35.445 INFO ProgressMeter - chr5:11412132 9.4 60491000 6418120.5 22:44:45.448 INFO ProgressMeter - chr5:40949949 9.6 61713000 6433966.7 22:44:56.444 INFO ProgressMeter - chr5:80947572 9.8 63865000 6533503.8 22:45:06.452 INFO ProgressMeter - chr5:132213984 9.9 66033000 6641945.1 22:45:30.152 INFO ProgressMeter - chr5:140504868 10.3 66956000 6477429.4 22:45:40.166 INFO ProgressMeter - chr5:149619022 10.5 67908000 6465140.1 22:45:50.169 INFO ProgressMeter - chr5:176646605 10.7 69620000 6524581.2 22:46:00.170 INFO ProgressMeter - chr6:8874913 10.8 70947000 6546677.6 22:46:10.174 INFO ProgressMeter - chr6:27811419 11.0 72006000 6543709.7 22:46:36.121 INFO ProgressMeter - chr6:31463923 11.4 72700000 6356960.4 22:46:46.126 INFO ProgressMeter - chr6:33540842 11.6 73325000 6319459.1 22:46:56.126 INFO ProgressMeter - chr6:41733003 11.8 74156000 6300576.5 22:47:06.136 INFO ProgressMeter - chr6:51682143 11.9 74957000 6279620.2 22:47:16.143 INFO ProgressMeter - chr6:88047797 12.1 76496000 6320242.4 22:47:26.948 INFO ProgressMeter - chr6:117634081 12.3 77943000 6345384.4 22:47:36.950 INFO ProgressMeter - chr6:147509192 12.5 79451000 6381546.6 22:47:46.951 INFO ProgressMeter - chr6:160708322 12.6 80450000 6376418.7 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745980-170745980 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745981-170745981 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745982-170745982 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745983-170745983 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745984-170745984 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745985-170745985 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745986-170745986 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745987-170745987 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745988-170745988 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745989-170745989 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745990-170745990 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745991-170745991 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745992-170745992 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745993-170745993 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745994-170745994 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745995-170745995 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745996-170745996 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745997-170745997 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745998-170745998 has an unknown base call (value: N). Skipping... 22:47:51.341 WARN AllelicCountCollector - The reference position at chr6:170745999-170745999 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746000-170746000 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746001-170746001 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746002-170746002 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746003-170746003 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746004-170746004 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746005-170746005 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746006-170746006 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746007-170746007 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746008-170746008 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746009-170746009 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746010-170746010 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746011-170746011 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746012-170746012 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746013-170746013 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746014-170746014 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746015-170746015 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746016-170746016 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746017-170746017 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746018-170746018 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746019-170746019 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746020-170746020 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746021-170746021 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746022-170746022 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746023-170746023 has an unknown base call (value: N). Skipping... 22:47:51.342 WARN AllelicCountCollector - The reference position at chr6:170746024-170746024 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746025-170746025 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746026-170746026 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746027-170746027 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746028-170746028 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746029-170746029 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746030-170746030 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746031-170746031 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746032-170746032 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746033-170746033 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746034-170746034 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746035-170746035 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746036-170746036 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746037-170746037 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746038-170746038 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746039-170746039 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746040-170746040 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746041-170746041 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746042-170746042 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746043-170746043 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746044-170746044 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746045-170746045 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746046-170746046 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746047-170746047 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746048-170746048 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746049-170746049 has an unknown base call (value: N). Skipping... 22:47:51.343 WARN AllelicCountCollector - The reference position at chr6:170746050-170746050 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746051-170746051 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746052-170746052 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746053-170746053 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746054-170746054 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746055-170746055 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746056-170746056 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746057-170746057 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746058-170746058 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746059-170746059 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746060-170746060 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746061-170746061 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746062-170746062 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746063-170746063 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746064-170746064 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746065-170746065 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746066-170746066 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746067-170746067 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746068-170746068 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746069-170746069 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746070-170746070 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746071-170746071 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746072-170746072 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746073-170746073 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746074-170746074 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746075-170746075 has an unknown base call (value: N). Skipping... 22:47:51.344 WARN AllelicCountCollector - The reference position at chr6:170746076-170746076 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746077-170746077 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746078-170746078 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746079-170746079 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746080-170746080 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746081-170746081 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746082-170746082 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746083-170746083 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746084-170746084 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746085-170746085 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746086-170746086 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746087-170746087 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746088-170746088 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746089-170746089 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746090-170746090 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746091-170746091 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746092-170746092 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746093-170746093 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746094-170746094 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746095-170746095 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746096-170746096 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746097-170746097 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746098-170746098 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746099-170746099 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746100-170746100 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746101-170746101 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746102-170746102 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746103-170746103 has an unknown base call (value: N). Skipping... 22:47:51.345 WARN AllelicCountCollector - The reference position at chr6:170746104-170746104 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746105-170746105 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746106-170746106 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746107-170746107 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746108-170746108 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746109-170746109 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746110-170746110 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746111-170746111 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746112-170746112 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746113-170746113 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746114-170746114 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746115-170746115 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746116-170746116 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746117-170746117 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746118-170746118 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746119-170746119 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746120-170746120 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746121-170746121 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746122-170746122 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746123-170746123 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746124-170746124 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746125-170746125 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746126-170746126 has an unknown base call (value: N). Skipping... 22:47:51.346 WARN AllelicCountCollector - The reference position at chr6:170746127-170746127 has an unknown base call (value: N). Skipping... 22:47:56.973 INFO ProgressMeter - chr7:2594774 12.8 81341000 6362802.0 22:48:08.415 INFO ProgressMeter - chr7:20615932 13.0 82370000 6348590.6 22:48:18.418 INFO ProgressMeter - chr7:38269677 13.1 83549000 6357766.6 22:48:28.423 INFO ProgressMeter - chr7:50595891 13.3 84424000 6343861.3 22:48:38.444 INFO ProgressMeter - chr7:69401367 13.5 85241000 6325854.9 22:48:48.445 INFO ProgressMeter - chr7:82952993 13.6 86213000 6319813.5 22:48:58.448 INFO ProgressMeter - chr7:99944015 13.8 87346000 6325562.3 22:49:08.523 INFO ProgressMeter - chr7:101034465 14.0 87685000 6273820.0 22:49:18.538 INFO ProgressMeter - chr7:105204909 14.1 88127000 6231028.9 22:49:28.538 INFO ProgressMeter - chr7:129608269 14.3 89437000 6250001.5 22:49:38.607 INFO ProgressMeter - chr7:142722441 14.5 90541000 6253810.4 22:49:48.611 INFO ProgressMeter - chr7:150951232 14.6 91228000 6229520.1 22:49:58.616 INFO ProgressMeter - chr8:10730087 14.8 92523000 6246819.7 22:50:08.620 INFO ProgressMeter - chr8:28731199 15.0 93920000 6270551.0 22:50:18.655 INFO ProgressMeter - chr8:43122165 15.1 94875000 6264361.0 22:50:45.923 INFO ProgressMeter - chr8:48914418 15.6 95073000 6094553.3 22:50:55.929 INFO ProgressMeter - chr8:64576910 15.8 95756000 6073409.1 22:51:05.932 INFO ProgressMeter - chr8:85373340 15.9 96737000 6071429.7 22:51:15.945 INFO ProgressMeter - chr8:97930657 16.1 97429000 6051478.2 22:51:25.955 INFO ProgressMeter - chr8:109381318 16.3 98097000 6030485.3 22:51:36.018 INFO ProgressMeter - chr8:125436795 16.4 98788000 6010982.9 22:51:46.086 INFO ProgressMeter - chr8:140551184 16.6 99454000 5990344.8 22:51:56.122 INFO ProgressMeter - chr8:143563203 16.8 99774000 5949676.9 22:52:06.122 INFO ProgressMeter - chr8:143937386 16.9 99927000 5900161.3 22:52:16.160 INFO ProgressMeter - chr8:144393792 17.1 100056000 5849996.5 22:52:26.161 INFO ProgressMeter - chr9:452027 17.3 100302000 5807774.0 22:52:36.173 INFO ProgressMeter - chr9:33328444 17.4 101653000 5829674.2 22:52:46.477 INFO ProgressMeter - chr9:39085759 17.6 102379000 5814048.6 22:52:48.318 WARN AllelicCountCollector - The reference position at chr9:61231967-61231967 has an unknown base call (value: N). Skipping... 22:52:48.318 WARN AllelicCountCollector - The reference position at chr9:61231968-61231968 has an unknown base call (value: N). Skipping... 22:52:48.319 WARN AllelicCountCollector - The reference position at chr9:61231969-61231969 has an unknown base call (value: N). Skipping... 22:52:48.319 WARN AllelicCountCollector - The reference position at chr9:61231970-61231970 has an unknown base call (value: N). Skipping... 22:52:48.319 WARN AllelicCountCollector - The reference position at chr9:61231971-61231971 has an unknown base call (value: N). Skipping... 22:52:48.319 WARN AllelicCountCollector - The reference position at chr9:61231972-61231972 has an unknown base call (value: N). Skipping... 22:52:48.319 WARN AllelicCountCollector - The reference position at chr9:61231973-61231973 has an unknown base call (value: N). Skipping... 22:52:48.320 WARN AllelicCountCollector - The reference position at chr9:61231974-61231974 has an unknown base call (value: N). Skipping... 22:52:48.320 WARN AllelicCountCollector - The reference position at chr9:61231975-61231975 has an unknown base call (value: N). Skipping... 22:52:48.320 WARN AllelicCountCollector - The reference position at chr9:61231976-61231976 has an unknown base call (value: N). Skipping... 22:52:48.320 WARN AllelicCountCollector - The reference position at chr9:61231977-61231977 has an unknown base call (value: N). Skipping... 22:52:48.320 WARN AllelicCountCollector - The reference position at chr9:61231978-61231978 has an unknown base call (value: N). Skipping... 22:52:48.320 WARN AllelicCountCollector - The reference position at chr9:61231979-61231979 has an unknown base call (value: N). Skipping... 22:52:48.320 WARN AllelicCountCollector - The reference position at chr9:61231980-61231980 has an unknown base call (value: N). Skipping... 22:52:48.320 WARN AllelicCountCollector - The reference position at chr9:61231981-61231981 has an unknown base call (value: N). Skipping... 22:52:48.321 WARN AllelicCountCollector - The reference position at chr9:61231982-61231982 has an unknown base call (value: N). Skipping... 22:52:48.321 WARN AllelicCountCollector - The reference position at chr9:61231983-61231983 has an unknown base call (value: N). Skipping... 22:52:48.321 WARN AllelicCountCollector - The reference position at chr9:61231984-61231984 has an unknown base call (value: N). Skipping... 22:52:48.321 WARN AllelicCountCollector - The reference position at chr9:61231985-61231985 has an unknown base call (value: N). Skipping... 22:52:48.321 WARN AllelicCountCollector - The reference position at chr9:61231986-61231986 has an unknown base call (value: N). Skipping... 22:52:48.321 WARN AllelicCountCollector - The reference position at chr9:61231987-61231987 has an unknown base call (value: N). Skipping... 22:52:48.321 WARN AllelicCountCollector - The reference position at chr9:61231988-61231988 has an unknown base call (value: N). Skipping... 22:52:48.321 WARN AllelicCountCollector - The reference position at chr9:61231989-61231989 has an unknown base call (value: N). Skipping... 22:52:48.321 WARN AllelicCountCollector - The reference position at chr9:61231990-61231990 has an unknown base call (value: N). Skipping... 22:52:48.321 WARN AllelicCountCollector - The reference position at chr9:61231991-61231991 has an unknown base call (value: N). Skipping... 22:52:48.321 WARN AllelicCountCollector - The reference position at chr9:61231992-61231992 has an unknown base call (value: N). Skipping... 22:52:48.322 WARN AllelicCountCollector - The reference position at chr9:61231993-61231993 has an unknown base call (value: N). Skipping... 22:52:48.322 WARN AllelicCountCollector - The reference position at chr9:61231994-61231994 has an unknown base call (value: N). Skipping... 22:52:48.322 WARN AllelicCountCollector - The reference position at chr9:61231995-61231995 has an unknown base call (value: N). Skipping... 22:52:48.322 WARN AllelicCountCollector - The reference position at chr9:61231996-61231996 has an unknown base call (value: N). Skipping... 22:52:48.322 WARN AllelicCountCollector - The reference position at chr9:61231997-61231997 has an unknown base call (value: N). Skipping... 22:52:48.322 WARN AllelicCountCollector - The reference position at chr9:61231998-61231998 has an unknown base call (value: N). Skipping... 22:52:48.322 WARN AllelicCountCollector - The reference position at chr9:61231999-61231999 has an unknown base call (value: N). Skipping... 22:52:48.322 WARN AllelicCountCollector - The reference position at chr9:61232000-61232000 has an unknown base call (value: N). Skipping... 22:52:48.322 WARN AllelicCountCollector - The reference position at chr9:61232001-61232001 has an unknown base call (value: N). Skipping... 22:52:48.322 WARN AllelicCountCollector - The reference position at chr9:61232002-61232002 has an unknown base call (value: N). Skipping... 22:52:48.323 WARN AllelicCountCollector - The reference position at chr9:61232003-61232003 has an unknown base call (value: N). Skipping... 22:52:48.323 WARN AllelicCountCollector - The reference position at chr9:61232004-61232004 has an unknown base call (value: N). Skipping... 22:52:48.323 WARN AllelicCountCollector - The reference position at chr9:61232005-61232005 has an unknown base call (value: N). Skipping... 22:52:48.323 WARN AllelicCountCollector - The reference position at chr9:61232006-61232006 has an unknown base call (value: N). Skipping... 22:52:48.323 WARN AllelicCountCollector - The reference position at chr9:61232007-61232007 has an unknown base call (value: N). Skipping... 22:52:48.323 WARN AllelicCountCollector - The reference position at chr9:61232008-61232008 has an unknown base call (value: N). Skipping... 22:52:48.323 WARN AllelicCountCollector - The reference position at chr9:61232009-61232009 has an unknown base call (value: N). Skipping... 22:52:48.323 WARN AllelicCountCollector - The reference position at chr9:61232010-61232010 has an unknown base call (value: N). Skipping... 22:52:48.323 WARN AllelicCountCollector - The reference position at chr9:61232011-61232011 has an unknown base call (value: N). Skipping... 22:52:48.323 WARN AllelicCountCollector - The reference position at chr9:61232012-61232012 has an unknown base call (value: N). Skipping... 22:52:48.323 WARN AllelicCountCollector - The reference position at chr9:61232013-61232013 has an unknown base call (value: N). Skipping... 22:52:49.907 WARN AllelicCountCollector - The reference position at chr9:67920553-67920553 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920554-67920554 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920555-67920555 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920556-67920556 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920557-67920557 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920558-67920558 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920559-67920559 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920560-67920560 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920561-67920561 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920562-67920562 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920563-67920563 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920564-67920564 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920565-67920565 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920566-67920566 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920567-67920567 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920568-67920568 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920569-67920569 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920570-67920570 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920571-67920571 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920572-67920572 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920573-67920573 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920574-67920574 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920575-67920575 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920576-67920576 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920577-67920577 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920578-67920578 has an unknown base call (value: N). Skipping... 22:52:49.908 WARN AllelicCountCollector - The reference position at chr9:67920579-67920579 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920580-67920580 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920581-67920581 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920582-67920582 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920583-67920583 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920584-67920584 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920585-67920585 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920586-67920586 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920587-67920587 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920588-67920588 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920589-67920589 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920590-67920590 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920591-67920591 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920592-67920592 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920593-67920593 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920594-67920594 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920595-67920595 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920596-67920596 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920597-67920597 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920598-67920598 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920599-67920599 has an unknown base call (value: N). Skipping... 22:52:49.909 WARN AllelicCountCollector - The reference position at chr9:67920600-67920600 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920601-67920601 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920602-67920602 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920603-67920603 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920604-67920604 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920605-67920605 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920606-67920606 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920607-67920607 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920608-67920608 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920609-67920609 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920610-67920610 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920611-67920611 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920612-67920612 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920613-67920613 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920614-67920614 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920615-67920615 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920616-67920616 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920617-67920617 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920618-67920618 has an unknown base call (value: N). Skipping... 22:52:49.910 WARN AllelicCountCollector - The reference position at chr9:67920619-67920619 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920620-67920620 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920621-67920621 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920622-67920622 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920623-67920623 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920624-67920624 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920625-67920625 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920626-67920626 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920627-67920627 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920628-67920628 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920629-67920629 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920630-67920630 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920631-67920631 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920632-67920632 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920633-67920633 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920634-67920634 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920635-67920635 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920636-67920636 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920637-67920637 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920638-67920638 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920639-67920639 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920640-67920640 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920641-67920641 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920642-67920642 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920643-67920643 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920644-67920644 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920645-67920645 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920646-67920646 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920647-67920647 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920648-67920648 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920649-67920649 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920650-67920650 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920651-67920651 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920652-67920652 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920653-67920653 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920654-67920654 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920655-67920655 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920656-67920656 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920657-67920657 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920658-67920658 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920659-67920659 has an unknown base call (value: N). Skipping... 22:52:49.911 WARN AllelicCountCollector - The reference position at chr9:67920660-67920660 has an unknown base call (value: N). Skipping... 22:52:49.912 WARN AllelicCountCollector - The reference position at chr9:67920661-67920661 has an unknown base call (value: N). Skipping... 22:52:49.912 WARN AllelicCountCollector - The reference position at chr9:67920662-67920662 has an unknown base call (value: N). Skipping... 22:52:49.912 WARN AllelicCountCollector - The reference position at chr9:67920663-67920663 has an unknown base call (value: N). Skipping... 22:52:49.912 WARN AllelicCountCollector - The reference position at chr9:67920664-67920664 has an unknown base call (value: N). Skipping... 22:52:49.912 WARN AllelicCountCollector - The reference position at chr9:67920665-67920665 has an unknown base call (value: N). Skipping... 22:52:49.912 WARN AllelicCountCollector - The reference position at chr9:67920666-67920666 has an unknown base call (value: N). Skipping... 22:52:49.912 WARN AllelicCountCollector - The reference position at chr9:67920667-67920667 has an unknown base call (value: N). Skipping... 22:52:49.912 WARN AllelicCountCollector - The reference position at chr9:67920668-67920668 has an unknown base call (value: N). Skipping... 22:52:49.912 WARN AllelicCountCollector - The reference position at chr9:67920669-67920669 has an unknown base call (value: N). Skipping... 22:52:49.912 WARN AllelicCountCollector - The reference position at chr9:67920670-67920670 has an unknown base call (value: N). Skipping... 22:52:49.912 WARN AllelicCountCollector - The reference position at chr9:67920671-67920671 has an unknown base call (value: N). Skipping... 22:52:49.913 WARN AllelicCountCollector - The reference position at chr9:67920672-67920672 has an unknown base call (value: N). Skipping... 22:52:49.913 WARN AllelicCountCollector - The reference position at chr9:67920673-67920673 has an unknown base call (value: N). Skipping... 22:52:49.913 WARN AllelicCountCollector - The reference position at chr9:67920674-67920674 has an unknown base call (value: N). Skipping... 22:52:49.913 WARN AllelicCountCollector - The reference position at chr9:67920675-67920675 has an unknown base call (value: N). Skipping... 22:52:49.913 WARN AllelicCountCollector - The reference position at chr9:67920676-67920676 has an unknown base call (value: N). Skipping... 22:52:49.913 WARN AllelicCountCollector - The reference position at chr9:67920677-67920677 has an unknown base call (value: N). Skipping... 22:52:49.913 WARN AllelicCountCollector - The reference position at chr9:67920678-67920678 has an unknown base call (value: N). Skipping... 22:52:49.913 WARN AllelicCountCollector - The reference position at chr9:67920679-67920679 has an unknown base call (value: N). Skipping... 22:52:49.913 WARN AllelicCountCollector - The reference position at chr9:67920680-67920680 has an unknown base call (value: N). Skipping... 22:52:49.913 WARN AllelicCountCollector - The reference position at chr9:67920681-67920681 has an unknown base call (value: N). Skipping... 22:52:49.913 WARN AllelicCountCollector - The reference position at chr9:67920682-67920682 has an unknown base call (value: N). Skipping... 22:52:49.913 WARN AllelicCountCollector - The reference position at chr9:67920683-67920683 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920684-67920684 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920685-67920685 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920686-67920686 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920687-67920687 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920688-67920688 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920689-67920689 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920690-67920690 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920691-67920691 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920692-67920692 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920693-67920693 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920694-67920694 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920695-67920695 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920696-67920696 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920697-67920697 has an unknown base call (value: N). Skipping... 22:52:49.914 WARN AllelicCountCollector - The reference position at chr9:67920698-67920698 has an unknown base call (value: N). Skipping... 22:52:49.915 WARN AllelicCountCollector - The reference position at chr9:67920699-67920699 has an unknown base call (value: N). Skipping... 22:52:49.915 WARN AllelicCountCollector - The reference position at chr9:67920700-67920700 has an unknown base call (value: N). Skipping... 22:52:49.915 WARN AllelicCountCollector - The reference position at chr9:67920701-67920701 has an unknown base call (value: N). Skipping... 22:52:49.915 WARN AllelicCountCollector - The reference position at chr9:67920702-67920702 has an unknown base call (value: N). Skipping... 22:52:56.483 INFO ProgressMeter - chr9:84702448 17.8 103836000 5841468.7 22:53:06.484 INFO ProgressMeter - chr9:97386412 17.9 104777000 5839647.5 22:53:42.312 INFO ProgressMeter - chr9:113283331 18.5 105810000 5707283.9 22:53:52.343 INFO ProgressMeter - chr9:126696035 18.7 106790000 5708660.0 22:54:02.350 INFO ProgressMeter - chr9:131121441 18.9 107593000 5700759.5 22:54:12.358 INFO ProgressMeter - chr9:136382322 19.0 108305000 5688213.1 22:54:22.394 INFO ProgressMeter - chr9:137158397 19.2 108576000 5652787.0 22:54:32.404 INFO ProgressMeter - chr10:7713464 19.4 109323000 5642666.7 22:54:42.428 INFO ProgressMeter - chr10:37169457 19.5 110882000 5674204.8 22:54:50.365 WARN AllelicCountCollector - The reference position at chr10:58267943-58267943 has an unknown base call (value: N). Skipping... 22:54:52.792 INFO ProgressMeter - chr10:65912557 19.7 112307000 5696771.1 22:55:02.805 INFO ProgressMeter - chr10:79507290 19.9 113463000 5707097.7 22:55:13.143 INFO ProgressMeter - chr10:100362858 20.1 115111000 5740242.7 22:55:23.191 INFO ProgressMeter - chr10:122593739 20.2 116714000 5771977.4 22:55:31.696 WARN AllelicCountCollector - The reference position at chr10:133740456-133740456 has an unknown base call (value: N). Skipping... 22:55:31.696 WARN AllelicCountCollector - The reference position at chr10:133740457-133740457 has an unknown base call (value: N). Skipping... 22:55:31.696 WARN AllelicCountCollector - The reference position at chr10:133740458-133740458 has an unknown base call (value: N). Skipping... 22:55:31.696 WARN AllelicCountCollector - The reference position at chr10:133740459-133740459 has an unknown base call (value: N). Skipping... 22:55:31.696 WARN AllelicCountCollector - The reference position at chr10:133740460-133740460 has an unknown base call (value: N). Skipping... 22:55:31.696 WARN AllelicCountCollector - The reference position at chr10:133740461-133740461 has an unknown base call (value: N). Skipping... 22:55:31.696 WARN AllelicCountCollector - The reference position at chr10:133740462-133740462 has an unknown base call (value: N). Skipping... 22:55:31.696 WARN AllelicCountCollector - The reference position at chr10:133740463-133740463 has an unknown base call (value: N). Skipping... 22:55:31.697 WARN AllelicCountCollector - The reference position at chr10:133740464-133740464 has an unknown base call (value: N). Skipping... 22:55:31.697 WARN AllelicCountCollector - The reference position at chr10:133740465-133740465 has an unknown base call (value: N). Skipping... 22:55:31.697 WARN AllelicCountCollector - The reference position at chr10:133740466-133740466 has an unknown base call (value: N). Skipping... 22:55:33.208 INFO ProgressMeter - chr11:409213 20.4 117590000 5767679.1 22:55:43.248 INFO ProgressMeter - chr11:1242933 20.6 117882000 5734936.4 22:55:53.258 INFO ProgressMeter - chr11:5948452 20.7 118677000 5727124.7 22:56:03.262 INFO ProgressMeter - chr11:10774130 20.9 119355000 5713868.5 22:56:13.265 INFO ProgressMeter - chr11:31817915 21.1 120561000 5725908.1 22:56:23.330 INFO ProgressMeter - chr11:47179338 21.2 121487000 5724281.6 22:56:33.333 INFO ProgressMeter - chr11:59504210 21.4 122382000 5721503.2 22:56:43.342 INFO ProgressMeter - chr11:62791649 21.6 123022000 5706916.4 22:56:53.347 INFO ProgressMeter - chr11:65622418 21.7 123686000 5693675.9 22:57:03.369 INFO ProgressMeter - chr11:67605139 21.9 124188000 5673163.2 22:57:13.371 INFO ProgressMeter - chr11:73297596 22.1 124884000 5661846.1 22:57:23.409 INFO ProgressMeter - chr11:86952715 22.2 125914000 5665570.5 22:57:33.409 INFO ProgressMeter - chr11:113275461 22.4 127459000 5692399.9 22:57:43.424 INFO ProgressMeter - chr11:119078419 22.6 128148000 5680822.8 22:58:24.019 INFO ProgressMeter - chr11:126336763 23.2 129015000 5552710.2 22:58:34.028 INFO ProgressMeter - chr12:1886070 23.4 129731000 5543724.2 22:58:44.051 INFO ProgressMeter - chr12:9203904 23.6 130784000 5549156.5
I'm not really seeing any error in this one (only a lot of warnings). Could you please advise on how to solve this or did I use the wrong input for the intervals?
Comments
19 comments
Hi Hanbing Song,
Thanks for writing in. Can you share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.
Let us know the workspace name, as well as the relevant submission and workflow IDs. We’ll be happy to take a closer look as soon as we can.
Best,
Samantha
Hi Samantha,
Thanks for your reply and I just shared our workspace with you. The workspace name is fhuanglab/WES_pipeline. In there you might see the latest failed job running 2-CNV_Somatic_Pair which I need help with.
Hi Hanbing Song,
Can you confirm the submission ID that you would like us to look into? I also noticed you posted on the GATK forum with a similar question - is that regarding the same submission here?
Best,
Samantha
Hi Samantha,
Yes, that was the same problem because I don't know which forum would be the proper one to post this.
The submission ID would be this one: 7878b8f7-2f4e-4c9e-9492-1052b0ce5c00.
Thank you
Hanbing
Hi Hanbing Song,
Thanks for confirming. I'll address both posts here if that's okay with you.
If you scroll further down through the backend log for the failed task, you'll see this error:
You are receiving this error because the Funcotator datasource you are using (v1.7.20200521) is not supported by the GATK version you're running (v4.1.7.0). Since you are using an older version of GATK, you should use the older datasources. See this bug report for more information.
Best,
Samantha
Hi Samantha,
Sure! I'll just reply to this thread then.
Yeah, that makes a lot of sense. Thank you for the insight! I just modified the funcotator datasource to the 1.6.20190124 version and restarted the job. However, I'm wondering if this would also be the cause of the PlotDenoisedCopyRatiosNormal step?
Hanbing
Hi Samantha,
I restarted the workflow this morning and so far some of the samples failed again on the plotdenoised step and the funcotator step. I changed the funcotator datasource and didn't see the previous error anymore. Now the error msg for funcotator became this one:
A USER ERROR has occurred: Bad input: Is the input a file of segment variant contexts? Variant context does not represent a copy number segment: [VC null @ chr1:23134065-23134079 Q. of type=SYMBOLIC alleles=[G*, <DEL>] attr={END=23134079, Num_Probes=1, Segment_Call=-, Segment_Mean=-29.897353} GT=[] filters=
And I noticed another strange thing in this run. Previously, some of the samples went through the plotdenoisedcopyrationormal steps and I was able to see the denoised CNV curve for the tumor samples. But for the other samples in the batch, this step failed and here is the log file.
Could you please advise what could cause this error?
2021/03/24 17:00:44 Starting container setup. 2021/03/24 17:00:47 Done container setup. 2021/03/24 17:00:50 Starting localization. 2021/03/24 17:00:58 Localization script execution started... 2021/03/24 17:00:58 Localizing input gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-DenoiseReadCountsNormal/RESPOND_60100060_C1_Non-Malignant.standardizedCR.tsv -> /cromwell_root/fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-DenoiseReadCountsNormal/RESPOND_60100060_C1_Non-Malignant.standardizedCR.tsv 2021/03/24 17:01:01 Localizing input gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-DenoiseReadCountsNormal/RESPOND_60100060_C1_Non-Malignant.denoisedCR.tsv -> /cromwell_root/fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-DenoiseReadCountsNormal/RESPOND_60100060_C1_Non-Malignant.denoisedCR.tsv Copying gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-DenoiseReadCountsNormal/RESPOND_60100060_C1_Non-Malignant.denoisedCR.tsv... / [0/1 files][ 0.0 B/ 12.3 MiB] 0% Done / [1/1 files][ 12.3 MiB/ 12.3 MiB] 100% Done Operation completed over 1 objects/12.3 MiB. 2021/03/24 17:01:03 Localizing input gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-PlotDenoisedCopyRatiosNormal/script -> /cromwell_root/script 2021/03/24 17:01:04 Localizing input gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/GRCh38.primary_assembly.genome.dict -> /cromwell_root/fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/GRCh38.primary_assembly.genome.dict 2021/03/24 17:01:05 Localization script execution complete. 2021/03/24 17:01:11 Done localization. 2021/03/24 17:01:12 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint=/bin/bash us.gcr.io/broad-gatk/gatk@sha256:192fedf9b9d65809da4a2954030269e3f311d296e6b5e4c6c7deec12c7fe84b2 /cromwell_root/script Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.42dbf577 17:01:16.740 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.7.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 17:01:17.082 INFO PlotDenoisedCopyRatios - ------------------------------------------------------------ 17:01:17.083 INFO PlotDenoisedCopyRatios - The Genome Analysis Toolkit (GATK) v4.1.7.0 17:01:17.083 INFO PlotDenoisedCopyRatios - For support and documentation go to https://software.broadinstitute.org/gatk/ 17:01:17.084 INFO PlotDenoisedCopyRatios - Executing as root@59c013a10564 on Linux v5.4.89+ amd64 17:01:17.084 INFO PlotDenoisedCopyRatios - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03 17:01:17.085 INFO PlotDenoisedCopyRatios - Start Date/Time: March 24, 2021 5:01:16 PM UTC 17:01:17.085 INFO PlotDenoisedCopyRatios - ------------------------------------------------------------ 17:01:17.085 INFO PlotDenoisedCopyRatios - ------------------------------------------------------------ 17:01:17.087 INFO PlotDenoisedCopyRatios - HTSJDK Version: 2.21.2 17:01:17.087 INFO PlotDenoisedCopyRatios - Picard Version: 2.21.9 17:01:17.087 INFO PlotDenoisedCopyRatios - HTSJDK Defaults.COMPRESSION_LEVEL : 2 17:01:17.087 INFO PlotDenoisedCopyRatios - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 17:01:17.089 INFO PlotDenoisedCopyRatios - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 17:01:17.089 INFO PlotDenoisedCopyRatios - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 17:01:17.089 INFO PlotDenoisedCopyRatios - Deflater: IntelDeflater 17:01:17.089 INFO PlotDenoisedCopyRatios - Inflater: IntelInflater 17:01:17.090 INFO PlotDenoisedCopyRatios - GCS max retries/reopens: 20 17:01:17.090 INFO PlotDenoisedCopyRatios - Requester pays: disabled 17:01:17.091 INFO PlotDenoisedCopyRatios - Initializing engine 17:01:17.091 INFO PlotDenoisedCopyRatios - Done initializing engine 17:01:17.094 INFO PlotDenoisedCopyRatios - Reading and validating input files... 17:01:19.638 INFO PlotDenoisedCopyRatios - Contigs above length threshold: {chr1=248956422, chr2=242193529, chr3=198295559, chr4=190214555, chr5=181538259, chr6=170805979, chr7=159345973, chr8=145138636, chr9=138394717, chr10=133797422, chr11=135086622, chr12=133275309, chr13=114364328, chr14=107043718, chr15=101991189, chr16=90338345, chr17=83257441, chr18=80373285, chr19=58617616, chr20=64444167, chr21=46709983, chr22=50818468, chrX=156040895, chrY=57227415, KI270728.1=1872759} 17:01:19.723 WARN PlotDenoisedCopyRatios - Contigs present in the file /cromwell_root/fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-DenoiseReadCountsNormal/RESPOND_60100060_C1_Non-Malignant.standardizedCR.tsv are missing from the sequence dictionary and will not be plotted. 17:01:19.882 WARN PlotDenoisedCopyRatios - Contigs present in the file /cromwell_root/fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-DenoiseReadCountsNormal/RESPOND_60100060_C1_Non-Malignant.denoisedCR.tsv are missing from the sequence dictionary and will not be plotted. 17:01:19.967 INFO PlotDenoisedCopyRatios - Writing plots to /cromwell_root/out... 17:01:22.052 INFO PlotDenoisedCopyRatios - PlotDenoisedCopyRatios complete. 17:01:22.052 INFO PlotDenoisedCopyRatios - Shutting down engine [March 24, 2021 5:01:22 PM UTC] org.broadinstitute.hellbender.tools.copynumber.plotting.PlotDenoisedCopyRatios done. Elapsed time: 0.09 minutes. Runtime.totalMemory()=389545984 Using GATK jar /root/gatk.jar defined in environment variable GATK_LOCAL_JAR Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx6000m -jar /root/gatk.jar PlotDenoisedCopyRatios --standardized-copy-ratios /cromwell_root/fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-DenoiseReadCountsNormal/RESPOND_60100060_C1_Non-Malignant.standardizedCR.tsv --denoised-copy-ratios /cromwell_root/fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-DenoiseReadCountsNormal/RESPOND_60100060_C1_Non-Malignant.denoisedCR.tsv --sequence-dictionary /cromwell_root/fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/GRCh38.primary_assembly.genome.dict --minimum-contig-length 1000000 --maximum-copy-ratio 4.0 --point-size-copy-ratio 0.2 --output out --output-prefix RESPOND_60100060_C1_Non-Malignant 2021/03/24 17:01:23 Starting delocalization. 2021/03/24 17:01:24 Delocalization script execution started... 2021/03/24 17:01:24 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-PlotDenoisedCopyRatiosNormal/memory_retry_rc 2021/03/24 17:01:24 Delocalizing output /cromwell_root/rc -> gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-PlotDenoisedCopyRatiosNormal/rc 2021/03/24 17:01:26 Delocalizing output /cromwell_root/stdout -> gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-PlotDenoisedCopyRatiosNormal/stdout 2021/03/24 17:01:27 Delocalizing output /cromwell_root/stderr -> gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-PlotDenoisedCopyRatiosNormal/stderr 2021/03/24 17:01:29 Delocalizing output /cromwell_root/out/RESPOND_60100060_C1_Non-Malignant.denoised.png -> gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-PlotDenoisedCopyRatiosNormal/out/RESPOND_60100060_C1_Non-Malignant.denoised.png 2021/03/24 17:01:30 Delocalizing output /cromwell_root/out/RESPOND_60100060_C1_Non-Malignant.standardizedMAD.txt -> gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-PlotDenoisedCopyRatiosNormal/out/RESPOND_60100060_C1_Non-Malignant.standardizedMAD.txt 2021/03/24 17:01:31 Delocalizing output /cromwell_root/out/RESPOND_60100060_C1_Non-Malignant.denoisedMAD.txt -> gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-PlotDenoisedCopyRatiosNormal/out/RESPOND_60100060_C1_Non-Malignant.denoisedMAD.txt 2021/03/24 17:01:33 Delocalizing output /cromwell_root/out/RESPOND_60100060_C1_Non-Malignant.scaledDeltaMAD.txt -> gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-PlotDenoisedCopyRatiosNormal/out/RESPOND_60100060_C1_Non-Malignant.scaledDeltaMAD.txt 2021/03/24 17:01:34 Delocalizing output /cromwell_root/out/RESPOND_60100060_C1_Non-Malignant.deltaMAD.txt -> gs://fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-PlotDenoisedCopyRatiosNormal/out/RESPOND_60100060_C1_Non-Malignant.deltaMAD.txt 2021/03/24 17:01:36 Delocalization script execution complete. 2021/03/24 17:01:37 Done delocalization.
Thanks so much!
Hanbing
Hi Hanbing Song,
Can you confirm the submission ID for the job where you are seeing this new error? I'll take a look and get back to you as soon as I can.
Best,
Samantha
Yes, sure! Sorry bout not including that. The job ID is a2756ae7-b331-4ea3-8c0b-0843a18aea88.
Hi Hanbing Song,
The new error in your FuncotateSegments task is happening because the segment being annotated is too short. There is an argument that specifies the minimum number of bases that a segment variant context must be in order to be annotated. The default value is 75 and this variant is of length 14, so it's failing. You will need to specify the
--min-num-bases-for-segment-funcotationargument and provide a number that is smaller than the smallest segment in your input data.Best,
Samantha
Hi Samantha,
Thanks so much for spotting this. However, I still ran into this error in this step PlotDenoisedCopyRatiosNormal. The problem is that I have 24 samples in this batch and 11 seemed to pass this step and I could see a CNV denoised plot generated. And I checked the step locally and did not run into any problem. Could you please take a look at this error? Also for the job a2756ae7-b331-4ea3-8c0b-0843a18aea88.
Contigs present in the file /cromwell_root/fc-9828bda3-33d6-40b9-ad27-544fb296a8e0/a2756ae7-b331-4ea3-8c0b-0843a18aea88/CNVSomaticPairWorkflow/3b3a80a3-218d-45e4-be09-c273522313ab/call-DenoiseReadCountsNormal/RESPOND_60100060_C1_Non-Malignant.standardizedCR.tsv are missing from the sequence dictionary and will not be plotted.
I'll restart another run reducing the --min-num-bases-for-segment-funcotation.
Thanks again,
Hanbing
Hi Hanbing Song,
Sorry for the delayed response. We are still looking into the error in the
PlotDenoisedCopyRatiosNormaltask as we think it may be a bug. We've reached out to GATK developers and will let you know once we hear back.I also noticed the following error you're receiving in the
FuncotateSegmentstask:A USER ERROR has occurred: min-num-bases-for-segment-funcotation is not a recognized option.You'll need to use at least version 4.1.8.0 because that is when themin-num-bases-for-segment-funcotationparameter was added. You'll need to use GATK version 4.1.8.0 as your GATK docker and use v4.1.8.0 of the WDL.Please let me know if you have any questions.
Best,
Samantha
Hi Samantha,
Thanks for following up on this issue and thanks for reaching out to GATKdevelopers for help!
Got it, I'll change the gatk version and test it out again soon. We just figured out which common site file to use for our CNV call so hopefully it'll smooth the outcome CNV curves a little bit.
Hanbing
Hi Hanbing Song,
Our developers noticed that you are using
hg38_v0_exome_calling_regions.v1.interval_listas the input intervals, which is not correct. You should be using an interval list that corresponds to your target kit.Best,
Samantha
Hi Samantha,
Thanks for pointing it out! But I only have a .bed file for our target kit. Is there a way of converting it to the interval_list format or .bed file also works?
In the meantime, in this workflow I was using, there was also a "common site" input. If I put the target kit in the input interval then what should I use for the common site?
I tested the workflow out in my local clusters for the steps which were problematic but they all worked fine, which is very confusing to me.
Thanks!
Hanbing
Hi Hanbing,
You can run the BedToIntervalList tool (or something like that) to get an interval list format. I'll have to see what the developers say about the common site file.
Best,
Samantha
Hi Samantha,
Thanks for your reply! I found that .bed file also worked when inserted as the interval. However, I kept hitting the same error during the denoisedcount step. Strangely, when I downloaded all the intermediate.tsv and .h5df files locally and tested gatk myself, everything seemed fine.
I'm wondering why that is. Is there a wall time or something? Locally, I was able to proceed until the plotting step and produce something like this. But apparently, this result indicates that I still need a lot of smoothing/denoising. Do you happen to see something similar in the past?
Thanks so much for following up on this and thanks for your time!
Hanbing
Hi Hanbing,
Can you share the submission ID for the job where you are seeing this?
Best,
Samantha
Hi Samantha,
Sorry, I have deleted the job folder a while back. But I can re-produce it on Terra and I'll reply with the submission ID when the job is done.
Thanks,
Hanbing
Please sign in to leave a comment.