file not found

gs://mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.fa.dict

The json parameter file has:

 "PreProcessingForVariantDiscovery_GATK4.ref_dict":"${workspace.chm13_dict}"

 and 

gsutil ls gs://mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.fa.dict

returns the file.

cromwell looks for a file chm13v2.0.dict, why? The json config file refers to 

workspace.chm13_dict and this links to 

Here is the log:

2022/05/21 01:33:17 Starting container setup. 2022/05/21 01:33:19 Done container setup. 2022/05/21 01:33:23 Starting localization. 2022/05/21 01:33:43 Localization script execution started... 2022/05/21 01:33:43 Localizing input gs://fc-94c0d9c9-5bbf-47c7-a83e-e3b14b5ea99c/e467c78b-6540-4523-b8e3-44e97e427c4f/PreProcessingForVariantDiscovery_GATK4/2caac1e0-3f33-4cf2-bb53-d10dff61e1ea/call-SortAndFixTags/OGI773_001511.CHM13.aligned.duplicate_marked.sorted.bai -> /cromwell_root/fc-94c0d9c9-5bbf-47c7-a83e-e3b14b5ea99c/e467c78b-6540-4523-b8e3-44e97e427c4f/PreProcessingForVariantDiscovery_GATK4/2caac1e0-3f33-4cf2-bb53-d10dff61e1ea/call-SortAndFixTags/OGI773_001511.CHM13.aligned.duplicate_marked.sorted.bai 2022/05/21 01:33:48 Localizing input gs://fc-94c0d9c9-5bbf-47c7-a83e-e3b14b5ea99c/e467c78b-6540-4523-b8e3-44e97e427c4f/PreProcessingForVariantDiscovery_GATK4/2caac1e0-3f33-4cf2-bb53-d10dff61e1ea/call-SortAndFixTags/OGI773_001511.CHM13.aligned.duplicate_marked.sorted.bam -> /cromwell_root/fc-94c0d9c9-5bbf-47c7-a83e-e3b14b5ea99c/e467c78b-6540-4523-b8e3-44e97e427c4f/PreProcessingForVariantDiscovery_GATK4/2caac1e0-3f33-4cf2-bb53-d10dff61e1ea/call-SortAndFixTags/OGI773_001511.CHM13.aligned.duplicate_marked.sorted.bam Copying gs://fc-94c0d9c9-5bbf-47c7-a83e-e3b14b5ea99c/e467c78b-6540-4523-b8e3-44e97e427c4f/PreProcessingForVariantDiscovery_GATK4/2caac1e0-3f33-4cf2-bb53-d10dff61e1ea/call-SortAndFixTags/OGI773_001511.CHM13.aligned.duplicate_marked.sorted.bam... / [0 files][ 0.0 B/ 25.6 GiB] - 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\ \ [0 files][ 21.6 GiB/ 25.6 GiB] 94.2 MiB/s | / / [0 files][ 21.7 GiB/ 25.6 GiB] 93.7 MiB/s - - [0 files][ 21.8 GiB/ 25.6 GiB] 93.0 MiB/s \ | | [0 files][ 21.9 GiB/ 25.6 GiB] 92.3 MiB/s / - - [0 files][ 22.0 GiB/ 25.6 GiB] 92.7 MiB/s \ \ [0 files][ 22.1 GiB/ 25.6 GiB] 93.1 MiB/s | / / [0 files][ 22.2 GiB/ 25.6 GiB] 93.0 MiB/s - \ \ [0 files][ 22.2 GiB/ 25.6 GiB] 93.4 MiB/s | | [0 files][ 22.3 GiB/ 25.6 GiB] 93.2 MiB/s / - - [0 files][ 22.4 GiB/ 25.6 GiB] 92.5 MiB/s \ | | [0 files][ 22.5 GiB/ 25.6 GiB] 91.6 MiB/s / / [0 files][ 22.6 GiB/ 25.6 GiB] 92.3 MiB/s - \ \ [0 files][ 22.7 GiB/ 25.6 GiB] 92.8 MiB/s | / / [0 files][ 22.8 GiB/ 25.6 GiB] 93.0 MiB/s - - [0 files][ 22.9 GiB/ 25.6 GiB] 93.2 MiB/s \ | | [0 files][ 23.0 GiB/ 25.6 GiB] 93.6 MiB/s / - - [0 files][ 23.1 GiB/ 25.6 GiB] 93.0 MiB/s \ \ [0 files][ 23.2 GiB/ 25.6 GiB] 92.7 MiB/s | / / [0 files][ 23.2 GiB/ 25.6 GiB] 93.2 MiB/s - \ \ [0 files][ 23.3 GiB/ 25.6 GiB] 93.7 MiB/s | | [0 files][ 23.4 GiB/ 25.6 GiB] 93.7 MiB/s / - - [0 files][ 23.5 GiB/ 25.6 GiB] 93.5 MiB/s \ | | [0 files][ 23.6 GiB/ 25.6 GiB] 92.4 MiB/s / / [0 files][ 23.7 GiB/ 25.6 GiB] 90.8 MiB/s - \ \ [0 files][ 23.8 GiB/ 25.6 GiB] 90.1 MiB/s | / / [0 files][ 23.8 GiB/ 25.6 GiB] 85.4 MiB/s - - [0 files][ 23.9 GiB/ 25.6 GiB] 76.1 MiB/s \ | | [0 files][ 23.9 GiB/ 25.6 GiB] 67.8 MiB/s / - - [0 files][ 24.0 GiB/ 25.6 GiB] 63.4 MiB/s \ \ [0 files][ 24.1 GiB/ 25.6 GiB] 63.6 MiB/s | / / [0 files][ 24.2 GiB/ 25.6 GiB] 68.4 MiB/s - \ \ [0 files][ 24.3 GiB/ 25.6 GiB] 77.8 MiB/s | | [0 files][ 24.4 GiB/ 25.6 GiB] 86.6 MiB/s / - - [0 files][ 24.5 GiB/ 25.6 GiB] 92.3 MiB/s \ | | [0 files][ 24.6 GiB/ 25.6 GiB] 92.8 MiB/s / / [0 files][ 24.6 GiB/ 25.6 GiB] 92.8 MiB/s - \ \ [0 files][ 24.7 GiB/ 25.6 GiB] 92.8 MiB/s | / / [0 files][ 24.8 GiB/ 25.6 GiB] 93.0 MiB/s - - [0 files][ 24.9 GiB/ 25.6 GiB] 92.6 MiB/s \ | | [0 files][ 25.0 GiB/ 25.6 GiB] 85.8 MiB/s / - - [0 files][ 25.0 GiB/ 25.6 GiB] 73.0 MiB/s \ \ [0 files][ 25.0 GiB/ 25.6 GiB] 60.3 MiB/s | / / [0 files][ 25.1 GiB/ 25.6 GiB] 47.6 MiB/s - \ \ [0 files][ 25.1 GiB/ 25.6 GiB] 35.1 MiB/s | | [0 files][ 25.2 GiB/ 25.6 GiB] 36.2 MiB/s / - - [0 files][ 25.2 GiB/ 25.6 GiB] 49.2 MiB/s \ | | [0 files][ 25.3 GiB/ 25.6 GiB] 62.0 MiB/s / / [0 files][ 25.4 GiB/ 25.6 GiB] 74.8 MiB/s - \ \ [0 files][ 25.5 GiB/ 25.6 GiB] 87.5 MiB/s | / / [0 files][ 25.6 GiB/ 25.6 GiB] 85.0 MiB/s - - [0 files][ 25.6 GiB/ 25.6 GiB] 72.1 MiB/s \ | | [0 files][ 25.6 GiB/ 25.6 GiB] 59.5 MiB/s / / [1 files][ 25.6 GiB/ 25.6 GiB] 15.8 MiB/s - Operation completed over 1 objects/25.6 GiB. 2022/05/21 01:39:30 Localizing input gs://fc-94c0d9c9-5bbf-47c7-a83e-e3b14b5ea99c/e467c78b-6540-4523-b8e3-44e97e427c4f/PreProcessingForVariantDiscovery_GATK4/2caac1e0-3f33-4cf2-bb53-d10dff61e1ea/call-BaseRecalibrator/shard-10/script -> /cromwell_root/script 2022/05/21 01:39:32 Localizing input gs://mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.fa.dict -> /cromwell_root/mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.fa.dict 2022/05/21 01:39:33 Localizing input gs://mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.fa -> /cromwell_root/mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.fa 2022/05/21 01:39:34 Localizing input gs://mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.fa.fai -> /cromwell_root/mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.fa.fai 2022/05/21 01:39:34 Localizing input gs://mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.dbsnp138.t2t-chm13-v2.0.vcf.gz.tbi -> /cromwell_root/mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.dbsnp138.t2t-chm13-v2.0.vcf.gz.tbi 2022/05/21 01:39:34 Localizing input gs://mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.known_indels.t2t-chm13-v2.0.vcf.gz.tbi -> /cromwell_root/mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.known_indels.t2t-chm13-v2.0.vcf.gz.tbi 2022/05/21 01:39:34 Localizing input gs://mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.dbsnp138.t2t-chm13-v2.0.vcf.gz -> /cromwell_root/mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.dbsnp138.t2t-chm13-v2.0.vcf.gz 2022/05/21 01:39:34 Localizing input gs://mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.known_indels.t2t-chm13-v2.0.vcf.gz -> /cromwell_root/mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.known_indels.t2t-chm13-v2.0.vcf.gz Copying gs://mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.fa... / [0 files][ 0.0 B/ 2.9 GiB] - - [0 files][ 50.5 MiB/ 2.9 GiB] \ | | [0 files][148.2 MiB/ 2.9 GiB] / / [0 files][244.4 MiB/ 2.9 GiB] - \ \ [0 files][335.2 MiB/ 2.9 GiB] | / / [0 files][431.6 MiB/ 2.9 GiB] - - [0 files][528.3 MiB/ 2.9 GiB] \ | | [0 files][620.8 MiB/ 2.9 GiB] / - - [0 files][716.0 MiB/ 2.9 GiB] \ \ [0 files][807.0 MiB/ 2.9 GiB] | / / [0 files][900.3 MiB/ 2.9 GiB] - \ \ [0 files][993.1 MiB/ 2.9 GiB] 92.8 MiB/s | | [0 files][ 1.1 GiB/ 2.9 GiB] 92.4 MiB/s / - - [0 files][ 1.2 GiB/ 2.9 GiB] 92.0 MiB/s \ | | [0 files][ 1.2 GiB/ 2.9 GiB] 92.9 MiB/s / / [0 files][ 1.3 GiB/ 2.9 GiB] 93.5 MiB/s - \ \ [0 files][ 1.4 GiB/ 2.9 GiB] 93.5 MiB/s | / / [0 files][ 1.5 GiB/ 2.9 GiB] 94.2 MiB/s - - [0 files][ 1.6 GiB/ 2.9 GiB] 94.0 MiB/s \ | | [0 files][ 1.7 GiB/ 2.9 GiB] 93.8 MiB/s / - - [0 files][ 1.8 GiB/ 2.9 GiB] 93.4 MiB/s \ \ [0 files][ 1.9 GiB/ 2.9 GiB] 93.9 MiB/s | / / [0 files][ 2.0 GiB/ 2.9 GiB] 93.9 MiB/s - \ \ [0 files][ 2.1 GiB/ 2.9 GiB] 94.3 MiB/s | | [0 files][ 2.2 GiB/ 2.9 GiB] 94.3 MiB/s / - - [0 files][ 2.2 GiB/ 2.9 GiB] 94.3 MiB/s \ | | [0 files][ 2.3 GiB/ 2.9 GiB] 93.8 MiB/s / / [0 files][ 2.4 GiB/ 2.9 GiB] 93.8 MiB/s - \ \ [0 files][ 2.5 GiB/ 2.9 GiB] 93.7 MiB/s | / / [0 files][ 2.6 GiB/ 2.9 GiB] 93.9 MiB/s - - [0 files][ 2.7 GiB/ 2.9 GiB] 93.8 MiB/s \ | | [0 files][ 2.8 GiB/ 2.9 GiB] 90.4 MiB/s / - - [0 files][ 2.8 GiB/ 2.9 GiB] 80.8 MiB/s \ \ [0 files][ 2.9 GiB/ 2.9 GiB] 71.0 MiB/s | / / [0 files][ 2.9 GiB/ 2.9 GiB] 63.5 MiB/s / [1 files][ 2.9 GiB/ 2.9 GiB] 33.0 MiB/s - Copying gs://mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.fa.fai... - [1 files][ 2.9 GiB/ 2.9 GiB] 33.0 MiB/s - [2 files][ 2.9 GiB/ 2.9 GiB] 32.2 MiB/s Copying gs://mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.dbsnp138.t2t-chm13-v2.0.vcf.gz.tbi... - [2 files][ 2.9 GiB/ 2.9 GiB] 32.1 MiB/s - [3 files][ 2.9 GiB/ 2.9 GiB] 31.5 MiB/s Copying gs://mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.known_indels.t2t-chm13-v2.0.vcf.gz.tbi... - [3 files][ 2.9 GiB/ 3.0 GiB] 31.4 MiB/s - [4 files][ 3.0 GiB/ 3.0 GiB] 30.5 MiB/s ==> NOTE: You are performing a sequence of gsutil operations that may run significantly faster if you instead use gsutil -m cp ... Please see the -m section under "gsutil help options" for further information about when gsutil -m can be advantageous. Copying gs://mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.dbsnp138.t2t-chm13-v2.0.vcf.gz... - [4 files][ 3.0 GiB/ 4.9 GiB] 30.4 MiB/s \ | | [4 files][ 3.0 GiB/ 4.9 GiB] 38.3 MiB/s / - - [4 files][ 3.1 GiB/ 4.9 GiB] 47.6 MiB/s \ \ [4 files][ 3.2 GiB/ 4.9 GiB] 80.9 MiB/s | / / [4 files][ 3.3 GiB/ 4.9 GiB] 84.3 MiB/s - \ \ [4 files][ 3.4 GiB/ 4.9 GiB] 94.9 MiB/s | | [4 files][ 3.5 GiB/ 4.9 GiB] 95.0 MiB/s / - - [4 files][ 3.6 GiB/ 4.9 GiB] 95.4 MiB/s \ | | [4 files][ 3.7 GiB/ 4.9 GiB] 95.0 MiB/s / / [4 files][ 3.8 GiB/ 4.9 GiB] 94.0 MiB/s - \ \ [4 files][ 3.9 GiB/ 4.9 GiB] 93.5 MiB/s | / / [4 files][ 4.0 GiB/ 4.9 GiB] 93.3 MiB/s - - [4 files][ 4.0 GiB/ 4.9 GiB] 93.3 MiB/s \ | | [4 files][ 4.1 GiB/ 4.9 GiB] 93.2 MiB/s / - - [4 files][ 4.2 GiB/ 4.9 GiB] 94.0 MiB/s \ \ [4 files][ 4.3 GiB/ 4.9 GiB] 94.3 MiB/s | / / [4 files][ 4.4 GiB/ 4.9 GiB] 94.0 MiB/s - \ \ [4 files][ 4.5 GiB/ 4.9 GiB] 93.9 MiB/s | | [4 files][ 4.6 GiB/ 4.9 GiB] 93.2 MiB/s / - - [4 files][ 4.7 GiB/ 4.9 GiB] 92.6 MiB/s \ | | [4 files][ 4.8 GiB/ 4.9 GiB] 92.2 MiB/s / / [4 files][ 4.9 GiB/ 4.9 GiB] 92.7 MiB/s - \ \ [5 files][ 4.9 GiB/ 4.9 GiB] 16.4 MiB/s | Copying gs://mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.known_indels.t2t-chm13-v2.0.vcf.gz... | [5 files][ 4.9 GiB/ 5.0 GiB] 13.2 MiB/s / / [5 files][ 5.0 GiB/ 5.0 GiB] 20.8 MiB/s - \ \ [5 files][ 5.0 GiB/ 5.0 GiB] 30.8 MiB/s \ [6 files][ 5.0 GiB/ 5.0 GiB] 26.0 MiB/s | Operation completed over 6 objects/5.0 GiB. 2022/05/21 01:40:45 Localization script execution complete. 2022/05/21 01:40:54 Done localization. 2022/05/21 01:40:55 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint=/bin/bash broadinstitute/gatk@sha256:8051adab0ff725e7e9c2af5997680346f3c3799b2df3785dd51d4abdd3da747b /cromwell_root/script Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell_root/tmp.c20a098c 01:41:08.457 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.8.1-local.jar!/com/intel/gkl/native/libgkl_compression.so 01:41:09.618 INFO BaseRecalibrator - ------------------------------------------------------------ 01:41:09.619 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.8.1 01:41:09.620 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 01:41:09.620 INFO BaseRecalibrator - Executing as root@ff13958b1342 on Linux v5.10.107+ amd64 01:41:09.621 INFO BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08 01:41:09.621 INFO BaseRecalibrator - Start Date/Time: May 21, 2022 1:41:08 AM GMT 01:41:09.621 INFO BaseRecalibrator - ------------------------------------------------------------ 01:41:09.622 INFO BaseRecalibrator - ------------------------------------------------------------ 01:41:09.622 INFO BaseRecalibrator - HTSJDK Version: 2.23.0 01:41:09.623 INFO BaseRecalibrator - Picard Version: 2.22.8 01:41:09.623 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 01:41:09.623 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 01:41:09.624 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 01:41:09.624 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 01:41:09.624 INFO BaseRecalibrator - Deflater: IntelDeflater 01:41:09.624 INFO BaseRecalibrator - Inflater: IntelInflater 01:41:09.625 INFO BaseRecalibrator - GCS max retries/reopens: 20 01:41:09.625 INFO BaseRecalibrator - Requester pays: disabled 01:41:09.625 INFO BaseRecalibrator - Initializing engine 01:41:09.653 INFO BaseRecalibrator - Shutting down engine [May 21, 2022 1:41:09 AM GMT] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=4151836672 *********************************************************************** A USER ERROR has occurred: Fasta dict file file:///cromwell_root/mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.dict for reference file:///cromwell_root/mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.fa does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it. *********************************************************************** Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace. Using GATK jar /gatk/gatk-package-4.1.8.1-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 -Xms4G -jar /gatk/gatk-package-4.1.8.1-local.jar BaseRecalibrator -R /cromwell_root/mbc-ngs-us-central1-standard/chm13v2.0/chm13v2.0.fa -I /cromwell_root/fc-94c0d9c9-5bbf-47c7-a83e-e3b14b5ea99c/e467c78b-6540-4523-b8e3-44e97e427c4f/PreProcessingForVariantDiscovery_GATK4/2caac1e0-3f33-4cf2-bb53-d10dff61e1ea/call-SortAndFixTags/OGI773_001511.CHM13.aligned.duplicate_marked.sorted.bam --use-original-qualities -O OGI773_001511.CHM13.recal_data.csv --known-sites /cromwell_root/mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.dbsnp138.t2t-chm13-v2.0.vcf.gz --known-sites /cromwell_root/mbc-ngs-us-central1-standard/chm13v2.0/Homo_sapiens_assembly38.known_indels.t2t-chm13-v2.0.vcf.gz -L chr11:1+ 2022/05/21 01:41:12 Starting delocalization. 2022/05/21 01:41:13 Delocalization script execution started... 2022/05/21 01:41:13 Delocalizing output /cromwell_root/memory_retry_rc -> gs://fc-94c0d9c9-5bbf-47c7-a83e-e3b14b5ea99c/e467c78b-6540-4523-b8e3-44e97e427c4f/PreProcessingForVariantDiscovery_GATK4/2caac1e0-3f33-4cf2-bb53-d10dff61e1ea/call-BaseRecalibrator/shard-10/memory_retry_rc 2022/05/21 01:41:16 Delocalizing output /cromwell_root/rc -> gs://fc-94c0d9c9-5bbf-47c7-a83e-e3b14b5ea99c/e467c78b-6540-4523-b8e3-44e97e427c4f/PreProcessingForVariantDiscovery_GATK4/2caac1e0-3f33-4cf2-bb53-d10dff61e1ea/call-BaseRecalibrator/shard-10/rc 2022/05/21 01:41:18 Delocalizing output /cromwell_root/stdout -> gs://fc-94c0d9c9-5bbf-47c7-a83e-e3b14b5ea99c/e467c78b-6540-4523-b8e3-44e97e427c4f/PreProcessingForVariantDiscovery_GATK4/2caac1e0-3f33-4cf2-bb53-d10dff61e1ea/call-BaseRecalibrator/shard-10/stdout 2022/05/21 01:41:20 Delocalizing output /cromwell_root/stderr -> gs://fc-94c0d9c9-5bbf-47c7-a83e-e3b14b5ea99c/e467c78b-6540-4523-b8e3-44e97e427c4f/PreProcessingForVariantDiscovery_GATK4/2caac1e0-3f33-4cf2-bb53-d10dff61e1ea/call-BaseRecalibrator/shard-10/stderr 2022/05/21 01:41:22 Delocalizing output /cromwell_root/OGI773_001511.CHM13.recal_data.csv -> gs://fc-94c0d9c9-5bbf-47c7-a83e-e3b14b5ea99c/e467c78b-6540-4523-b8e3-44e97e427c4f/PreProcessingForVariantDiscovery_GATK4/2caac1e0-3f33-4cf2-bb53-d10dff61e1ea/call-BaseRecalibrator/shard-10/OGI773_001511.CHM13.recal_data.csv Required file output '/cromwell_root/OGI773_001511.CHM13.recal_data.csv' does not exist. GO TO FILE