No suitable codecs found
I am trying to run GetPileupSummaries, but when running the script I get the error related to no suitable codecs found.
Here is the code:
gatk GetPileupSummaries -I SRR13147304_good.bam -V 1000GENOMES-phase_3.gvf.gz -L 1000GENOMES-phase_3.gvf.gz -O pileups.table
Using GATK jar /home/carlosbarron/Downloads/gatk-4.2.6.1/gatk-package-4.2.6.1-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 -jar /home/carlosbarron/Downloads/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar GetPileupSummaries -I SRR13147304_good.bam -V 1000GENOMES-phase_3.gvf.gz -L 1000GENOMES-phase_3.gvf.gz -O pileups.table
23:06:49.247 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/carlosbarron/Downloads/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
23:06:49.731 INFO GetPileupSummaries - ------------------------------------------------------------
23:06:49.731 INFO GetPileupSummaries - The Genome Analysis Toolkit (GATK) v4.2.6.1
23:06:49.732 INFO GetPileupSummaries - For support and documentation go to https://software.broadinstitute.org/gatk/
23:06:49.732 INFO GetPileupSummaries - Executing as carlosbarron@carlosbarron-HP-Laptop-15-ef1xxx on Linux v5.15.0-33-generic amd64
23:06:49.732 INFO GetPileupSummaries - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_312-8u312-b07-0ubuntu1~20.04-b07
23:06:49.732 INFO GetPileupSummaries - Start Date/Time: June 21, 2022 11:06:49 PM EDT
23:06:49.732 INFO GetPileupSummaries - ------------------------------------------------------------
23:06:49.732 INFO GetPileupSummaries - ------------------------------------------------------------
23:06:49.733 INFO GetPileupSummaries - HTSJDK Version: 2.24.1
23:06:49.733 INFO GetPileupSummaries - Picard Version: 2.27.1
23:06:49.733 INFO GetPileupSummaries - Built for Spark Version: 2.4.5
23:06:49.733 INFO GetPileupSummaries - HTSJDK Defaults.COMPRESSION_LEVEL : 2
23:06:49.734 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
23:06:49.734 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
23:06:49.734 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
23:06:49.734 INFO GetPileupSummaries - Deflater: IntelDeflater
23:06:49.734 INFO GetPileupSummaries - Inflater: IntelInflater
23:06:49.734 INFO GetPileupSummaries - GCS max retries/reopens: 20
23:06:49.734 INFO GetPileupSummaries - Requester pays: disabled
23:06:49.735 INFO GetPileupSummaries - Initializing engine
23:06:50.115 INFO GetPileupSummaries - Shutting down engine
[June 21, 2022 11:06:50 PM EDT] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=450363392
***********************************************************************
A USER ERROR has occurred: Cannot read file:///home/carlosbarron/Documents/Sequencias/1000GENOMES-phase_3.gvf.gz because no suitable codecs found
After that, I tried to get an index for the gvf file using gatk IndexFeatureFile, nevertheless, when running the program I got the same error. I also tried to gunzip my gvf.gz file and then gzip again, thinking of a mistake of the compress method, but still, I get the same error when running the code.
Could someone help me, please?
Comments
1 comment
Hi Carlos,
Thank you for writing in about this issue. Can you share the workspace where you are seeing this issue with Terra Support by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.
Please provide us with
We’ll be happy to take a closer look as soon as we can!
Kind regards,
Josh
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