no suitable codecs found

[ChiaraF32]

Hi,

I am running the RNA variant caller module on a small (9 sample) cohort of fibroblast samples.

I keep running into the following error message:

[June 2, 2023 at 1:08:48 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1056964608
***********************************************************************

A USER ERROR has occurred: Cannot read file:///data/tmp_drop/tmp.oE0SdFCFKy.gz because no suitable codecs found

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
01:08:48.704 WARN  IntelInflater - Zero Bytes Written : 0
01:08:48.704 WARN  IntelInflater - Zero Bytes Written : 0
01:08:48.733 WARN  IntelInflater - Zero Bytes Written : 0
01:08:48.733 WARN  IntelInflater - Zero Bytes Written : 0
01:08:48.740 WARN  IntelInflater - Zero Bytes Written : 0
01:08:48.740 WARN  IntelInflater - Zero Bytes Written : 0
01:08:48.791 INFO  BaseRecalibrator - Shutting down engine
[June 2, 2023 at 1:08:48 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1056964608
***********************************************************************

A USER ERROR has occurred: Cannot read file:///data/tmp_drop/tmp.fRWVSCdByB.gz because no suitable codecs found

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Waiting at most 10 seconds for missing files.
01:08:48.838 INFO  BaseRecalibrator - Shutting down engine
[June 2, 2023 at 1:08:48 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1056964608
***********************************************************************

A USER ERROR has occurred: Cannot read file:///data/tmp_drop/tmp.WUQXm7VROa.gz because no suitable codecs found

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
01:08:49.059 INFO  BaseRecalibrator - Shutting down engine
[June 2, 2023 at 1:08:49 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1056964608
***********************************************************************

A USER ERROR has occurred: Cannot read file:///data/tmp_drop/tmp.I0w0tpzYv2.gz because no suitable codecs found

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
01:08:49.125 INFO  BaseRecalibrator - Shutting down engine
[June 2, 2023 at 1:08:49 AM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1056964608
***********************************************************************

A USER ERROR has occurred: Cannot read file:///data/tmp_drop/tmp.vh4zajDu2N.gz because no suitable codecs found

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
MissingOutputException in rule bqsr in line 446 of /data/drop/FibroGTEx/Scripts/rnaVariantCalling/pipeline/Snakefile:
Job Missing files after 10 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/data/drop/FibroGTEx/output/processed_data/rnaVariantCalling/out/bqsr/D21-0076_recal.table completed successfully, but some output files are missing. 51
Waiting at most 10 seconds for missing files.
MissingOutputException in rule bqsr in line 446 of /data/drop/FibroGTEx/Scripts/rnaVariantCalling/pipeline/Snakefile:
Job Missing files after 10 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/data/drop/FibroGTEx/output/processed_data/rnaVariantCalling/out/bqsr/D19-1541_recal.table completed successfully, but some output files are missing. 19
Waiting at most 10 seconds for missing files.
MissingOutputException in rule bqsr in line 446 of /data/drop/FibroGTEx/Scripts/rnaVariantCalling/pipeline/Snakefile:
Job Missing files after 10 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/data/drop/FibroGTEx/output/processed_data/rnaVariantCalling/out/bqsr/D19-0176_recal.table completed successfully, but some output files are missing. 67
Waiting at most 10 seconds for missing files.
MissingOutputException in rule bqsr in line 446 of /data/drop/FibroGTEx/Scripts/rnaVariantCalling/pipeline/Snakefile:
Job Missing files after 10 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/data/drop/FibroGTEx/output/processed_data/rnaVariantCalling/out/bqsr/D19-1542_recal.table completed successfully, but some output files are missing. 75
Waiting at most 10 seconds for missing files.
MissingOutputException in rule bqsr in line 446 of /data/drop/FibroGTEx/Scripts/rnaVariantCalling/pipeline/Snakefile:
Job Missing files after 10 seconds. This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait:
/data/drop/FibroGTEx/output/processed_data/rnaVariantCalling/out/bqsr/D19-1525_recal.table completed successfully, but some output files are missing. 83
INFO	2023-06-02 01:44:57	ReorderSam	Wrote 185781545 reads
INFO	2023-06-02 01:54:36	ReorderSam	Wrote 227607274 reads
[Fri Jun 02 02:10:04 UTC 2023] picard.sam.ReorderSam done. Elapsed time: 61.34 minutes.
Runtime.totalMemory()=633339904
Tool returned:
0
[Fri Jun  2 02:10:04 2023]

My run command is:

snakemake --cores 14 --default-resources "tmpdir='/data/tmp_drop'" "mem_mb=60000" --latency-wait 10 &> 2_Fibro_VC_June.log

I increased the latency wait time incase the error was due to filesystem latency.

I have attached my config file and full log file.

2_Fibro_VC_June.txt
config.txt

Distribution: Ubuntu 18.04.5

Thanks!

[ischeller]

Hi @ChiaraF32 ,
sorry for the late reply. I saw that in your log file there is also this error:
bcftools: error while loading shared libraries: libgsl.so.25: cannot open shared object file: No such file or directory.
So possibly the final error is a result of this first error. Here it seems that this error is related to the conda installation of bcftools, maybe following one of the suggestions there helps you as well.