Mutect2 PoN best practice pipeline failed with GenomicsDBImport 'A USER ERROR has occurred: Failed to create reader from file' ERROR

August 07, 2020 07:21
Edited

Sorry if I posted twice. I posted it again because the previous post was pending approval. Maybe I inserted too many links in it.

Main Problem：

Mutect2 PoN best practice pipeline executed with WDL+Cromwell failed with GenomicsDBImport 'A USER ERROR has occurred: Failed to create reader from file' ERROR

Any Comments or Suggestions on How to Solve the Error are Highly Appreciated.

Can you please provide
a) GATK version used （docker 4.1.8.0）
b) Exact GATK commands used

config=${bindir}/cromwell.mutect2.conf
cromwell_engine=${bindir}/cromwell-49.jar
wdlscript=${bindir}/gatk4-somatic-snvs-indels-master/mutect2_pon.wdl

importzip=${outputdir}/imports.zip
json=${outputdir}/zb.mutect2.pon.json

java -jar -Dconfig.file=${config} ${cromwell_engine} run ${wdlscript} --imports ${importzip} --inputs ${json} > pon.log 2>&1

c) The entire error log if applicable. Too Long, I just provided the part I thought necessary.

I am running *gatk4-somatic-snvs-indels* best practice archived at:
gatk-workflows/gatk4-somatic-snvs-indels

to call snvs+indels in WES paired samples.

It said that the pipeline was tested successfully on:
GATK version 4.1.4.1
Cromwell version v47

and I am running it on my local machine with:
GATK version 4.1.8.0
Cromwell version v49
because I succeed with version 4.1.8.0 gatk on running *gatk4-data-processing* best practice archived at:
gatk-workflows/gatk4-data-processing

but when I was running *gatk4-somatic-snvs-indels* to build a panel of normals, I ran into several errors:
1. The 1st error was *solved *after I deleted the line:
"Mutect2_Panel.Mutect2.variants_for_contamination":"gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf"
in the provided json file:

gatk-workflows/gatk4-somatic-snvs-indels/blob/master/mutect2_pon.inputs.json

Nowhere in the mutect_2_pon.wdl file "Mutect2_Panel.Mutect2.variants_for_contamination" was claimed as a input, so I guess that this input unexpectedly triggered the imported *mutect2.wdl* to execute "call MergePileupSummaries as MergeTumorPileups" part, which gives an empty output and causes an error.

P.S. Maybe "Mutect2_Panel.Mutect2.variants_for_contamination_idx" should be provided instead of delete "Mutect2_Panel.Mutect2.variants_for_contamination"

2. the 2nd error was an already reported one, but ....
the error message was "genomicsDBImport .A USER ERROR has occurred: Failed to create reader from file"
It was reported in：
a. gatk.broadinstitute.org/hc/en-us/community/posts/360056249211-genomicsDBImport-A-USER-ERROR-has-occurred-Failed-to-create-reader-from-file

caused by wrong file formats, but all the files in my execution were generated by the gatk archived pipeline. So this post doesn't solved my problem

b. gatkforums.broadinstitute.org/gatk/discussion/23966/failed-to-create-reader-error-in-genomicsdbimport

caused by missing vcf index file but index file does exist in the cromwell execution directory.

Then I checked if gatk 4.1.8.0 and 4.1.4.0 version of *gatk genomicsDBImport* tools used different file format as input：
4.1.4.0 gatk.broadinstitute.org/hc/en-us/articles/360036712071-GenomicsDBImport

4.1.8.0 gatk.broadinstitute.org/hc/en-us/articles/360046222251-GenomicsDBImport

there are several updates but the input option remain unchanged.

the entire wdl execution log file is too long to be pasted here.[5000 lines] I am very willing to post any infomation here if necessary.

As I see, the pipeline exit during CreatePanel. 'CreatePanel call' calls 'CreatePanel task' calls 'gatk GenomicsDBImport' and failed.

[First 300 bytes]:Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2_Panel/6b0d1f07-0af7-4df1-bd2e-eef952b5254e/call-CreatePanel/shard-2/attempt-3/tmp.acdf7c8b
15:29:51.117 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.8.0-local.jar!/com/intel/gkl/n
Job Mutect2_Panel.CreatePanel:12:3 exited with return code 2 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /data/user/object/mutect2.pons/cromwell-executions/Mutect2_Panel/6b0d1f07-0af7-4df1-bd2e-eef952b5254e/call-CreatePanel/shard-12/attempt-3/execution/stderr.

the stderr message mentioned in the log file is:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2_Panel/8a515b6f-89d2-4e2c-9adf-bcb612a520c2/call-CreatePanel/shard-0/attempt-3/tmp.d645415d
13:17:59.638 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.8.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jul 17, 2020 1:17:59 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
13:17:59.813 INFO GenomicsDBImport - ------------------------------------------------------------
13:17:59.814 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.8.0
13:17:59.814 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
13:17:59.814 INFO GenomicsDBImport - Executing as root@466abf09f44a on Linux v4.18.0-147.8.1.el8_1.x86_64 amd64
13:17:59.814 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_242-8u242-b08-0ubuntu3~18.04-b08
13:17:59.814 INFO GenomicsDBImport - Start Date/Time: July 17, 2020 1:17:59 PM GMT
13:17:59.814 INFO GenomicsDBImport - ------------------------------------------------------------
13:17:59.814 INFO GenomicsDBImport - ------------------------------------------------------------
13:17:59.815 INFO GenomicsDBImport - HTSJDK Version: 2.22.0
13:17:59.815 INFO GenomicsDBImport - Picard Version: 2.22.8
13:17:59.815 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:17:59.815 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:17:59.815 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:17:59.815 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:17:59.815 INFO GenomicsDBImport - Deflater: IntelDeflater
13:17:59.815 INFO GenomicsDBImport - Inflater: IntelInflater
13:17:59.815 INFO GenomicsDBImport - GCS max retries/reopens: 20
13:17:59.815 INFO GenomicsDBImport - Requester pays: disabled
13:17:59.815 INFO GenomicsDBImport - Initializing engine
13:17:59.832 INFO GenomicsDBImport - Shutting down engine
[July 17, 2020 1:17:59 PM GMT] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1132986368
***********************************************************************

A USER ERROR has occurred: Failed to create reader from file:///data/user/zbraw_freashn/mutect2.pons/cromwell-executions/Mutect2_Panel/8a515b6f-89d2-4e2c-9adf-bcb612a520c2/call-Mutect2/shard-0/Mutect2/e296cf4a-1a6f-4f79-b252-473197857114/call-Filter/execution/samplename[concealed].b37-filtered.vcf

***********************************************************************
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 /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 -jar /root/gatk.jar GenomicsDBImport --genomicsdb-workspace-path pon_db -R /cromwell-executions/Mutect2_Panel/8a515b6f-89d2-4e2c-9adf-bcb612a520c2/call-CreatePanel/shard-0/attempt-3/inputs/1559445236/human_g1k_v37_decoy.fasta -V /data/user/zbraw_freashn/mutect2.pons/cromwell-executions/Mutect2_Panel/8a515b6f-89d2-4e2c-9adf-bcb612a520c2/call-Mutect2/shard-0/Mutect2/e296cf4a-1a6f-4f79-b252-473197857114/call-Filter/execution/samplename[concealed].b37-filtered.vcf -V /data/user/zbraw_freashn/mutect2.pons/cromwell-executions/Mutect2_Panel/8a515b6f-89d2-4e2c-9adf-bcb612a520c2/call-Mutect2/shard-1/Mutect2/bff47bb1-702b-4bfc-829f-52ef94e3fa98/call-Filter/execution/samplename[concealed].b37-filtered.vcf -V /data/user/zbraw_freashn/mutect2.pons/cromwell-executions/Mutect2_Panel/8a515b6f-89d2-4e2c-9adf-bcb612a520c2/call-Mutect2/shard-2/Mutect2/0371d5cd-dcdb-4290-b9d4-021573f9675a/call-Filter/execution/samplename[concealed].b37-filtered.vcf -V /data/user/zbraw_freashn/mutect2.pons/cromwell-executions/Mutect2_Panel/8a515b6f-89d2-4e2c-9adf-bcb612a520c2/call-Mutect2/shard-3/Mutect2/b3fb5a46-eb33-402c-9508-522017ada5dd/call-Filter/execution/samplename[concealed].b37-filtered.vcf -V /data/user/zbraw_freashn/mutect2.pons/cromwell-executions/Mutect2_Panel/8a515b6f-89d2-4e2c-9adf-bcb612a520c2/call-Mutect2/shard-4/Mutect2/921c9f3f-2b08-403d-8ef3-2f949bcf9c0c/call-Filter/execution/samplename[concealed].b37-filtered.vcf -V /data/user/zbraw_freashn/mutect2.pons/cromwell-executions/Mutect2_Panel/8a515b6f-89d2-4e2c-9adf-bcb612a520c2/call-Mutect2/shard-5/Mutect2/c55aaa1a-e3ea-4e60-9477-d5d2cfea595d/call-Filter/execution/samplename[concealed].b37-filtered.vcf -V /data/user/zbraw_freashn/mutect2.pons/cromwell-executions/Mutect2_Panel/8a515b6f-89d2-4e2c-9adf-bcb612a520c2/call-Mutect2/shard-6/Mutect2/562a6add-ac63-4199-813b-6d7f6e49d3f7/call-Filter/execution/samplename[concealed].b37-filtered.vcf -L /cromwell-executions/Mutect2_Panel/8a515b6f-89d2-4e2c-9adf-bcb612a520c2/call-CreatePanel/shard-0/attempt-3/inputs/1617384629/0000-scattered.interval_list
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The problematic command line is:

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 /root/gatk.jar GenomicsDBImport --genomicsdb-workspace-path pon_db -R /cromwell-executions/Mutect2_Panel/6b0d1f07-0af7-4df1-bd2e-eef952b5254e/call-CreatePanel/shard-0/attempt-3/inputs/1559445236/human_g1k_v37_decoy.fasta -V /data/user/object/mutect2.pons/cromwell-executions/Mutect2_Panel/6b0d1f07-0af7-4df1-bd2e-eef952b5254e/call-Mutect2/shard-0/Mutect2/72a2075c-b6f4-46c5-892a-f95885518121/call-Filter/execution/samplename[concealed].b37-filtered.vcf -V /data/user/object/mutect2.pons/cromwell-executions/Mutect2_Panel/6b0d1f07-0af7-4df1-bd2e-eef952b5254e/call-Mutect2/shard-1/Mutect2/571a1129-fec6-44eb-8b98-e8c91f2a1d70/call-Filter/execution/samplename[concealed].b37-filtered.vcf -V /data/user/object/mutect2.pons/cromwell-executions/Mutect2_Panel/6b0d1f07-0af7-4df1-bd2e-eef952b5254e/call-Mutect2/shard-2/Mutect2/daa95ba0-e4aa-423a-8970-2f66119ff914/call-Filter/execution/samplename[concealed].b37-filtered.vcf -V /data/user/object/mutect2.pons/cromwell-executions/Mutect2_Panel/6b0d1f07-0af7-4df1-bd2e-eef952b5254e/call-Mutect2/shard-3/Mutect2/ddb7d2fb-f764-4667-9ed6-52159d527b31/call-Filter/execution/samplename[concealed].b37-filtered.vcf -V /data/user/object/mutect2.pons/cromwell-executions/Mutect2_Panel/6b0d1f07-0af7-4df1-bd2e-eef952b5254e/call-Mutect2/shard-4/Mutect2/c587c2a2-4f6d-45c7-a296-99813dc4f0f6/call-Filter/execution/samplename[concealed].b37-filtered.vcf -V /data/user/object/mutect2.pons/cromwell-executions/Mutect2_Panel/6b0d1f07-0af7-4df1-bd2e-eef952b5254e/call-Mutect2/shard-5/Mutect2/e3f328e4-15a3-41f5-98e6-f4e381e2c9b0/call-Filter/execution/samplename[concealed].b37-filtered.vcf -V /data/user/object/mutect2.pons/cromwell-executions/Mutect2_Panel/6b0d1f07-0af7-4df1-bd2e-eef952b5254e/call-Mutect2/shard-6/Mutect2/1102f3d0-0de1-4feb-9b93-9c9b0ba79b79/call-Filter/execution/samplename[concealed].b37-filtered.vcf -L /cromwell-executions/Mutect2_Panel/6b0d1f07-0af7-4df1-bd2e-eef952b5254e/call-CreatePanel/shard-0/attempt-3/inputs/1890662442/0000-scattered.interval_list

I found the vcf files of each sample, and instead of running it as a part of the wdl pipeline, I ran it independently on the command line as follows:

gatk --java-options "-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" GenomicsDBImport --genomicsdb-workspace-path pon_db -R /data/wangzw/zbraw_freashn/input/human_g1k_v37_decoy.fasta -V ./100336AZW1.b37-filtered.vcf -V ./104260AZW1.b37-filtered.vcf -V ./104261AZW1.b37-filtered.vcf -V ./105023AZW1.b37-filtered.vcf -V ./105603AZW1.b37-filtered.vcf -V ./11T001353W.b37-filtered.vcf -V ./11T004419W.b37-filtered.vcf -L /data/wangzw/zbraw_freashn/input/common_sites.interval_list

The command is now executable (while has not finished yet). The log is:

Using GATK jar /root/WZW/20200512_wes_p3/bin/gatk-4.1.8.0/gatk-package-4.1.8.0-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 -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 /root/WZW/20200512_wes_p3/bin/gatk-4.1.8.0/gatk-package-4.1.8.0-local.jar GenomicsDBImport --genomicsdb-workspace-path pon_db -R /data/user/project/input/human_g1k_v37_decoy.fasta -V ./samplename[concealed].b37-filtered.vcf -V ./samplename[concealed].b37-filtered.vcf -V ./samplename[concealed].b37-filtered.vcf -V ./samplename[concealed].b37-filtered.vcf -V ./samplename[concealed].b37-filtered.vcf -V ./samplename[concealed].b37-filtered.vcf -V ./samplename[concealed].b37-filtered.vcf -L /data/user/project/input/common_sites.interval_list
10:32:03.046 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/root/WZW/20200512_wes_p3/bin/gatk-4.1.8.0/gatk-package-4.1.8.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Jul 20, 2020 10:32:03 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
10:32:03.210 INFO GenomicsDBImport - ------------------------------------------------------------
10:32:03.210 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.8.0
10:32:03.210 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
10:32:03.210 INFO GenomicsDBImport - Executing as root@ljlab on Linux v4.18.0-147.8.1.el8_1.x86_64 amd64
10:32:03.210 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v11.0.1+13-LTS
10:32:03.211 INFO GenomicsDBImport - Start Date/Time: July 20, 2020 at 10:32:03 AM CST
10:32:03.211 INFO GenomicsDBImport - ------------------------------------------------------------
10:32:03.211 INFO GenomicsDBImport - ------------------------------------------------------------
10:32:03.211 INFO GenomicsDBImport - HTSJDK Version: 2.22.0
10:32:03.211 INFO GenomicsDBImport - Picard Version: 2.22.8
10:32:03.211 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
10:32:03.211 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:32:03.211 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:32:03.211 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:32:03.212 INFO GenomicsDBImport - Deflater: IntelDeflater
10:32:03.212 INFO GenomicsDBImport - Inflater: IntelInflater
10:32:03.212 INFO GenomicsDBImport - GCS max retries/reopens: 20
10:32:03.212 INFO GenomicsDBImport - Requester pays: disabled
10:32:03.212 INFO GenomicsDBImport - Initializing engine
10:32:03.488 INFO FeatureManager - Using codec IntervalListCodec to read file file:///data/user/project/input/common_sites.interval_list
10:32:33.850 INFO IntervalArgumentCollection - Processing 11034962 bp from intervals
10:32:34.371 WARN GenomicsDBImport - A large number of intervals were specified. Using more than 100 intervals in a single import is not recommended and can cause performance to suffer. If GVCF data only exists within those intervals, performance can be improved by aggregating intervals with the merge-input-intervals argument.
10:32:34.392 INFO GenomicsDBImport - Done initializing engine
10:32:34.603 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.3.0-e701905
10:32:34.604 INFO GenomicsDBImport - Vid Map JSON file will be written to /data/user/project/mutect2.pons/cromwell-executions/Mutect2_Panel/50f317ea-4193-4d6d-86cf-b647e9fedd5e/pon_db/vidmap.json
10:32:34.604 INFO GenomicsDBImport - Callset Map JSON file will be written to /data/user/project/mutect2.pons/cromwell-executions/Mutect2_Panel/50f317ea-4193-4d6d-86cf-b647e9fedd5e/pon_db/callset.json
10:32:34.604 INFO GenomicsDBImport - Complete VCF Header will be written to /data/user/project/mutect2.pons/cromwell-executions/Mutect2_Panel/50f317ea-4193-4d6d-86cf-b647e9fedd5e/pon_db/vcfheader.vcf
10:32:34.604 INFO GenomicsDBImport - Importing to workspace - /data/user/project/mutect2.pons/cromwell-executions/Mutect2_Panel/50f317ea-4193-4d6d-86cf-b647e9fedd5e/pon_db
10:32:34.604 INFO ProgressMeter - Starting traversal
10:32:34.604 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute

10 comments

Jason Cerrato

July 21, 2020 20:52
Hi WangZiwei,

Thanks for writing in. I'll take a look at this and get back to you as soon as I can.

Kind regards,

Jason
1

Comment actions Permalink
Jason Cerrato

July 30, 2020 20:48
Hi WangZiwei,

Can you confirm which version of the Mutect2 workflow you are using?

https://dockstore.org/my-workflows/github.com/broadinstitute/gatk/mutect2

Examining the versions of the workflow, we don't currently have a 4.1.8.0 version. Can you confirm whether this workflow works when you use a version with the equivalent GATK version - for example, version 4.1.6.0 of Mutect2 with the 4.1.6.0 GATK4 docker.

Kind regards,

Jason
0

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WangZiwei

August 03, 2020 13:55
Hi Jason Cerrato

Sorry for replying late.

I did arbitarily change the gatk4 version to 4.1.8.0, I will keep the workflow as it is and try to run it again.

The workflow I used is the one archived in https://github.com/gatk-workflows/gatk4-somatic-snvs-indels

It said that the pipeline was tested successfully on:
GATK version 4.1.4.1
Cromwell version v47

and I am running it on my local machine with:
GATK version 4.1.8.0
Cromwell version v49

Have a nice day!

Wang Ziwei
0

Comment actions Permalink
Jason Cerrato

August 04, 2020 12:57
Hi Wang,

Please let us know how it goes!

Kind regards,

Jason
0

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WangZiwei

August 05, 2020 14:11
Edited

Hi Jason Cerrato ,

I switched to gatk 4.1.4.1 docker but still got an error at "GetPileupSummaries" step and exit, I believe it is involved in detecting variants for contamination things.

Here is the Cromwell execution log file. I pick the part I think important.

### GetPileupSummaries
# These must be created, even if they remain empty, as cromwell doesn't support optional output
touch tumor-pileups.table
touch normal-pileups.table

if [[ ! -z "/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5/inputs/1139317085/variants_for_contamination.vcf" ]]; then
gatk --java-options "-Xmx3000m" GetPileupSummaries -R /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5/inputs/1139317085/human_g1k_v37_decoy.fasta -I /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5/inputs/-1577115655/11T004419WB1.b37.bam --interval-set-rule INTERSECTION -L /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5/inputs/429898421/0005-scattered.interval_list \
-V /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5/inputs/1139317085/variants_for_contamination.vcf -L /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5/inputs/1139317085/variants_for_contamination.vcf -O tumor-pileups.table

if [[ ! -z "" ]]; then
gatk --java-options "-Xmx3000m" GetPileupSummaries -R /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5/inputs/1139317085/human_g1k_v37_decoy.fasta -I --interval-set-rule INTERSECTION -L /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5/inputs/429898421/0005-scattered.interval_list \
-V /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5/inputs/1139317085/variants_for_contamination.vcf -L /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5/inputs/1139317085/variants_for_contamination.vcf -O normal-pileups.table
fi
fi[0m
[2020-08-05 11:39:32,41] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m98326f95[0mMutect2.M2:5:1]: executing: docker run \
--rm -i \
\
--entrypoint /bin/bash \
-v /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5:/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5 \
broadinstitute/gatk@sha256:f80d33060cb4872d29b9a248b193d267f838b1a636c5a6120aaa45b08a1f09e9 /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-5/Mutect2/98326f95-58f7-452c-88d1-3c51a0a61f55/call-M2/shard-5/execution/script
[2020-08-05 11:39:35,32] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m98326f95[0mMutect2.M2:5:1]: job id: 27762
[2020-08-05 11:39:35,32] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m98326f95[0mMutect2.M2:5:1]: Status change from - to WaitingForReturnCode
[2020-08-05 11:41:49,75] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m98326f95[0mMutect2.M2:7:1]: Status change from WaitingForReturnCode to Done
[2020-08-05 11:42:13,53] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m98326f95[0mMutect2.M2:2:1]: Status change from WaitingForReturnCode to Done
[2020-08-05 11:43:48,28] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m98326f95[0mMutect2.M2:9:1]: Status change from WaitingForReturnCode to Done
[2020-08-05 11:44:11,52] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m98326f95[0mMutect2.M2:5:1]: Status change from WaitingForReturnCode to Done
[2020-08-05 11:44:13,71] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m98326f95[0mMutect2.M2:0:1]: Status change from WaitingForReturnCode to Done
[2020-08-05 11:44:15,68] [info] WorkflowManagerActor Workflow b8e8d572-a4de-44fd-b726-95519a96be86 failed (during ExecutingWorkflowState): Job Mutect2.M2:8:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/execution/stderr.
[First 300 bytes]:Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/tmp.ed7dbd30
03:09:09.139 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/
Job Mutect2.M2:3:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-3/execution/stderr.
[First 300 bytes]:Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-3/tmp.feb9ba54
03:09:50.997 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/
Job Mutect2.M2:4:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-4/execution/stderr.
[First 300 bytes]:Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-4/tmp.9f9e661e
03:10:07.070 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/
Job Mutect2.M2:6:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-6/execution/stderr.
[First 300 bytes]:Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-6/tmp.49492ce3
03:11:03.142 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/

here is the stderrs from GetPileupSummaries. I read the log above, saw lines like

"Check the content of stderr for potential additional information: /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/execution/stderr."

the stderr says :

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/tmp.ed7dbd30
03:09:09.139 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Aug 05, 2020 3:09:09 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
03:09:09.333 INFO GetSampleName - ------------------------------------------------------------
03:09:09.334 INFO GetSampleName - The Genome Analysis Toolkit (GATK) v4.1.4.1
03:09:09.334 INFO GetSampleName - For support and documentation go to https://software.broadinstitute.org/gatk/
03:09:09.334 INFO GetSampleName - Executing as root@3422bf65747c on Linux v4.18.0-147.8.1.el8_1.x86_64 amd64
03:09:09.334 INFO GetSampleName - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03
03:09:09.335 INFO GetSampleName - Start Date/Time: August 5, 2020 3:09:09 AM UTC
03:09:09.335 INFO GetSampleName - ------------------------------------------------------------
03:09:09.335 INFO GetSampleName - ------------------------------------------------------------
03:09:09.335 INFO GetSampleName - HTSJDK Version: 2.21.0
03:09:09.335 INFO GetSampleName - Picard Version: 2.21.2
03:09:09.335 INFO GetSampleName - HTSJDK Defaults.COMPRESSION_LEVEL : 2
03:09:09.335 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
03:09:09.336 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
03:09:09.336 INFO GetSampleName - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
03:09:09.336 INFO GetSampleName - Deflater: IntelDeflater
03:09:09.336 INFO GetSampleName - Inflater: IntelInflater
03:09:09.336 INFO GetSampleName - GCS max retries/reopens: 20
03:09:09.336 INFO GetSampleName - Requester pays: disabled
03:09:09.336 INFO GetSampleName - Initializing engine
03:09:09.625 INFO GetSampleName - Done initializing engine
03:09:09.626 INFO ProgressMeter - Starting traversal
03:09:09.627 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
03:09:09.627 INFO ProgressMeter - unmapped 0.0 0 NaN
03:09:09.627 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
03:09:09.628 INFO GetSampleName - Shutting down engine
[August 5, 2020 3:09:09 AM UTC] org.broadinstitute.hellbender.tools.GetSampleName done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1109917696
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 -Xmx3000m -jar /root/gatk.jar GetSampleName -R /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/1139317085/human_g1k_v37_decoy.fasta -I /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/-1577115655/105023AZW1B1.b37.bam -O tumor_name.txt -encode
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/tmp.ed7dbd30
03:09:11.985 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Aug 05, 2020 3:09:12 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
03:09:12.182 INFO Mutect2 - ------------------------------------------------------------
03:09:12.183 INFO Mutect2 - The Genome Analysis Toolkit (GATK) v4.1.4.1
03:09:12.183 INFO Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
03:09:12.183 INFO Mutect2 - Executing as root@3422bf65747c on Linux v4.18.0-147.8.1.el8_1.x86_64 amd64
03:09:12.183 INFO Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03
03:09:12.183 INFO Mutect2 - Start Date/Time: August 5, 2020 3:09:11 AM UTC
03:09:12.183 INFO Mutect2 - ------------------------------------------------------------
03:09:12.183 INFO Mutect2 - ------------------------------------------------------------
03:09:12.184 INFO Mutect2 - HTSJDK Version: 2.21.0
03:09:12.184 INFO Mutect2 - Picard Version: 2.21.2
03:09:12.184 INFO Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
03:09:12.184 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
03:09:12.184 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
03:09:12.184 INFO Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
03:09:12.184 INFO Mutect2 - Deflater: IntelDeflater
03:09:12.184 INFO Mutect2 - Inflater: IntelInflater
03:09:12.184 INFO Mutect2 - GCS max retries/reopens: 20
03:09:12.184 INFO Mutect2 - Requester pays: disabled
03:09:12.184 INFO Mutect2 - Initializing engine
03:09:12.485 INFO FeatureManager - Using codec IntervalListCodec to read file file:///cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/-878894379/0008-scattered.interval_list
03:09:12.777 INFO IntervalArgumentCollection - Processing 3294456 bp from intervals
03:09:12.838 INFO Mutect2 - Done initializing engine
03:09:12.861 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/gatk/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_utils.so
03:09:12.863 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/gatk/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
03:09:12.909 INFO IntelPairHmm - Using CPU-supported AVX-512 instructions
03:09:12.909 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
03:09:12.909 INFO IntelPairHmm - Available threads: 16
03:09:12.909 INFO IntelPairHmm - Requested threads: 4
03:09:12.909 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
03:09:12.948 INFO ProgressMeter - Starting traversal
03:09:12.948 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
03:09:22.960 INFO ProgressMeter - 17:2371055 0.2 820 4914.1
03:09:33.021 INFO ProgressMeter - 17:7385417 0.3 2400 7173.8
03:09:43.027 INFO ProgressMeter - 17:15641311 0.5 3930 7839.4
03:09:53.059 INFO ProgressMeter - 17:27982579 0.7 5590 8361.8
03:10:04.528 INFO ProgressMeter - 17:34801361 0.9 6540 7607.6
03:10:16.382 INFO ProgressMeter - 17:39274556 1.1 7720 7302.1
03:10:26.457 INFO ProgressMeter - 17:39538151 1.2 7840 6399.2
03:10:36.481 INFO ProgressMeter - 17:47388674 1.4 10040 7211.5
03:10:46.497 INFO ProgressMeter - 17:66985168 1.6 12460 7991.6
03:10:56.507 INFO ProgressMeter - 17:78326740 1.7 14530 8418.4
03:11:07.543 INFO ProgressMeter - 18:9888020 1.9 16080 8419.2
03:11:17.607 INFO ProgressMeter - 18:21739763 2.1 16900 8134.2
03:11:27.717 INFO ProgressMeter - 18:55221492 2.2 18440 8209.6
03:11:37.732 INFO ProgressMeter - 19:1041830 2.4 19870 8234.3
03:11:48.391 INFO ProgressMeter - 19:4511793 2.6 21350 8241.0
03:11:58.491 INFO ProgressMeter - 19:8993007 2.8 22810 8267.3
03:12:08.502 INFO ProgressMeter - 19:10402465 2.9 23450 8014.6
03:12:18.508 INFO ProgressMeter - 19:14774230 3.1 25040 8096.6
03:12:24.046 INFO Mutect2 - 165884 read(s) filtered by: (((((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonChimericOriginalAlignmentReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND ReadLengthReadFilter) AND GoodCigarReadFilter) AND WellformedReadFilter)
165884 read(s) filtered by: ((((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonChimericOriginalAlignmentReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter) AND ReadLengthReadFilter) AND GoodCigarReadFilter)
165884 read(s) filtered by: (((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonChimericOriginalAlignmentReadFilter)
AND NonZeroReferenceLengthAlignmentReadFilter) AND ReadLengthReadFilter)
165884 read(s) filtered by: ((((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonChimericOriginalAlignmentReadFilter) AND NonZeroReferenceLengthAlignmentReadFilter)
165884 read(s) filtered by: (((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter) AND NonChimericOriginalAlignmentReadFilter)
165884 read(s) filtered by: ((((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter) AND PassesVendorQualityCheckReadFilter)
165884 read(s) filtered by: (((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter) AND NotDuplicateReadFilter)
163842 read(s) filtered by: ((((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter) AND NotSecondaryAlignmentReadFilter)
163842 read(s) filtered by: (((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter) AND MappedReadFilter)
163842 read(s) filtered by: ((MappingQualityReadFilter AND MappingQualityAvailableReadFilter) AND MappingQualityNotZeroReadFilter)
163842 read(s) filtered by: (MappingQualityReadFilter AND MappingQualityAvailableReadFilter)
163842 read(s) filtered by: MappingQualityReadFilter 
2042 read(s) filtered by: NotDuplicateReadFilter

03:12:24.046 INFO ProgressMeter - 19:17014371 3.2 25731 8078.9
03:12:24.047 INFO ProgressMeter - Traversal complete. Processed 25731 total regions in 3.2 minutes.
03:12:24.093 INFO VectorLoglessPairHMM - Time spent in setup for JNI call : 0.195592328
03:12:24.093 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 29.540971090000003
03:12:24.093 INFO SmithWatermanAligner - Total compute time in java Smith-Waterman : 28.41 sec
03:12:24.094 INFO Mutect2 - Shutting down engine
[August 5, 2020 3:12:24 AM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 3.20 minutes.
Runtime.totalMemory()=1353187328
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 -Xmx3000m -jar /root/gatk.jar Mutect2 -R /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/1139317085/human_g1k_v37_decoy.fasta -I /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/-1577115655/105023AZW1B1.b37.bam -tumor 105023AZW1B1 -L /crom
well-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/-878894379/0008-scattered.interval_list -O output.vcf --max-mnp-distance 0
Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/tmp.ed7dbd30
03:12:26.395 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Aug 05, 2020 3:12:26 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
03:12:26.550 INFO GetPileupSummaries - ------------------------------------------------------------
03:12:26.550 INFO GetPileupSummaries - The Genome Analysis Toolkit (GATK) v4.1.4.1
03:12:26.550 INFO GetPileupSummaries - For support and documentation go to https://software.broadinstitute.org/gatk/
03:12:26.551 INFO GetPileupSummaries - Executing as root@3422bf65747c on Linux v4.18.0-147.8.1.el8_1.x86_64 amd64
03:12:26.551 INFO GetPileupSummaries - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03
03:12:26.551 INFO GetPileupSummaries - Start Date/Time: August 5, 2020 3:12:26 AM UTC
03:12:26.551 INFO GetPileupSummaries - ------------------------------------------------------------
03:12:26.551 INFO GetPileupSummaries - ------------------------------------------------------------
03:12:26.551 INFO GetPileupSummaries - HTSJDK Version: 2.21.0
03:12:26.551 INFO GetPileupSummaries - Picard Version: 2.21.2
03:12:26.552 INFO GetPileupSummaries - HTSJDK Defaults.COMPRESSION_LEVEL : 2
03:12:26.552 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
03:12:26.552 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
03:12:26.552 INFO GetPileupSummaries - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
03:12:26.552 INFO GetPileupSummaries - Deflater: IntelDeflater
03:12:26.552 INFO GetPileupSummaries - Inflater: IntelInflater
03:12:26.552 INFO GetPileupSummaries - GCS max retries/reopens: 20
03:12:26.552 INFO GetPileupSummaries - Requester pays: disabled
03:12:26.552 INFO GetPileupSummaries - Initializing engine
03:12:26.863 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/1139317085/variants_for_contamination.vcf
03:12:26.884 INFO FeatureManager - Using codec IntervalListCodec to read file file:///cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/-878894379/0008-scattered.interval_list
03:12:27.292 INFO FeatureManager - Using codec VCFCodec to read file file:///cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/1139317085/variants_for_contamination.vcf
03:12:28.605 INFO GetPileupSummaries - Shutting down engine
[August 5, 2020 3:12:28 AM UTC] org.broadinstitute.hellbender.tools.walkers.contamination.GetPileupSummaries done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1470627840
USAGE: GetPileupSummaries [arguments]

Tabulates pileup metrics for inferring contamination
Version:4.1.4.1


Required Arguments:

--input,-I:String BAM/SAM/CRAM file containing reads This argument must be specified at least once.
Required.

--intervals,-L:String One or more genomic intervals over which to operate This argument must be specified at
least once. Required.

--output,-O:File The output table Required.

--variant,-V:FeatureInput A VCF file containing variants and allele frequencies Required.


Optional Arguments:

--add-output-sam-program-record,-add-output-sam-program-record:Boolean
If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible
values: {true, false}

--add-output-vcf-command-line,-add-output-vcf-command-line:Boolean
If true, adds a command line header line to created VCF files. Default value: true.
Possible values: {true, false}

--arguments_file:File read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.

--cloud-index-prefetch-buffer,-CIPB:Integer
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to
cloudPrefetchBuffer if unset. Default value: -1.

--cloud-prefetch-buffer,-CPB:Integer
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40.

--create-output-bam-index,-OBI:Boolean
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default
value: true. Possible values: {true, false}

--create-output-bam-md5,-OBM:Boolean
If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false.
Possible values: {true, false}

--create-output-variant-index,-OVI:Boolean
If true, create a VCF index when writing a coordinate-sorted VCF file. Default value:
true. Possible values: {true, false}

--create-output-variant-md5,-OVM:Boolean
If true, create a a MD5 digest any VCF file created. Default value: false. Possible
values: {true, false}

--disable-bam-index-caching,-DBIC:Boolean
If true, don't cache bam indexes, this will reduce memory requirements but may harm
performance if many intervals are specified. Caching is automatically disabled if there
are no intervals specified. Default value: false. Possible values: {true, false}

--disable-read-filter,-DF:String
Read filters to be disabled before analysis This argument may be specified 0 or more
times. Default value: null. Possible Values: {GoodCigarReadFilter, MappedReadFilter,
MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
MateOnSameContigOrNoMappedMateReadFilter, NonZeroReferenceLengthAlignmentReadFilter,
NotDuplicateReadFilter, PassesVendorQualityCheckReadFilter, PrimaryLineReadFilter,
WellformedReadFilter}

--disable-sequence-dictionary-validation,-disable-sequence-dictionary-validation:Boolean
If specified, do not check the sequence dictionaries from our inputs for compatibility.
Use at your own risk! Default value: false. Possible values: {true, false}

--exclude-intervals,-XL:StringOne or more genomic intervals to exclude from processing This argument may be specified 0
or more times. Default value: null.

--gatk-config-file:String A configuration file to use with the GATK. Default value: null.

--gcs-max-retries,-gcs-retries:Integer
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
connection Default value: 20.

--gcs-project-for-requester-pays:String
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
accessed. Default value: .

--help,-h:Boolean display the help message Default value: false. Possible values: {true, false}

--interval-exclusion-padding,-ixp:Integer
Amount of padding (in bp) to add to each interval you are excluding. Default value: 0.

--interval-merging-rule,-imr:IntervalMergingRule
Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL,
OVERLAPPING_ONLY}

--interval-padding,-ip:IntegerAmount of padding (in bp) to add to each interval you are including. Default value: 0.

--interval-set-rule,-isr:IntervalSetRule
Set merging approach to use for combining interval inputs Default value: UNION. Possible
values: {UNION, INTERSECTION}

--lenient,-LE:Boolean Lenient processing of VCF files Default value: false. Possible values: {true, false}

--max-depth-per-sample,-max-depth-per-sample:Integer
Maximum number of reads to retain per sample per locus. Reads above this threshold will be
downsampled. Set to 0 to disable. Default value: 0.

--maximum-population-allele-frequency,-max-af:Double
Maximum population allele frequency of sites to consider. Default value: 0.2.

--min-mapping-quality,-mmq:Integer
Minimum read mapping quality Default value: 50.

--minimum-population-allele-frequency,-min-af:Double
Minimum population allele frequency of sites to consider. A low value increases accuracy
at the expense of speed. Default value: 0.01.

--QUIET:Boolean Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}

--read-filter,-RF:String Read filters to be applied before analysis This argument may be specified 0 or more
times. Default value: null. Possible Values: {AlignmentAgreesWithHeaderReadFilter,
AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator,
FirstOfPairReadFilter, FragmentLengthReadFilter, GoodCigarReadFilter,
HasReadGroupReadFilter, IntervalOverlapReadFilter, LibraryReadFilter, MappedReadFilter,
MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter,
MateOnSameContigOrNoMappedMateReadFilter, MateUnmappedAndUnmappedReadFilter,
MetricsReadFilter, NonChimericOriginalAlignmentReadFilter,
NonZeroFragmentLengthReadFilter, NonZeroReferenceLengthAlignmentReadFilter,
NotDuplicateReadFilter, NotOpticalDuplicateReadFilter, NotSecondaryAlignmentReadFilter,
NotSupplementaryAlignmentReadFilter, OverclippedReadFilter, PairedReadFilter,
PassesVendorQualityCheckReadFilter, PlatformReadFilter, PlatformUnitReadFilter,
PrimaryLineReadFilter, ProperlyPairedReadFilter, ReadGroupBlackListReadFilter,
ReadGroupReadFilter, ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter,
ReadNameReadFilter, ReadStrandFilter, SampleReadFilter, SecondOfPairReadFilter,
SeqIsStoredReadFilter, SoftClippedReadFilter, ValidAlignmentEndReadFilter,
ValidAlignmentStartReadFilter, WellformedReadFilter}

--read-index,-read-index:String
Indices to use for the read inputs. If specified, an index must be provided for every read
input and in the same order as the read inputs. If this argument is not specified, the
path to the index for each input will be inferred automatically. This argument may be
specified 0 or more times. Default value: null.

--read-validation-stringency,-VS:ValidationStringency
Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default
stringency value SILENT can improve performance when processing a BAM file in which
variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default
value: SILENT. Possible values: {STRICT, LENIENT, SILENT}

--reference,-R:String Reference sequence Default value: null.

--seconds-between-progress-updates,-seconds-between-progress-updates:Double
Output traversal statistics every time this many seconds elapse Default value: 10.0.

--sequence-dictionary,-sequence-dictionary:String
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a
.dict file. Default value: null.

--sites-only-vcf-output:Boolean
If true, don't emit genotype fields when writing vcf file output. Default value: false.
Possible values: {true, false}

--tmp-dir:GATKPathSpecifier Temp directory to use. Default value: null.

--use-jdk-deflater,-jdk-deflater:Boolean
Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false.
Possible values: {true, false}

--use-jdk-inflater,-jdk-inflater:Boolean
Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false.
Possible values: {true, false}

--verbosity,-verbosity:LogLevel
Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}

--version:Boolean display the version number for this tool Default value: false. Possible values: {true,
false}


Advanced Arguments:

--disable-tool-default-read-filters,-disable-tool-default-read-filters:Boolean
Disable all tool default read filters (WARNING: many tools will not function correctly
without their default read filters on) Default value: false. Possible values: {true,
false}

--showHidden,-showHidden:Boolean
display hidden arguments Default value: false. Possible values: {true, false}


***********************************************************************

A USER ERROR has occurred: Argument -L, --interval-set-rule has a bad value: [/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/-878894379/0008-scattered.interval_list, /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/1139317085/variants_for_contamination.vcf],INTERSECTION. The specified intervals had an empty intersection

***********************************************************************
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 /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 -Xmx3000m -jar /root/gatk.jar GetPileupSummaries -R /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/1139317085/human_g1k_v37_decoy.fasta -I /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/-1577115655/105023AZW1B1.b37.bam --interval-set-rule INTERSECTION -L /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/-878894379/0008-scattered.interval_list -V /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/1139317085/variants_for_contamination.vcf -L /cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/1139317085/variants_for_contamination.vcf -O tumor-pileups.table

I believe:

A USER ERROR has occurred: Argument -L, --interval-set-rule has a bad value

and

The specified intervals had an empty intersection

maybe are important for solving the error but currently i have no idea. Could you please give some comments? Did I feed the pipeline with wrong files?

I am analysing wes data and I am creating a panel of normal. the interval_list file is provided by the vendor and i lifted it over from hg19 to b37. the variants_for_contamination file was provided as guided.

Jason Cerrato

August 05, 2020 20:53
Hi WangZiwei,

I believe you are correct in your understanding.

/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/-878894379/0008-scattered.interval_list,

/cromwell-executions/Mutect2_Panel/b8e8d572-a4de-44fd-b726-95519a96be86/call-Mutect2/shard-2/Mutect2/152d431e-30f4-4ff9-9fdf-edb71e56f86d/call-M2/shard-8/inputs/1139317085/variants_for_contamination.vcf],INTERSECTION. The specified intervals had an empty intersection

Can you examine these files to confirm that your interval list is not malformed or that the vcf is not missing a region defined by the interval file?

Kind regards,
Jason
0

Comment actions Permalink

WangZiwei

August 07, 2020 08:03
Edited

Hi Jason Cerrato

I found these 2 files have no intersection. I think it is because I generate variants_for_contamination.vcf in a wrong way.

so I add -L xgen_exome_panel_v2_targets_b37_somatic.interval_list to the original command

gatk SelectVariants -V af-only-gnomad.raw.sites.vcf --restrict-alleles-to BIALLELIC --select "AF > 0.01" -O variants_for_contamination.vcf

Also，I added a few lines in what I believe is an incomplete json example provided by gatk github ( https://github.com/gatk-workflows/gatk4-somatic-snvs-indels/blob/master/mutect2_pon.inputs.json ) including:

"Mutect2_Panel.Mutect2.variants_for_contamination_idx":"***.vcf.idx",
and
"Mutect2_Panel.gnomad_idx":"***.vcf.idx",

then using gatk docker 4.1.4.1

then everything went well until I got an error which seems to be the one I posted at the very beginning :(

the cromwell log is:

[2020-08-07 10:39:22,74] [info] WorkflowManagerActor Workflow 9e7a9c3b-b2e2-4293-ba67-9e16c377ceea failed (during ExecutingWorkflowState): Job Mutect2_Panel.CreatePanel:14:3 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: [2020-08-07 10:39:22,74] [info] WorkflowManagerActor Workflow 9e7a9c3b-b2e2-4293-ba67-9e16c377ceea failed (during ExecutingWorkflowState): Job Mutect2_Panel.CreatePanel:14:3 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-CreatePanel/shard-14/attempt-3/execution/stderr.
[First 300 bytes]:Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-CreatePanel/shard-14/attempt-3/tmp.56457799
02:39:09.785 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/
Job Mutect2_Panel.CreatePanel:3:3 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-CreatePanel/shard-3/attempt-3/execution/stderr.
[First 300 bytes]:Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-CreatePanel/shard-3/attempt-3/tmp.37d2ea68

Then I check the stderr file:

Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-CreatePanel/shard-14/attempt-3/tmp.56457799
02:39:09.785 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
Aug 07, 2020 2:39:09 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
02:39:09.954 INFO GenomicsDBImport - ------------------------------------------------------------
02:39:09.954 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.4.1
02:39:09.954 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
02:39:09.954 INFO GenomicsDBImport - Executing as root@ca39d0ac02bf on Linux v4.18.0-147.8.1.el8_1.x86_64 amd64
02:39:09.954 INFO GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03
02:39:09.955 INFO GenomicsDBImport - Start Date/Time: August 7, 2020 2:39:09 AM UTC
02:39:09.955 INFO GenomicsDBImport - ------------------------------------------------------------
02:39:09.955 INFO GenomicsDBImport - ------------------------------------------------------------
02:39:09.955 INFO GenomicsDBImport - ------------------------------------------------------------
02:39:09.955 INFO GenomicsDBImport - ------------------------------------------------------------
02:39:09.955 INFO GenomicsDBImport - HTSJDK Version: 2.21.0
02:39:09.955 INFO GenomicsDBImport - Picard Version: 2.21.2
02:39:09.955 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
02:39:09.955 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
02:39:09.955 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
02:39:09.955 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
02:39:09.955 INFO GenomicsDBImport - Deflater: IntelDeflater
02:39:09.955 INFO GenomicsDBImport - Inflater: IntelInflater
02:39:09.955 INFO GenomicsDBImport - GCS max retries/reopens: 20
02:39:09.955 INFO GenomicsDBImport - Requester pays: disabled
02:39:09.955 INFO GenomicsDBImport - Initializing engine
02:39:09.969 INFO GenomicsDBImport - Shutting down engine
[August 7, 2020 2:39:09 AM UTC] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1213202432
***********************************************************************

A USER ERROR has occurred: Failed to create reader from file:///data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-Filter/execution/104260AZW1B1.b37-filtered.vcf

***********************************************************************
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 /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 -jar /root/gatk.jar GenomicsDBImport --genomicsdb-workspace-path pon_db -R /cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-CreatePanel/shard-14/attempt-3/inputs/1139317085/human_g1k_v37_decoy.fasta -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-Filter/execution/104260AZW1B1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-1/Mutect2/2d66bc71-b554-46ca-990a-0f00b48120d5/call-Filter/execution/104261AZW1B1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-2/Mutect2/46f0a611-cdd3-4ee0-8709-a09fb0be65ab/call-Filter/execution/105023AZW1B1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-3/Mutect2/8de36acc-9da7-475c-91c7-7ac5d8cc7483/call-Filter/execution/105603AZW1B1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-4/Mutect2/95de0c5a-b6d4-4930-8b2c-c6cbf7594952/call-Filter/execution/11T001353WB1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-5/Mutect2/c573175f-22e4-4716-a9c3-8ea5789b9235/call-Filter/execution/11T004419WB1.b37-filtered.vcf -L /cromwell-executions/Mutect2_Pa
nel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-CreatePanel/shard-14/attempt-3/inputs/2088407395/0014-scattered.interval_list

the vcf: 104260AZW1B1.b37-filtered.vcf

looks like:

##fileformat=VCFv4.2
##FILTER=<ID=base_qual,Description="alt median base quality">
##FILTER=<ID=clustered_events,Description="Clustered events observed in the tumor">
##FILTER=<ID=contamination,Description="contamination">
##FILTER=<ID=duplicate,Description="evidence for alt allele is overrepresented by apparent duplicates">
##FILTER=<ID=fragment,Description="abs(ref - alt) median fragment length">
##FILTER=<ID=germline,Description="Evidence indicates this site is germline, not somatic">
##FILTER=<ID=haplotype,Description="Variant near filtered variant on same haplotype.">
##FILTER=<ID=low_allele_frac,Description="Allele fraction is below specified threshold">
##FILTER=<ID=map_qual,Description="ref - alt median mapping quality">
##FILTER=<ID=multiallelic,Description="Site filtered because too many alt alleles pass tumor LOD">
##FILTER=<ID=n_ratio,Description="Ratio of N to alt exceeds specified ratio">
##FILTER=<ID=normal_artifact,Description="artifact_in_normal">
##FILTER=<ID=numt_chimera,Description="NuMT variant with too many ALT reads originally from autosome">
##FILTER=<ID=numt_novel,Description="Alt depth is below expected coverage of NuMT in autosome">
##FILTER=<ID=orientation,Description="orientation bias detected by the orientation bias mixture model">
##FILTER=<ID=panel_of_normals,Description="Blacklisted site in panel of normals">
##FILTER=<ID=position,Description="median distance of alt variants from end of reads">
##FILTER=<ID=slippage,Description="Site filtered due to contraction of short tandem repeat region">
##FILTER=<ID=strand_bias,Description="Evidence for alt allele comes from one read direction only">
##FILTER=<ID=strict_strand,Description="Evidence for alt allele is not represented in both directions">
##FILTER=<ID=weak_evidence,Description="Mutation does not meet likelihood threshold">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=AF,Number=A,Type=Float,Description="Allele fractions of alternate alleles in the tumor">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=F1R2,Number=R,Type=Integer,Description="Count of reads in F1R2 pair orientation supporting each allele">
##FORMAT=<ID=F2R1,Number=R,Type=Integer,Description="Count of reads in F2R1 pair orientation supporting each allele">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another; will always be heterozygous and is not intended to describe called alleles">
##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##FORMAT=<ID=PS,Number=1,Type=Integer,Description="Phasing set (typically the position of the first variant in the set)">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##GATKCommandLine=<ID=FilterMutectCalls,CommandLine="FilterMutectCalls --output 104260AZW1B1.b37-filtered.vcf --stats /cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-Filter/inputs/-1431848726/merged.stats --filtering-stats filtering.stats --contamination-table /cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-Filter/inputs/594308847/contamination.table --tumor-segmentation /cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-Filter/inputs/594308847/segments.table --variant /cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-Filter/inputs/-930748415/104260AZW1B1.b37-unfiltered.vcf --reference /cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-Filter/inputs/1139317085/human_g1k_v37_decoy.fasta --threshold-strategy OPTIMAL_F_SCORE --f-score-beta 1.0 --false-discovery-rate 0.05 --initial-threshold 0.1 --mitochondria-mode false --max-events-in-region 2 --max-alt-allele-count 1 --unique-alt-read-count 0 --min-median-mapping-quality 30 --min-median-base-quality 20 --max-median-fragment-length-difference 10000 --min-median-read-position 1 --max-n-ratio Infinity --min-reads-per-strand 0 --autosomal-coverage 0.0 --max-numt-fraction 0.85 --min-allele-fraction 0.0 --contamination-estimate 0.0 --log-snv-prior -13.815510557964275 --log-indel-prior -16.11809565095832 --log-artifact-prior -2.302585092994046 --normal-p-value-threshold 0.001 --min-slippage-length 8 --pcr-slippage-rate 0.1 --distance-on-haplotype 100 --long-indel-length 5 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="4.1.4.1",Date="August 7, 2020 2:36:06 AM UTC">
##GATKCommandLine=<ID=Mutect2,CommandLine="Mutect2 --tumor-sample 104260AZW1B1 --max-mnp-distance 0 --output output.vcf --intervals /cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-M2/shard-3/inputs/-1960942214/0003-scattered.interval_list --input /cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-M2/shard-3/inputs/-1577115655/104260AZW1B1.b37.bam --reference /cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-M2/shard-3/inputs/1139317085/human_g1k_v37_decoy.fasta --f1r2-median-mq 50 --f1r2-min-bq 20 --f1r2-max-depth 200 --genotype-pon-sites false --genotype-germline-sites false --af-of-alleles-not-in-resource -1.0 --mitochondria-mode false --tumor-lod-to-emit 3.0 --initial-tumor-lod 2.0 --pcr-snv-qual 40 --pcr-indel-qual 40 --max-population-af 0.01 --downsampling-stride 1 --callable-depth 10 --max-suspicious-reads-per-alignment-start 0 --normal-lod 2.2 --ignore-itr-artifacts false --gvcf-lod-band -2.5 --gvcf-lod-band -2.0 --gvcf-lod-band -1.5 --gvcf-lod-band -1.0 --gvcf-lod-band -0.5 --gvcf-lod-band 0.0 --gvcf-lod-band 0.5 --gvcf-lod-band 1.0 --minimum-allele-fraction 0.0 --independent-mates false --disable-adaptive-pruning false --dont-trim-active-regions false --max-extension 25 --padding-around-indels 150 --padding-around-snps 20 --kmer-size 10 --kmer-size 25 --dont-increase-kmer-sizes-for-cycles false --allow-non-unique-kmers-in-ref false --num-pruning-samples 1 --min-dangling-branch-length 4 --recover-all-dangling-branches false --max-num-haplotypes-in-population 128 --min-pruning 2 --adaptive-pruning-initial-error-rate 0.001 --pruning-lod-threshold 2.302585092994046 --max-unpruned-variants 100 --linked-de-bruijn-graph false --debug-assembly false --debug-graph-transformations false --capture-assembly-failure-bam false --error-correct-reads false --kmer-length-for-read-error-correction 25 --min-observations-for-kmer-to-be-solid 20 --likelihood-calculation-engine PairHMM --base-quality-score-threshold 18 --pair-hmm-gap-continuation-penalty 10 --pair-hmm-implementation FASTEST_AVAILABLE --pcr-indel-model CONSERVATIVE --phred-scaled-global-read-mismapping-rate 45 --native-pair-hmm-threads 4 --native-pair-hmm-use-double-precision false --bam-writer-type CALLED_HAPLOTYPES --dont-use-soft-clipp
ed-bases false --min-base-quality-score 10 --smith-waterman JAVA --emit-ref-confidence NONE --force-call-filtered-alleles false --min-assembly-region-size 50 --max-assembly-region-size 300 --assembly-region-padding 100 --max-reads-per-alignment-start 50 --active-probability-threshold 0.002 --max-prob-propagation-distance 50 --force-active false --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --verbosity INFO --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false --max-read-length 2147483647 --min-read-length 30 --minimum-mapping-quality 20 --disable-tool-default-annotations false --enable-all-annotations false",Version="4.1.4.1",Date="August 7, 2020 2:02:57 AM UTC">
##INFO=<ID=CONTQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to contamination">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=ECNT,Number=1,Type=Integer,Description="Number of events in this haplotype">
##INFO=<ID=GERMQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not germline variants">
##INFO=<ID=MBQ,Number=R,Type=Integer,Description="median base quality">
##INFO=<ID=MFRL,Number=R,Type=Integer,Description="median fragment length">
##INFO=<ID=MMQ,Number=R,Type=Integer,Description="median mapping quality">
##INFO=<ID=MPOS,Number=A,Type=Integer,Description="median distance from end of read">
##INFO=<ID=NALOD,Number=A,Type=Float,Description="Negative log 10 odds of artifact in normal with same allele fraction as tumor">
##INFO=<ID=NCount,Number=1,Type=Integer,Description="Count of N bases in the pileup">
##INFO=<ID=NLOD,Number=A,Type=Float,Description="Normal log 10 likelihood ratio of diploid het or hom alt genotypes">
##INFO=<ID=OCM,Number=1,Type=Integer,Description="Number of alt reads whose original alignment doesn't match the current contig.">
##INFO=<ID=PON,Number=0,Type=Flag,Description="site found in panel of normals">
##INFO=<ID=POPAF,Number=A,Type=Float,Description="negative log 10 population allele frequencies of alt alleles">
##INFO=<ID=ROQ,Number=1,Type=Float,Description="Phred-scaled qualities that alt allele are not due to read orientation artifact">
##INFO=<ID=RPA,Number=.,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=SEQQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles are not sequencing errors">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=STRANDQ,Number=1,Type=Integer,Description="Phred-scaled quality of strand bias artifact">
##INFO=<ID=STRQ,Number=1,Type=Integer,Description="Phred-scaled quality that alt alleles in STRs are not polymerase slippage errors">
##INFO=<ID=TLOD,Number=A,Type=Float,Description="Log 10 likelihood ratio score of variant existing versus not existing">
##INFO=<ID=UNIQ_ALT_READ_COUNT,Number=1,Type=Integer,Description="Number of ALT reads with unique start and mate end positions at a variant site">
##MutectVersion=2.2
##contig=<ID=1,length=249250621>
##contig=<ID=2,length=243199373>
##contig=<ID=3,length=198022430>
##contig=<ID=4,length=191154276>
##contig=<ID=5,length=180915260>
##contig=<ID=6,length=171115067>
##contig=<ID=7,length=159138663>
##contig=<ID=8,length=146364022>
##contig=<ID=9,length=141213431>
##contig=<ID=10,length=135534747>
##contig=<ID=11,length=135006516>
##contig=<ID=12,length=133851895>
##contig=<ID=13,length=115169878>
##contig=<ID=14,length=107349540>
##contig=<ID=15,length=102531392>
##contig=<ID=16,length=90354753>
##contig=<ID=17,length=81195210>
##contig=<ID=18,length=78077248>
##contig=<ID=19,length=59128983>
##contig=<ID=20,length=63025520>
##contig=<ID=21,length=48129895>
##contig=<ID=22,length=51304566>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##contig=<ID=MT,length=16569>
##contig=<ID=GL000207.1,length=4262>
##contig=<ID=GL000226.1,length=15008>
##contig=<ID=GL000229.1,length=19913>
##contig=<ID=GL000231.1,length=27386>
##contig=<ID=GL000210.1,length=27682>
##contig=<ID=GL000239.1,length=33824>
##contig=<ID=GL000235.1,length=34474>
##contig=<ID=GL000201.1,length=36148>
##contig=<ID=GL000247.1,length=36422>
##contig=<ID=GL000245.1,length=36651>
##contig=<ID=GL000197.1,length=37175>
##contig=<ID=GL000203.1,length=37498>
##contig=<ID=GL000246.1,length=38154>
##contig=<ID=GL000249.1,length=38502>
##contig=<ID=GL000196.1,length=38914>
##contig=<ID=GL000248.1,length=39786>
##contig=<ID=GL000244.1,length=39929>
##contig=<ID=GL000238.1,length=39939>
##contig=<ID=GL000202.1,length=40103>
##contig=<ID=GL000234.1,length=40531>
##contig=<ID=GL000232.1,length=40652>
##contig=<ID=GL000206.1,length=41001>
##contig=<ID=GL000240.1,length=41933>
##contig=<ID=GL000236.1,length=41934>
##contig=<ID=GL000241.1,length=42152>
##contig=<ID=GL000243.1,length=43341>
##contig=<ID=GL000242.1,length=43523>
##contig=<ID=GL000230.1,length=43691>
##contig=<ID=GL000237.1,length=45867>
##contig=<ID=GL000233.1,length=45941>
##contig=<ID=GL000204.1,length=81310>
##contig=<ID=GL000198.1,length=90085>
##contig=<ID=GL000208.1,length=92689>
##contig=<ID=GL000191.1,length=106433>
##contig=<ID=GL000227.1,length=128374>
##contig=<ID=GL000228.1,length=129120>
##contig=<ID=GL000214.1,length=137718>
##contig=<ID=GL000221.1,length=155397>
##contig=<ID=GL000209.1,length=159169>
##contig=<ID=GL000218.1,length=161147>
##contig=<ID=GL000220.1,length=161802>
##contig=<ID=GL000213.1,length=164239>
##contig=<ID=GL000211.1,length=166566>
##contig=<ID=GL000199.1,length=169874>
##contig=<ID=GL000217.1,length=172149>
##contig=<ID=GL000216.1,length=172294>
##contig=<ID=GL000215.1,length=172545>
##contig=<ID=GL000205.1,length=174588>
##contig=<ID=GL000219.1,length=179198>
##contig=<ID=GL000224.1,length=179693>
##contig=<ID=GL000223.1,length=180455>
##contig=<ID=GL000195.1,length=182896>
##contig=<ID=GL000212.1,length=186858>
##contig=<ID=GL000222.1,length=186861>
##contig=<ID=GL000200.1,length=187035>
##contig=<ID=GL000193.1,length=189789>
##contig=<ID=GL000194.1,length=191469>
##contig=<ID=GL000225.1,length=211173>
##contig=<ID=GL000192.1,length=547496>
##contig=<ID=NC_007605,length=171823>
##contig=<ID=hs37d5,length=35477943>
##filtering_status=These calls have been filtered by FilterMutectCalls to label false positives with a list of failed filters and true positives with PASS.
##source=FilterMutectCalls
##source=Mutect2
##tumor_sample=104260AZW1B1
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 104260AZW1B1
1 69270 . A G . map_qual CONTQ=93;DP=32;ECNT=1;GERMQ=93;MBQ=0,30;MFRL=0,375;MMQ=60,25;MPOS=44;POPAF=7.30;SEQQ=93;STRANDQ=80;TLOD=92.78 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,30:0.970:30:0,16:0,14:0,0,30,0
1 69511 . A G . PASS CONTQ=93;DP=213;ECNT=1;GERMQ=93;MBQ=0,30;MFRL=0,252;MMQ=60,45;MPOS=44;POPAF=7.30;SEQQ=93;STRANDQ=93;TLOD=593.82 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:0,206:0.994:206:0,117:0,88:0,0,122,84
1 69735 . A G . map_qual CONTQ=93;DP=73;ECNT=1;GERMQ=93;MBQ=30,30;MFRL=337,518;MMQ=25,25;MPOS=45;POPAF=7.30;SEQQ=30;STRANDQ=21;TLOD=7.92 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:64,6:0.097:70:36,3:26,3:13,51,4,2
1 69849 . G A . map_qual;strand_bias CONTQ=93;DP=47;ECNT=2;GERMQ=88;MBQ=30,30;MFRL=439,555;MMQ=25,27;MPOS=30;POPAF=7.30;SEQQ=8;STRANDQ=1;TLOD=5.67 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:41,4:0.106:45:23,3:18,1:13,28,4,0
1 69897 . T C . map_qual CONTQ=93;DP=33;ECNT=2;GERMQ=52;MBQ=30,30;MFRL=449,439;MMQ=27,27;MPOS=29;POPAF=7.30;SEQQ=93;STRANDQ=93;TLOD=77.31 GT:AD:AF:DP:F1R2:F2R1:SB 0/1:4,27:0.849:31:2,15:2,11:4,0,9,18

I found nothing strange.

Post https://gatk.broadinstitute.org/hc/en-us/community/posts/360056249211-genomicsDBImport-A-USER-ERROR-has-occurred-Failed-to-create-reader-from-file said that the error occurs when vcf.idx is not provided or wrongly provided.

so I checked the directory:

# ls -1 /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-Filter/execution/
104260AZW1B1.b37-filtered.vcf
104260AZW1B1.b37-filtered.vcf.idx
filtering.stats
rc
script
script.background
script.submit
stderr
stderr.background
stdout
stdout.background

and found that the idx file was there.

Then I ran the command without docker:

# gatk --java-options "-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" GenomicsDBImport --genomicsdb-workspace-path pon_db -R ../cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-CreatePanel/shard-14/attempt-3/inputs/1139317085/human_g1k_v37_decoy.fasta -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-Filter/execution/104260AZW1B1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-1/Mutect2/2d66bc71-b554-46ca-990a-0f00b48120d5/call-Filter/execution/104261AZW1B1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-2/Mutect2/46f0a611-cdd3-4ee0-8709-a09fb0be65ab/call-Filter/execution/105023AZW1B1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-3/Mutect2/8de36acc-9da7-475c-91c7-7ac5d8cc7483/call-Filter/execution/105603AZW1B1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-4/Mutect2/95de0c5a-b6d4-4930-8b2c-c6cbf7594952/call-Filter/execution/11T001353WB1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-5/Mutect2/c573175f-22e4-4716-a9c3-8ea5789b9235/call-Filter/execution/11T004419WB1.b37-filtered.vcf -L ../cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-CreatePanel/shard-14/attempt-3/inputs/2088407395/0014-scattered.interval_list
Using GATK jar /root/WZW/20200512_wes_p3/bin/gatk-4.1.8.0/gatk-package-4.1.8.0-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 -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 /root/WZW/20200512_wes_p3/bin/gatk-4.1.8.0/gatk-package-4.1.8.0-local.jar GenomicsDBImport --genomicsdb-workspace-path pon_db -R ../cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-CreatePanel/shard-14/attempt-3/inputs/1139317085/human_g1k_v37_decoy.fasta -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-0/Mutect2/a464b61a-d581-42ab-849a-37ea62602991/call-Filter/execution/104260AZW1B1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-1/Mutect2/2d66bc71-b554-46ca-990a-0f00b48120d5/call-Filter/execution/104261AZW1B1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-2/Mutect2/46f0a611-cdd3-4ee0-8709-a09fb0be65ab/call-Filter/execution/105023AZW1B1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-3/Mutect2/8de36acc-9da7-475c-91c7-7ac5d8cc7483/call-Filter/execution/105603AZW1B1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-4/Mutect2/95de0c5a-b6d4-4930-8b2c-c6cbf7594952/call-Filter/execution/11T001353WB1.b37-filtered.vcf -V /data/wangzw/wes_normals/cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-Mutect2/shard-5/Mutect2/c573175f-22e4-4716-a9c3-8ea5789b9235/call-Filter/execution/11T004419WB1.b37-filtered.vcf -L ../cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-CreatePanel/shard-14/attempt-3/inputs/2088407395/0014-scattered.interval_list
11:22:50.040 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/root/WZW/20200512_wes_p3/bin/gatk-4.1.8.0/gatk-package-4.1.8.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Aug 07, 2020 11:22:50 AM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
11:22:50.152 INFO GenomicsDBImport - ------------------------------------------------------------
11:22:50.152 INFO GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.1.8.0
11:22:50.152 INFO GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
11:22:50.152 INFO GenomicsDBImport - Executing as root@ljlab on Linux v4.18.0-147.8.1.el8_1.x86_64 amd64
11:22:50.152 INFO GenomicsDBImport - Java runtime: Java HotSpot(TM) 64-Bit Server VM v13-ea+33
11:22:50.152 INFO GenomicsDBImport - Start Date/Time: August 7, 2020 at 11:22:50 AM CST
11:22:50.152 INFO GenomicsDBImport - ------------------------------------------------------------
11:22:50.152 INFO GenomicsDBImport - ------------------------------------------------------------
11:22:50.153 INFO GenomicsDBImport - HTSJDK Version: 2.22.0
11:22:50.153 INFO GenomicsDBImport - Picard Version: 2.22.8
11:22:50.153 INFO GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:22:50.153 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:22:50.153 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:22:50.153 INFO GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:22:50.153 INFO GenomicsDBImport - Deflater: IntelDeflater
11:22:50.153 INFO GenomicsDBImport - Inflater: IntelInflater
11:22:50.153 INFO GenomicsDBImport - GCS max retries/reopens: 20
11:22:50.153 INFO GenomicsDBImport - Requester pays: disabled
11:22:50.154 INFO GenomicsDBImport - Initializing engine
11:22:50.372 INFO FeatureManager - Using codec IntervalListCodec to read file file:///data/wangzw/wes_normals/test/../cromwell-executions/Mutect2_Panel/9e7a9c3b-b2e2-4293-ba67-9e16c377ceea/call-CreatePanel/shard-14/attempt-3/inputs/2088407395/0014-scattered.interval_list
11:22:50.387 INFO IntervalArgumentCollection - Processing 248361646 bp from intervals
11:22:50.407 INFO GenomicsDBImport - Done initializing engine
11:22:50.620 INFO GenomicsDBLibLoader - GenomicsDB native library version : 1.3.0-e701905
11:22:50.621 INFO GenomicsDBImport - Vid Map JSON file will be written to /data/wangzw/wes_normals/test/pon_db/vidmap.json
11:22:50.621 INFO GenomicsDBImport - Callset Map JSON file will be written to /data/wangzw/wes_normals/test/pon_db/callset.json
11:22:50.621 INFO GenomicsDBImport - Complete VCF Header will be written to /data/wangzw/wes_normals/test/pon_db/vcfheader.vcf
11:22:50.621 INFO GenomicsDBImport - Importing to workspace - /data/wangzw/wes_normals/test/pon_db
11:22:50.621 INFO ProgressMeter - Starting traversal
11:22:50.621 INFO ProgressMeter - Current Locus Elapsed Minutes Batches Processed Batches/Minute
11:22:50.788 INFO GenomicsDBImport - Importing batch 1 with 6 samples
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
11:22:51.179 INFO GenomicsDBImport - Importing batch 1 with 6 samples
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
11:22:51.840 INFO GenomicsDBImport - Importing batch 1 with 6 samples
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
11:22:52.169 INFO GenomicsDBImport - Importing batch 1 with 6 samples
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
[E::bcf_get_info_values] Trying to get 32-bit int data from a field which contains 64 bit values
11:22:52.404 INFO GenomicsDBImport - Done importing batch 1/1
11:22:52.405 INFO ProgressMeter - 18:1 0.0 1 33.6
11:22:52.405 INFO ProgressMeter - Traversal complete. Processed 1 total batches in 0.0 minutes.
11:22:52.405 INFO GenomicsDBImport - Import completed!
11:22:52.405 INFO GenomicsDBImport - Shutting down engine
[August 7, 2020 at 11:22:52 AM CST] org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=322961408
Tool returned:
true
(gatk)

the command finished successfully... ⊙ˍ⊙|||

I thought if it could be run successfully in command line, it could also be run successfully in docker. Now the situation is quite confusing.

Do you have any idea about the "GenomicsDBImport : Failed to create reader from file" Error? The error message is unspecified.

For the moment, I believe I have prepared all files correctly.

here is my panel_of_normal.json:

{
"Mutect2_Panel.pon_name":"panel_of_normal",
"Mutect2_Panel.normal_bams":["104260AZW1B1.b37.bam","104261AZW1B1.b37.bam","105023AZW1B1.b37.bam","105603AZW1B1.b37.bam","11T001353WB1.b37.bam","11T004419WB1.b37.bam"],
"Mutect2_Panel.normal_bais":["104260AZW1B1.b37.bai","104261AZW1B1.b37.bai","105023AZW1B1.b37.bai","105603AZW1B1.b37.bai","11T001353WB1.b37.bai","11T004419WB1.b37.bai"],

"Mutect2_Panel.ref_fasta":"/data/wangzw/gatk-workflow/input/human_g1k_v37_decoy.fasta",
"Mutect2_Panel.ref_fai":"/data/wangzw/gatk-workflow/input/human_g1k_v37_decoy.fasta.fai",
"Mutect2_Panel.ref_dict":"/data/wangzw/gatk-workflow/input/human_g1k_v37_decoy.dict",
"Mutect2_Panel.scatter_count":10,

"Mutect2_Panel.intervals":"/data/wangzw/gatk-workflow/input/xgen_exome_panel_v2_targets_b37_somatic.interval_list",
"Mutect2_Panel.Mutect2.variants_for_contamination":"/data/wangzw/gatk-workflow/input/variants_for_contamination.vcf",
"Mutect2_Panel.Mutect2.variants_for_contamination_idx":"/data/wangzw/gatk-workflow/input/variants_for_contamination.vcf.idx",
"Mutect2_Panel.gnomad":"/data/wangzw/gatk-workflow/input/af-only-gnomad.raw.sites.vcf",
"Mutect2_Panel.gnomad_idx":"/data/wangzw/gatk-workflow/input/af-only-gnomad.raw.sites.vcf.idx",

"Mutect2_Panel.gatk_docker":"broadinstitute/gatk:4.1.4.1"
}

Many thanks.

Wang Ziwei

WangZiwei

August 07, 2020 06:49
Hi Jason Cerrato

My reply seems to be pending approval. I wonder if you could see it.

Regards.

Wang Ziwei
0

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Jason Cerrato

August 07, 2020 13:58
Hi WangZiwei,

I am able to see your reply. I'll take a look and get back to you as soon as I am able.

Kind regards,

Jason
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Jason Cerrato

September 25, 2020 19:05
Hi Wang Ziwei,

Apologies for the delay on this issue. Did you happen to isolate the root cause of the discrepancy you were experiencing between running on command line and running in the docker?

Kind regards,

Jason
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