File "/opt/conda/lib/python3.7/subprocess.py", line 347, in check_call raise CalledProcessError(retcode, cmd) #106
Comments
|
hi,
if you go to the directory for the task that failed:
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/
Do you see any stderr or stdout files that have more information about the
error?
Another thing you might try is to run the singularity image in 'shell' mode
and try running this command directly:
samtools faidx
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/inputs/817306935/ref_genome.fa
--region-file
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/tmp.0d731215/positions.fa
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/tmp.0d731215/faidx_output.fa
and see what the error message is, if any.
That'll help us figure out the next steps.
best,
~brian
…On Thu, Jan 13, 2022 at 12:32 AM Yuanqing Yan ***@***.***> wrote:
Hi,
I use singularity (version 3.8.1), ctat_mutations.v3.2.0.simg and the
testing read files to call the mutation. The pipeline fails in "Annotating
VCF: Calculating ED" step. Do you have any idea how it can be fixed?
The command I used is as below:
singularity exec -e -B pwd:/data -B
/work/reference/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir:/ctat_genome_lib_dir:ro
/work/singularityImage/ctat_mutations.v3.2.0.simg
/usr/local/src/ctat-mutations/ctat_mutations --left
/data/fastq/reads_1.fastq.gz --right /data/fastq/reads_2.fastq.gz
--sample_id test --output /data/out --cpu 1 --genome_lib_dir
/ctat_genome_lib_dir
The error message is:
echo "########### Annotate BLAT ED #############"
/usr/local/src/ctat-mutations/src/annotate_ED.py
--input_vcf
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/inputs/-1226801460/test.splice_distance.vcf.gz
--output_vcf test.blat_ED.vcf
--reference
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/inputs/817306935/ref_genome.fa
--temp_dir $TMPDIR
--threads 16
bgzip -c test.blat_ED.vcf > test.blat_ED.vcf.gz
tabix test.blat_ED.vcf.gz
[2022-01-13 04:39:05,29] [info] BackgroundConfigAsyncJobExecutionActor
[1561a942annotate_variants_wf.annotate_blat_ED:NA:1]: executing:
/usr/bin/env bash
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/execution/script
[2022-01-13 04:39:06,67] [info] BackgroundConfigAsyncJobExecutionActor
[1561a942annotate_variants_wf.annotate_blat_ED:NA:1]: job id: 148068
[2022-01-13 04:39:06,68] [info] BackgroundConfigAsyncJobExecutionActor
[1561a942annotate_variants_wf.annotate_blat_ED:NA:1]: Status change from -
to Done
[2022-01-13 04:39:23,67] [info] WorkflowManagerActor Workflow
ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb failed (during
ExecutingWorkflowState): Job annotate_variants_wf.annotate_blat_ED:NA: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/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/execution/stderr.
[First 3000 bytes]:+ echo '########### Annotate BLAT ED #############'
- /usr/local/src/ctat-mutations/src/annotate_ED.py --input_vcf
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/inputs/-1226801460/test.splice_distance.vcf.gz
--output_vcf test.blat_ED.vcf --reference
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/inputs/817306935/ref_genome.fa
--temp_dir
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/tmp.0d731215
--threads 16
22:39:05 : INFO :
################################
Annotating VCF: Calculating ED
################################
22:39:05 : INFO : Processing VCF Positions
22:39:06 : INFO : Running samtools faidx
Traceback (most recent call last):
File "/usr/local/src/ctat-mutations/src/annotate_ED.py", line 165, in
main()
File "/usr/local/src/ctat-mutations/src/annotate_ED.py", line 84, in main
subprocess.check_call(cmd, shell=True)
File "/opt/conda/lib/python3.7/subprocess.py", line 347, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'samtools faidx
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/inputs/817306935/ref_genome.fa
--region-file
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/tmp.0d731215/positions.fa
>
/data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/tmp.0d731215/faidx_output.fa'
returned non-zero exit status 1.
[2022-01-13 04:39:23,68] [info] WorkflowManagerActor
WorkflowActor-ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb is in a terminal state:
WorkflowFailedState
[2022-01-13 04:40:49,23] [info] SingleWorkflowRunnerActor workflow
finished with status 'Failed'.
[2022-01-13 04:40:52,89] [info] SingleWorkflowRunnerActor writing metadata
to /tmp/tmpmghzfeby.json
[2022-01-13 04:40:52,92] [info] Workflow polling stopped
[2022-01-13 04:40:52,93] [info] Shutting down WorkflowStoreActor - Timeout
= 5 seconds
[2022-01-13 04:40:52,93] [info] 0 workflows released by cromid-69e661a
[2022-01-13 04:40:52,93] [info] Aborting all running workflows.
[2022-01-13 04:40:52,94] [info] Shutting down WorkflowLogCopyRouter -
Timeout = 5 seconds
[2022-01-13 04:40:52,94] [info] WorkflowStoreActor stopped
[2022-01-13 04:40:52,95] [info] Shutting down JobExecutionTokenDispenser -
Timeout = 5 seconds
[2022-01-13 04:40:52,95] [info] WorkflowLogCopyRouter stopped
[2022-01-13 04:40:52,95] [info] JobExecutionTokenDispenser stopped
[2022-01-13 04:40:52,95] [info] Shutting down WorkflowManagerActor -
Timeout = 3600 seconds
[2022-01-13 04:40:52,95] [info] WorkflowManagerActor All workflows finished
[2022-01-13 04:40:52,95] [info] WorkflowManagerActor stopped
[2022-01-13 04:40:53,23] [info] Connection pools shut down
[2022-01-13 04:40:53,23] [info] Shutting down SubWorkflowStoreActor -
Timeout = 1800 seconds
[2022-01-13 04:40:53,23] [info] Shutting down JobStoreActor - Timeout =
1800 seconds
[2022-01-13 04:40:53,24] [info] Shutting down CallCacheWriteActor -
Timeout = 1800 seconds
[2022-01-13 04:40:53,24] [info] CallCacheWriteActor Shutting down: 0
queued messages to process
[2022-01-13 04:40:53,24] [info] Shutting down ServiceRegistryActor -
Timeout = 1800 seconds
[2022-01-13 04:40:53,24] [info] Shutting down DockerHashActor - Timeout =
1800 seconds
[2022-01-13 04:40:53,27] [info] Shutting down IoProxy - Timeout = 1800
seconds
[2022-01-13 04:40:53,27] [info] SubWorkflowStoreActor stopped
[2022-01-13 04:40:53,27] [info] JobStoreActor stopped
[2022-01-13 04:40:53,27] [info] CallCacheWriteActor stopped
[2022-01-13 04:40:53,27] [info] IoProxy stopped
[2022-01-13 04:40:53,29] [info] Shutting down connection pool:
curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256
closed=false
[2022-01-13 04:40:53,30] [info] WriteMetadataActor Shutting down: 0 queued
messages to process
[2022-01-13 04:40:53,32] [info] KvWriteActor Shutting down: 0 queued
messages to process
[2022-01-13 04:40:53,32] [info] ServiceRegistryActor stopped
[2022-01-13 04:40:53,32] [info] Shutting down connection pool:
curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256
closed=false
[2022-01-13 04:40:53,34] [info] DockerHashActor stopped
[2022-01-13 04:40:53,32] [info] Shutting down connection pool:
curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256
closed=false
[2022-01-13 04:40:53,32] [info] Shutting down connection pool:
curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256
closed=false
[2022-01-13 04:40:53,38] [info] Database closed
[2022-01-13 04:40:53,39] [info] Stream materializer shut down
[2022-01-13 04:40:53,40] [info] WDL HTTP import resolver closed
Workflow ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb transitioned to state Failed
Thanks so much.
—
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--
--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>
|
|
Thanks for your information, Brian. I fixed my previous issue already by feeding the correct input fastq files. However, another issue comes to the "VariantFiltration" module. Please see the message of "[2022-01-13 20:20:41,90] ", "[2022-01-13 20:20:59,58]" and "[2022-01-13 20:21:44,54]". Thanks again. [2022-01-13 20:20:41,16] [info] WorkflowExecutionActor-9068f826-411f-49a0-90cb-ce09f29efed4 [9068f826]: Starting ctat_mutations.VariantFiltration monitor_script.sh &boosting_method="XGBoost" if [ "$boosting_method" == "none" ]; then else fi
|
|
hi,
it looks like there's too few variants here to do boosting on. If you're
running a tiny test data set through, this can happen. To turn off
boosting, use the parameter --boosting_method none
it should resume where it left off when you give it the additional option.
best,
~b
…On Thu, Jan 13, 2022 at 3:56 PM Yuanqing Yan ***@***.***> wrote:
Thanks for your information, Brian.
I fixed my previous issue already by feeding the correct input fastq
files. However, another issue comes to the "VariantFiltration" module.
Please see the message of "[2022-01-13 20:20:41,90] ", "[2022-01-13
20:20:59,58]" and "[2022-01-13 20:21:44,54]". Thanks again.
[2022-01-13 20:20:41,16] [info]
WorkflowExecutionActor-9068f826-411f-49a0-90cb-ce09f29efed4 [9068f826]:
Starting ctat_mutations.VariantFiltration
[2022-01-13 20:20:41,89] [info] Assigned new job execution tokens to the
following groups: 9068f826: 1
[2022-01-13 20:20:41,90] [info]
9068f826-411f-49a0-90cb-ce09f29efed4-EngineJobExecutionActor-ctat_mutations.VariantFiltration:NA:1
[9068f826]: Could not copy a suitable cache hit for
9068f826:ctat_mutations.VariantFiltration👎1. No copy attempts were made.
[2022-01-13 20:20:41,90] [warn] BackgroundConfigAsyncJobExecutionActor
[9068f826ctat_mutations.VariantFiltration:NA:1]: Unrecognized runtime
attribute keys: preemptible, disks, docker, cpu, memory
[2022-01-13 20:20:41,91] [warn] Localization via hard link has failed:
/data/out/cromwell-executions/ctat_mutations/9068f826-411f-49a0-90cb-ce09f29efed4/call-VariantFiltration/inputs/817306935/ref_genome.fa.fai
-> /ctat_genome_lib_dir/ref_genome.fa.fai: Invalid cross-device link
[2022-01-13 20:20:41,91] [warn] Localization via hard link has failed:
/data/out/cromwell-executions/ctat_mutations/9068f826-411f-49a0-90cb-ce09f29efed4/call-VariantFiltration/inputs/817306935/ref_genome.fa
-> /ctat_genome_lib_dir/ref_genome.fa: Invalid cross-device link
[2022-01-13 20:20:41,91] [warn] Localization via hard link has failed:
/data/out/cromwell-executions/ctat_mutations/9068f826-411f-49a0-90cb-ce09f29efed4/call-VariantFiltration/inputs/817306935/ref_genome.dict
-> /ctat_genome_lib_dir/ref_genome.dict: Invalid cross-device link
[2022-01-13 20:20:41,92] [info] BackgroundConfigAsyncJobExecutionActor
[9068f826ctat_mutations.VariantFiltration:NA:1]: set -ex
monitor_script.sh &
boosting_method="XGBoost"
if [ "$boosting_method" == "none" ]; then
gatk --java-options "-Xmx2500m" \
VariantFiltration \
--R /data/out/cromwell-executions/ctat_mutations/9068f826-411f-49a0-90cb-ce09f29efed4/call-VariantFiltration/inputs/817306935/ref_genome.fa \
--V /data/out/cromwell-executions/ctat_mutations/9068f826-411f-49a0-90cb-ce09f29efed4/call-VariantFiltration/inputs/328445994/test.vcf.gz \
--window 35 \
--cluster 3 \
--filter-name "FS" \
--filter "FS > 30.0" \
--filter-name "QD" \
--filter "QD < 2.0" \
--filter-name "SPLICEDIST" \
--filter "DJ < 3" \
-O tmp.vcf
gatk --java-options "-Xmx2500m" \
SelectVariants \
--R /data/out/cromwell-executions/ctat_mutations/9068f826-411f-49a0-90cb-ce09f29efed4/call-VariantFiltration/inputs/817306935/ref_genome.fa \
--V tmp.vcf \
-select-type SNP \
--exclude-filtered \
-O test.XGBoost-classifier.vcf.gz
else
##############
## snps first:
/usr/local/src/ctat-mutations/src/annotated_vcf_to_feature_matrix.py \
--vcf /data/out/cromwell-executions/ctat_mutations/9068f826-411f-49a0-90cb-ce09f29efed4/call-VariantFiltration/inputs/328445994/test.vcf.gz \
--features AC,ALT,BaseQRankSum,DJ,DP,ED,Entropy,ExcessHet,FS,Homopolymer,LEN,MLEAF,MMF,QUAL,REF,RPT,RS,ReadPosRankSum,SAO,SOR,TCR,TDM,VAF,VMMF \
--snps \
\
--output XGBoost.snps.feature_matrix
/usr/local/src/ctat-mutations/src/VariantBoosting/Apply_ML.py \
--feature_matrix XGBoost.snps.feature_matrix \
--snps \
--features AC,ALT,BaseQRankSum,DJ,DP,ED,Entropy,ExcessHet,FS,Homopolymer,LEN,MLEAF,MMF,QUAL,REF,RPT,RS,ReadPosRankSum,SAO,SOR,TCR,TDM,VAF,VMMF \
--predictor classifier \
--model XGBoost \
--output XGBoost.classifier.snps.feature_matrix.wPreds
##############
## indels next
/usr/local/src/ctat-mutations/src/annotated_vcf_to_feature_matrix.py \
--vcf /data/out/cromwell-executions/ctat_mutations/9068f826-411f-49a0-90cb-ce09f29efed4/call-VariantFiltration/inputs/328445994/test.vcf.gz \
--features AC,ALT,BaseQRankSum,DJ,DP,ED,Entropy,ExcessHet,FS,Homopolymer,LEN,MLEAF,MMF,QUAL,REF,RPT,RS,ReadPosRankSum,SAO,SOR,TCR,TDM,VAF,VMMF \
--indels \
\
--output XGBoost.indels.feature_matrix
/usr/local/src/ctat-mutations/src/VariantBoosting/Apply_ML.py \
--feature_matrix XGBoost.indels.feature_matrix \
--indels \
--features AC,ALT,BaseQRankSum,DJ,DP,ED,Entropy,ExcessHet,FS,Homopolymer,LEN,MLEAF,MMF,QUAL,REF,RPT,RS,ReadPosRankSum,SAO,SOR,TCR,TDM,VAF,VMMF \
--predictor classifier \
--model XGBoost \
--output XGBoost.classifier.indels.feature_matrix.wPreds
#########
## combine predictions into single output vcf
/usr/local/src/ctat-mutations/src/extract_boosted_vcf.py \
--vcf_in /data/out/cromwell-executions/ctat_mutations/9068f826-411f-49a0-90cb-ce09f29efed4/call-VariantFiltration/inputs/328445994/test.vcf.gz \
--boosted_variants_matrix XGBoost.classifier.snps.feature_matrix.wPreds XGBoost.classifier.indels.feature_matrix.wPreds\
--vcf_out XGBoost.classifier.vcf
bgzip -c XGBoost.classifier.vcf > test.XGBoost-classifier.vcf.gz
fi
[2022-01-13 20:20:41,93] [info] BackgroundConfigAsyncJobExecutionActor
[9068f826ctat_mutations.VariantFiltration:NA:1]: executing: /usr/bin/env
bash
/data/out/cromwell-executions/ctat_mutations/9068f826-411f-49a0-90cb-ce09f29efed4/call-VariantFiltration/execution/script
[2022-01-13 20:20:43,80] [info] BackgroundConfigAsyncJobExecutionActor
[9068f826ctat_mutations.VariantFiltration:NA:1]: job id: 441113
[2022-01-13 20:20:43,80] [info] BackgroundConfigAsyncJobExecutionActor
[9068f826ctat_mutations.VariantFiltration:NA:1]: Status change from - to
WaitingForReturnCode
[2022-01-13 20:20:58,15] [info] BackgroundConfigAsyncJobExecutionActor
[9068f826ctat_mutations.VariantFiltration:NA:1]: Status change from
WaitingForReturnCode to Done
[2022-01-13 20:20:59,58] [info] WorkflowManagerActor Workflow
9068f826-411f-49a0-90cb-ce09f29efed4 failed (during
ExecutingWorkflowState): Job ctat_mutations.VariantFiltration:NA: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/out/cromwell-executions/ctat_mutations/9068f826-411f-49a0-90cb-ce09f29efed4/call-VariantFiltration/execution/stderr.
[First 3000 bytes]:+ boosting_method=XGBoost
- '[' XGBoost == none ']'
- /usr/local/src/ctat-mutations/src/annotated_vcf_to_feature_matrix.py
--vcf
/data/out/cromwell-executions/ctat_mutations/9068f826-411f-49a0-90cb-ce09f29efed4/call-VariantFiltration/inputs/328445994/test.vcf.gz
--features
AC,ALT,BaseQRankSum,DJ,DP,ED,Entropy,ExcessHet,FS,Homopolymer,LEN,MLEAF,MMF,QUAL,REF,RPT,RS,ReadPosRankSum,SAO,SOR,TCR,TDM,VAF,VMMF
--snps --output XGBoost.snps.feature_matrix
14:20:43 : INFO : -restricting feature matrix to SNPS
14:20:43 : INFO : Loading input VCF ...
14:20:43 : INFO : Preprocess Data ...
14:20:43 : INFO : Number of variants loaded: 40
14:20:43 : INFO : -restricting to snps
14:20:43 : INFO : -number of variants now: 39
14:20:43 : INFO : -writing feature data matrix to:
XGBoost.snps.feature_matrix
- /usr/local/src/ctat-mutations/src/VariantBoosting/Apply_ML.py
--feature_matrix XGBoost.snps.feature_matrix --snps --features
AC,ALT,BaseQRankSum,DJ,DP,ED,Entropy,ExcessHet,FS,Homopolymer,LEN,MLEAF,MMF,QUAL,REF,RPT,RS,ReadPosRankSum,SAO,SOR,TCR,TDM,VAF,VMMF
--predictor classifier --model XGBoost --output
XGBoost.classifier.snps.feature_matrix.wPreds
14:20:44 : INFO :
##########################
Running CTAT Boosting
##########################
14:20:44 : INFO : Preprocess Data ...
14:20:44 : INFO : Removing RNAediting sites ...
14:20:44 : INFO : Number of variants after removing RNAediting sites:
37
14:20:44 : INFO : -examining AC
14:20:44 : INFO : -AC has 2 uniq entries
14:20:44 : INFO : -examining ALT
14:20:44 : INFO : -ALT has 3 uniq entries
14:20:44 : INFO : -examining BaseQRankSum
14:20:44 : INFO : -BaseQRankSum has 24 uniq entries
14:20:44 : INFO : -examining DJ
14:20:44 : INFO : -DJ has 36 uniq entries
14:20:44 : INFO : -examining DP
14:20:44 : INFO : -DP has 30 uniq entries
14:20:44 : INFO : -examining ED
14:20:44 : INFO : -ED has 4 uniq entries
14:20:44 : INFO : -examining Entropy
14:20:44 : INFO : -Entropy has 9 uniq entries
14:20:44 : INFO : -examining ExcessHet
14:20:44 : INFO : -ExcessHet has 1 uniq entries
14:20:44 : INFO : -pruning feature column ExcessHet as theres no
complexity
14:20:44 : INFO : -examining FS
14:20:44 : INFO : -FS has 16 uniq entries
14:20:44 : INFO : -examining Homopolymer
14:20:44 : INFO : -Homopolymer has 2 uniq entries
14:20:44 : INFO : -examining LEN
14:20:44 : INFO : -LEN has 1 uniq entries
14:20:44 : INFO : -pruning feature column LEN as theres no complexity
14:20:44 : INFO : -examining MLEAF
14:20:44 : INFO : -MLEAF has 2 uniq entries
14:20:44 : INFO : -examining MMF
14:20:44 : INFO : -MMF has 9 uniq entries
14:20:44 : INFO : -examining QUAL
14:20:44 : INFO : -QUAL has 34 uniq entries
14:20:44 : INFO : -examining REF
14:20:44 : INFO : -REF has 3 uniq entries
14:20:44 : INFO : -examining RPT
14:20:44 : INFO : -RPT has 2 uniq entries
14:20:44 : INFO : -examining RS
14:20:44 : INFO : -RS has 2 uniq entries
14:20:44 : INFO : -examining ReadPosRankSum
14:20:44 : INFO : -ReadPosRankSum has 24 uniq entries
1
[2022-01-13 20:20:59,58] [info] WorkflowManagerActor
WorkflowActor-9068f826-411f-49a0-90cb-ce09f29efed4 is in a terminal state:
WorkflowFailedState
[2022-01-13 20:21:44,54] [info] SingleWorkflowRunnerActor workflow
finished with status 'Failed'.
[2022-01-13 20:21:49,36] [info] SingleWorkflowRunnerActor writing
metadata to /tmp/tmphx1uw4l9.json
[2022-01-13 20:21:49,40] [info] Workflow polling stopped
[2022-01-13 20:21:49,42] [info] Shutting down WorkflowStoreActor -
Timeout = 5 seconds
[2022-01-13 20:21:49,42] [info] Shutting down WorkflowLogCopyRouter -
Timeout = 5 seconds
[2022-01-13 20:21:49,42] [info] Shutting down
JobExecutionTokenDispenser - Timeout = 5 seconds
[2022-01-13 20:21:49,42] [info] 0 workflows released by cromid-f9579d5
[2022-01-13 20:21:49,42] [info] Aborting all running workflows.
[2022-01-13 20:21:49,43] [info] JobExecutionTokenDispenser stopped
[2022-01-13 20:21:49,43] [info] WorkflowStoreActor stopped
[2022-01-13 20:21:49,43] [info] WorkflowLogCopyRouter stopped
[2022-01-13 20:21:49,43] [info] Shutting down WorkflowManagerActor -
Timeout = 3600 seconds
[2022-01-13 20:21:49,43] [info] WorkflowManagerActor All workflows
finished
[2022-01-13 20:21:49,43] [info] WorkflowManagerActor stopped
[2022-01-13 20:21:49,66] [info] Connection pools shut down
[2022-01-13 20:21:49,66] [info] Shutting down SubWorkflowStoreActor -
Timeout = 1800 seconds
[2022-01-13 20:21:49,66] [info] Shutting down JobStoreActor - Timeout
= 1800 seconds
[2022-01-13 20:21:49,66] [info] Shutting down CallCacheWriteActor -
Timeout = 1800 seconds
[2022-01-13 20:21:49,66] [info] Shutting down ServiceRegistryActor -
Timeout = 1800 seconds
[2022-01-13 20:21:49,66] [info] Shutting down DockerHashActor -
Timeout = 1800 seconds
[2022-01-13 20:21:49,66] [info] Shutting down IoProxy - Timeout = 1800
seconds
[2022-01-13 20:21:49,66] [info] SubWorkflowStoreActor stopped
[2022-01-13 20:21:49,66] [info] CallCacheWriteActor Shutting down: 0
queued messages to process
[2022-01-13 20:21:49,66] [info] JobStoreActor stopped
[2022-01-13 20:21:49,66] [info] CallCacheWriteActor stopped
[2022-01-13 20:21:49,66] [info] KvWriteActor Shutting down: 0 queued
messages to process
[2022-01-13 20:21:49,66] [info] IoProxy stopped
[2022-01-13 20:21:49,66] [info] WriteMetadataActor Shutting down: 0
queued messages to process
[2022-01-13 20:21:49,66] [info] ServiceRegistryActor stopped
[2022-01-13 20:21:49,67] [info] DockerHashActor stopped
[2022-01-13 20:21:49,71] [info] Database closed
[2022-01-13 20:21:49,71] [info] Stream materializer shut down
[2022-01-13 20:21:49,72] [info] WDL HTTP import resolver closed
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Hi,
I use singularity (version 3.8.1), ctat_mutations.v3.2.0.simg and the testing read files to call the mutation. The pipeline fails in "Annotating VCF: Calculating ED" step. Do you have any idea how it can be fixed?
The command I used is as below:
singularity exec -e -B
pwd:/data -B /work/reference/GRCh38_gencode_v37_CTAT_lib_Mar012021.plug-n-play/ctat_genome_lib_build_dir:/ctat_genome_lib_dir:ro /work/singularityImage/ctat_mutations.v3.2.0.simg /usr/local/src/ctat-mutations/ctat_mutations --left /data/fastq/reads_1.fastq.gz --right /data/fastq/reads_2.fastq.gz --sample_id test --output /data/out --cpu 1 --genome_lib_dir /ctat_genome_lib_dirThe error message is:
echo "########### Annotate BLAT ED #############"
/usr/local/src/ctat-mutations/src/annotate_ED.py
--input_vcf /data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/inputs/-1226801460/test.splice_distance.vcf.gz
--output_vcf test.blat_ED.vcf
--reference /data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/inputs/817306935/ref_genome.fa
--temp_dir $TMPDIR
--threads 16
[2022-01-13 04:39:05,29] [info] BackgroundConfigAsyncJobExecutionActor [1561a942annotate_variants_wf.annotate_blat_ED:NA:1]: executing: /usr/bin/env bash /data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/execution/script
[2022-01-13 04:39:06,67] [info] BackgroundConfigAsyncJobExecutionActor [1561a942annotate_variants_wf.annotate_blat_ED:NA:1]: job id: 148068
[2022-01-13 04:39:06,68] [info] BackgroundConfigAsyncJobExecutionActor [1561a942annotate_variants_wf.annotate_blat_ED:NA:1]: Status change from - to Done
[2022-01-13 04:39:23,67] [info] WorkflowManagerActor Workflow ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb failed (during ExecutingWorkflowState): Job annotate_variants_wf.annotate_blat_ED:NA: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/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/execution/stderr.
[First 3000 bytes]:+ echo '########### Annotate BLAT ED #############'
22:39:05 : INFO :
################################
Annotating VCF: Calculating ED
################################
22:39:05 : INFO : Processing VCF Positions
22:39:06 : INFO : Running samtools faidx
Traceback (most recent call last):
File "/usr/local/src/ctat-mutations/src/annotate_ED.py", line 165, in
main()
File "/usr/local/src/ctat-mutations/src/annotate_ED.py", line 84, in main
subprocess.check_call(cmd, shell=True)
File "/opt/conda/lib/python3.7/subprocess.py", line 347, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'samtools faidx /data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/inputs/817306935/ref_genome.fa --region-file /data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/tmp.0d731215/positions.fa > /data/testOut/cromwell-executions/ctat_mutations/ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb/call-AnnotateVariants/annotate_variants_wf/1561a942-9e30-4a55-a098-9e091e8fbdfd/call-annotate_blat_ED/tmp.0d731215/faidx_output.fa' returned non-zero exit status 1.
[2022-01-13 04:39:23,68] [info] WorkflowManagerActor WorkflowActor-ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb is in a terminal state: WorkflowFailedState
[2022-01-13 04:40:49,23] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2022-01-13 04:40:52,89] [info] SingleWorkflowRunnerActor writing metadata to /tmp/tmpmghzfeby.json
[2022-01-13 04:40:52,92] [info] Workflow polling stopped
[2022-01-13 04:40:52,93] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
[2022-01-13 04:40:52,93] [info] 0 workflows released by cromid-69e661a
[2022-01-13 04:40:52,93] [info] Aborting all running workflows.
[2022-01-13 04:40:52,94] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
[2022-01-13 04:40:52,94] [info] WorkflowStoreActor stopped
[2022-01-13 04:40:52,95] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
[2022-01-13 04:40:52,95] [info] WorkflowLogCopyRouter stopped
[2022-01-13 04:40:52,95] [info] JobExecutionTokenDispenser stopped
[2022-01-13 04:40:52,95] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
[2022-01-13 04:40:52,95] [info] WorkflowManagerActor All workflows finished
[2022-01-13 04:40:52,95] [info] WorkflowManagerActor stopped
[2022-01-13 04:40:53,23] [info] Connection pools shut down
[2022-01-13 04:40:53,23] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
[2022-01-13 04:40:53,23] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
[2022-01-13 04:40:53,24] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
[2022-01-13 04:40:53,24] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
[2022-01-13 04:40:53,24] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
[2022-01-13 04:40:53,24] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
[2022-01-13 04:40:53,27] [info] Shutting down IoProxy - Timeout = 1800 seconds
[2022-01-13 04:40:53,27] [info] SubWorkflowStoreActor stopped
[2022-01-13 04:40:53,27] [info] JobStoreActor stopped
[2022-01-13 04:40:53,27] [info] CallCacheWriteActor stopped
[2022-01-13 04:40:53,27] [info] IoProxy stopped
[2022-01-13 04:40:53,29] [info] Shutting down connection pool: curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
[2022-01-13 04:40:53,30] [info] WriteMetadataActor Shutting down: 0 queued messages to process
[2022-01-13 04:40:53,32] [info] KvWriteActor Shutting down: 0 queued messages to process
[2022-01-13 04:40:53,32] [info] ServiceRegistryActor stopped
[2022-01-13 04:40:53,32] [info] Shutting down connection pool: curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
[2022-01-13 04:40:53,34] [info] DockerHashActor stopped
[2022-01-13 04:40:53,32] [info] Shutting down connection pool: curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
[2022-01-13 04:40:53,32] [info] Shutting down connection pool: curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
[2022-01-13 04:40:53,38] [info] Database closed
[2022-01-13 04:40:53,39] [info] Stream materializer shut down
[2022-01-13 04:40:53,40] [info] WDL HTTP import resolver closed
Workflow ffd9aa99-405b-4bc0-bf96-4e61a4f09dbb transitioned to state Failed
Thanks so much.
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