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can't use cwl step to create empty_dir anymore #205

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ionox0 opened this issue Jul 26, 2019 · 1 comment
Open

can't use cwl step to create empty_dir anymore #205

ionox0 opened this issue Jul 26, 2019 · 1 comment
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invalid This doesn't seem right

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@ionox0
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ionox0 commented Jul 26, 2019

need to understand this better

upgraded to Toil 3.19, made a change to ResolveIndirect logic as described here:

DataBiosphere/toil#2499 (comment)

Then got this error for Abra:

Exception in thread "main" java.nio.file.NoSuchFileException: /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FY/Toil-ionox0_0.0.8dev_test/5500-FY_TD-dmplib-1-1.1.13/tmp/tmpZy1gIX/stg1f502640-97b7-4379-bf94-bfae0e541b12/empty_dir/abra2_4dd0a31a-385a-47b3-be31-900950e07b3b5123542356085170296

Maybe the change caused this. Guess it's not a viable solution.

@ionox0 ionox0 added the invalid This doesn't seem right label Jul 31, 2019
@ionox0
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ionox0 commented Aug 19, 2019

Happened again:

DEBUG:toil.batchSystems.abstractGridEngineBatchSystem:Running ['bsub', '-cwd', '.', '-J', 'toil_job_192', '-R', 'select[mem > 7] rusage[mem=7]', '-M', '7', '-n', '8', '-o', u'/home/johnsoni/juno_ACCESS/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/toil-ed8f824a-824e-46aa-9ee2-33f1f224acac-ec01b17d-7096-41d9-bdd7-747ad82c936f/toil_job_192_batch_lsf_%J_std_output.log', '-e', u'/home/johnsoni/juno_ACCESS/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/toil-ed8f824a-824e-46aa-9ee2-33f1f224acac-ec01b17d-7096-41d9-bdd7-747ad82c936f/toil_job_192_batch_lsf_%J_std_error.log', '-S', '1', '-app', 'anyOS', '-R', 'select[type==CentOS7]', '/home/johnsoni/virtualenvs/pipeline_1.2.2-toil-ionox0-0.0.9/bin/_toil_worker file:///home/johnsoni/pipeline_1.2.2/ACCESS-Pipeline/cwl_tools/abra/abra.cwl file:/home/johnsoni/juno_ACCESS/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/jobstore-d78ef934-c06a-11e9-b1e7-ec0d9a88a22a kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA']
--
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        /ifs/depot/resources/dmp/data/pubdata/hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --sc \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        100,30,80,15 \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --sga \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        8,32,48,1 \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --targets \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stgc1eadbdc-bfba-4b58-bebb-717cc3f92bb3/C-0558N9.fci.bed.srt \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --threads \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        12 \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --tmpdir \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stgc781dc41-8ccd-4346-a54c-6724f81581ec/empty_dir \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --ws \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        800,700
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO:cwltool:[job abra.cwl] /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/toil-ed8f824a-824e-46aa-9ee2-33f1f224acac-d7d5f745-2014-4455-aa2c-e896e925dfa8/tmpS1jDxE/6258f6af-fa9f-4c0e-a1bc-19a6325b003f/tt0f1vP/tmp-outepTAJV$ /opt/common/CentOS_6/java/jdk1.8.0_31/bin/java \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        -Xmx50g \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        -Djava.io.tmpdir=/juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stgc781dc41-8ccd-4346-a54c-6724f81581ec/empty_dir \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        -jar \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        /opt/common/CentOS_6/abra2/abra2-2.17/abra2-2.17.jar \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --ca \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        10,1 \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --cons \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --index \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --in \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stg85c08b79-0378-4287-960f-ff17d54ccdfe/C-0558N9-L001-d_cl_aln_srt_MD.bam,/juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stg957f7beb-27f4-49dc-943f-b4a8ff4db7c6/C-0558N9-L002-d_cl_aln_srt_MD.bam \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --mad \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        1000 \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --mmr \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        0.1 \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --out \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        C-0558N9-L001-d_cl_aln_srt_MD_IR.bam,C-0558N9-L002-d_cl_aln_srt_MD_IR.bam \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --ref \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        /ifs/depot/resources/dmp/data/pubdata/hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --sc \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        100,30,80,15 \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --sga \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        8,32,48,1 \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --targets \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stgc1eadbdc-bfba-4b58-bebb-717cc3f92bb3/C-0558N9.fci.bed.srt \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --threads \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        12 \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --tmpdir \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stgc781dc41-8ccd-4346-a54c-6724f81581ec/empty_dir \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        --ws \
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        800,700
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/scratch/5500-FZ-1.1.14_zJW6zJ_18450
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	Abra version: 2.17
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	Abra params: [/opt/common/CentOS_6/abra2/abra2-2.17/abra2-2.17.jar --ca 10,1 --cons --index --in /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stg85c08b79-0378-4287-960f-ff17d54ccdfe/C-0558N9-L001-d_cl_aln_srt_MD.bam,/juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stg957f7beb-27f4-49dc-943f-b4a8ff4db7c6/C-0558N9-L002-d_cl_aln_srt_MD.bam --mad 1000 --mmr 0.1 --out C-0558N9-L001-d_cl_aln_srt_MD_IR.bam,C-0558N9-L002-d_cl_aln_srt_MD_IR.bam --ref /ifs/depot/resources/dmp/data/pubdata/hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta --sc 100,30,80,15 --sga 8,32,48,1 --targets /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stgc1eadbdc-bfba-4b58-bebb-717cc3f92bb3/C-0558N9.fci.bed.srt --threads 12 --tmpdir /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stgc781dc41-8ccd-4346-a54c-6724f81581ec/empty_dir --ws 800,700]
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	ABRA version: 2.17
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	input0: /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stg85c08b79-0378-4287-960f-ff17d54ccdfe/C-0558N9-L001-d_cl_aln_srt_MD.bam
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	input0: /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stg957f7beb-27f4-49dc-943f-b4a8ff4db7c6/C-0558N9-L002-d_cl_aln_srt_MD.bam
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	output0: C-0558N9-L001-d_cl_aln_srt_MD_IR.bam
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	output0: C-0558N9-L002-d_cl_aln_srt_MD_IR.bam
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	regions: /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stgc1eadbdc-bfba-4b58-bebb-717cc3f92bb3/C-0558N9.fci.bed.srt
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	reference: /ifs/depot/resources/dmp/data/pubdata/hg-fasta/VERSIONS/hg19/Homo_sapiens_assembly19.fasta
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	num threads: 12
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	minEdgeFrequency: 0
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    minNodeFrequncy: 1
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    minContigLength: -1
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    minBaseQuality: 20
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    minReadCandidateFraction: 0.01
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    maxAverageRegionDepth: 1000
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    minEdgeRatio: 0.01
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	paired end: true
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	isSkipAssembly: false
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	useSoftClippedReads: true
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	SW scoring: [8, 32, 48, 1]
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	Soft clip params: [100, 30, 80, 15]
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	Java version: 1.8.0_31
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	hostname: jb09
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO	Sun Aug 18 00:10:25 EDT 2019	SG match,mismatch,gap_open_penalty,gap_extend_penalty: 8,-32,-48,-1
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    Exception in thread "main" java.nio.file.NoSuchFileException: /juno/work/bergerm1/MSK-ACCESS/ACCESS-Projects/5500-FZ/5500-FZ_copy_6/5500-FZ-1.1.14/tmp/tmp2vATeh/stgc781dc41-8ccd-4346-a54c-6724f81581ec/empty_dir/abra2_e395573e-5374-4780-af6c-ae58a1a524256645442456157179718
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    	at sun.nio.fs.UnixException.translateToIOException(UnixException.java:86)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    	at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:102)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    	at sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:107)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    	at sun.nio.fs.UnixFileSystemProvider.createDirectory(UnixFileSystemProvider.java:384)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    	at java.nio.file.Files.createDirectory(Files.java:674)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    	at java.nio.file.TempFileHelper.create(TempFileHelper.java:136)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    	at java.nio.file.TempFileHelper.createTempDirectory(TempFileHelper.java:173)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    	at java.nio.file.Files.createTempDirectory(Files.java:991)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    	at abra.ReAligner.init(ReAligner.java:1647)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    	at abra.ReAligner.reAlign(ReAligner.java:166)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    	at abra.ReAligner.run(ReAligner.java:1833)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    	at abra.Abra.main(Abra.java:12)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    Could not collect memory usage, job ended before monitoring began.
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    INFO:cwltool:Could not collect memory usage, job ended before monitoring began.
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    [job abra.cwl] completed permanentFail
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    WARNING:cwltool:[job abra.cwl] completed permanentFail
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    DEBUG:toil.fileStores.abstractFileStore:LOG-TO-MASTER: Job files/for-job/kind-CWLWorkflow/instanceMtEXK7/cleanup/file-IQ0Zug/stream used 62.63% (74.0 GB [79481871872B] used, 118.2 GB [126902861824B] requested) at the end of its run.
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    DEBUG:toil.deferred:Running own deferred functions
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    DEBUG:toil.deferred:Out of deferred functions!
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    DEBUG:toil.deferred:Running orphaned deferred functions
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    Traceback (most recent call last):
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA      File "/home/johnsoni/virtualenvs/pipeline_1.2.2-toil-ionox0-0.0.9/lib/python2.7/site-packages/toil/worker.py", line 337, in workerScript
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA      File "/home/johnsoni/virtualenvs/pipeline_1.2.2-toil-ionox0-0.0.9/lib/python2.7/site-packages/toil/job.py", line 1389, in _runner
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        returnValues = self._run(jobGraph, fileStore)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA      File "/home/johnsoni/virtualenvs/pipeline_1.2.2-toil-ionox0-0.0.9/lib/python2.7/site-packages/toil/job.py", line 1328, in _run
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        return self.run(fileStore)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA      File "/home/johnsoni/virtualenvs/pipeline_1.2.2-toil-ionox0-0.0.9/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 574, in run
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA        raise cwltool.errors.WorkflowException(status)
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    WorkflowException: permanentFail
WARNING:toil.leader:kind-file_home_johnsoni_pipeline_1.2.2_ACCESS-Pipeline_cwl_tools_abra_abra.cwl/instancecA1ocA    ERROR:toil.worker:Exiting the worker because of a failed job on host jb09

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