DavyCats
commented
4 years ago The pipeline uses the size of the input files to estimate the amount of time needed to run certain tasks. To do so the size function from WDL was used to retrieve the file sizes. There was a bug in cromwell, however, which caused this to fail on relative input paths (as are used in the tests). This should be fixed in the latest cromwell release.
The requirements-test.txt file is currently a bit outdated, as we were using a patched cromwell version in the automated testing, which had to be installed separately.
If you remove the >=48 from the requirements-test.txt and rebuild the conda environment, then you will most likely be able to run the tests.
EngineerReversed
I ran
pytest --kwdfor testing out all workflows but all of them failed and only 30 passed. I specifically tested it out forRna3PairedEndVariantCallingworkflow and I got the following error.Package versions
``` _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 0_gnu conda-forge appdirs 1.4.3 py_1 conda-forge argcomplete 1.11.1 pyh9f0ad1d_1 conda-forge asn1crypto 1.3.0 py37hc8dfbb8_1 conda-forge attrs 19.3.0 py_0 conda-forge biowdl-input-converter 0.2.1 py_0 bioconda brotlipy 0.7.0 py37h8f50634_1000 conda-forge bzip2 1.0.8 h516909a_2 conda-forge ca-certificates 2020.6.20 hecda079_0 conda-forge certifi 2020.6.20 py37hc8dfbb8_0 conda-forge cffi 1.14.0 py37hd463f26_0 conda-forge chardet 3.0.4 py37hc8dfbb8_1006 conda-forge coloredlogs 14.0 py37hc8dfbb8_1 conda-forge cromwell 48 0 conda-forge cryptography 2.9.2 py37hb09aad4_0 conda-forge docker-py 4.2.2 py37hc8dfbb8_0 conda-forge docker-pycreds 0.4.0 py_0 conda-forge findutils 4.6.0 h14c3975_1000 conda-forge gettext 0.19.8.1 hc5be6a0_1002 conda-forge humanfriendly 8.2 py37hc8dfbb8_0 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge importlib-metadata 1.7.0 py37hc8dfbb8_0 conda-forge importlib_metadata 1.7.0 0 conda-forge jsonschema 3.2.0 py37hc8dfbb8_1 conda-forge krb5 1.17.1 hfafb76e_1 conda-forge lark-parser 0.8.5 pyh9f0ad1d_0 conda-forge ld_impl_linux-64 2.34 h53a641e_5 conda-forge libcurl 7.71.0 hcdd3856_0 conda-forge libdeflate 1.6 h516909a_0 conda-forge libedit 3.1.20191231 h46ee950_0 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc-ng 9.2.0 h24d8f2e_2 conda-forge libgomp 9.2.0 h24d8f2e_2 conda-forge libssh2 1.9.0 hab1572f_2 conda-forge libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge miniwdl 0.7.5 py_0 conda-forge more-itertools 8.4.0 py_0 conda-forge ncurses 6.1 hf484d3e_1002 conda-forge openjdk 8.0.192 h516909a_1005 conda-forge openssl 1.1.1g h516909a_0 conda-forge packaging 20.4 pyh9f0ad1d_0 conda-forge pip 20.1.1 py_1 conda-forge pluggy 0.13.1 py37hc8dfbb8_2 conda-forge py 1.9.0 pyh9f0ad1d_0 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pygtail 0.11.1 py_0 conda-forge pyopenssl 19.1.0 py_1 conda-forge pyparsing 2.4.7 pyh9f0ad1d_0 conda-forge pyrsistent 0.16.0 py37h8f50634_0 conda-forge pysam 0.16.0.1 py37hc501bad_0 bioconda pysocks 1.7.1 py37hc8dfbb8_1 conda-forge pytest 5.4.3 py37hc8dfbb8_0 conda-forge pytest-workflow 1.4.0 py_0 conda-forge python 3.7.6 cpython_h8356626_6 conda-forge python-json-logger 0.1.11 py_0 conda-forge python_abi 3.7 1_cp37m conda-forge pyyaml 5.3.1 py37h8f50634_0 conda-forge readline 8.0 hf8c457e_0 conda-forge regex 2020.6.8 py37h8f50634_0 conda-forge requests 2.24.0 pyh9f0ad1d_0 conda-forge ruamel.yaml 0.16.6 py37h8f50634_1 conda-forge ruamel.yaml.clib 0.2.0 py37h8f50634_1 conda-forge setuptools 47.3.1 py37hc8dfbb8_0 conda-forge six 1.15.0 pyh9f0ad1d_0 conda-forge sqlite 3.32.3 hcee41ef_0 conda-forge tk 8.6.10 hed695b0_0 conda-forge urllib3 1.25.9 py_0 conda-forge wcwidth 0.2.5 pyh9f0ad1d_0 conda-forge websocket-client 0.57.0 py37hc8dfbb8_1 conda-forge wheel 0.34.2 py_1 conda-forge xdg 4.0.1 py_1 conda-forge xz 5.2.5 h516909a_0 conda-forge yaml 0.2.5 h516909a_0 conda-forge zipp 3.1.0 py_0 conda-forge zlib 1.2.11 h516909a_1006 conda-forge ```I am using a _Ubuntu 18.04.3 LTS (GNU/Linux 4.15.0-72-generic x8664)
Full error stack trace
``` [2020-07-03 00:27:33,97] [info] Running with database db.url = jdbc:hsqldb:mem:fb4e23cb-5eb9-494b-ae42-1d9af7d01aab;shutdown=false;hsqldb.tx=mvcc [2020-07-03 00:27:39,37] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000 [2020-07-03 00:27:39,38] [info] [RenameWorkflowOptionsInMetadata] 100% [2020-07-03 00:27:39,44] [info] Running with database db.url = jdbc:hsqldb:mem:d1976698-78aa-47bf-b7ce-e2d98a2e4308;shutdown=false;hsqldb.tx=mvcc [2020-07-03 00:27:39,74] [info] Slf4jLogger started [2020-07-03 00:27:39,86] [info] Workflow heartbeat configuration: { "cromwellId" : "cromid-e524f6a", "heartbeatInterval" : "2 minutes", "ttl" : "10 minutes", "failureShutdownDuration" : "5 minutes", "writeBatchSize" : 10000, "writeThreshold" : 10000 } [2020-07-03 00:27:39,89] [info] Metadata summary refreshing every 1 second. [2020-07-03 00:27:39,91] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds. [2020-07-03 00:27:39,91] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds. [2020-07-03 00:27:39,91] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds. [2020-07-03 00:27:39,91] [[38;5;220mwarn[0m] 'docker.hash-lookup.gcr-api-queries-per-100-seconds' is being deprecated, use 'docker.hash-lookup.gcr.throttle' instead (see reference.conf) [2020-07-03 00:27:39,97] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds. [2020-07-03 00:27:40,09] [info] SingleWorkflowRunnerActor: Version 48 [2020-07-03 00:27:40,09] [info] SingleWorkflowRunnerActor: Submitting workflow [2020-07-03 00:27:40,13] [info] Unspecified type (Unspecified version) workflow 5c8eec74-dace-4680-a79b-b5ca0d003def submitted [2020-07-03 00:27:40,15] [info] SingleWorkflowRunnerActor: Workflow submitted [38;5;2m5c8eec74-dace-4680-a79b-b5ca0d003def[0m [2020-07-03 00:27:40,15] [info] 1 new workflows fetched by cromid-e524f6a: 5c8eec74-dace-4680-a79b-b5ca0d003def [2020-07-03 00:27:40,16] [info] WorkflowManagerActor Starting workflow [38;5;2m5c8eec74-dace-4680-a79b-b5ca0d003def[0m [2020-07-03 00:27:40,17] [info] WorkflowManagerActor Successfully started WorkflowActor-5c8eec74-dace-4680-a79b-b5ca0d003def [2020-07-03 00:27:40,17] [info] Retrieved 1 workflows from the WorkflowStoreActor [2020-07-03 00:27:40,20] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes. [2020-07-03 00:27:40,25] [info] MaterializeWorkflowDescriptorActor [[38;5;2m5c8eec74[0m]: Parsing workflow as WDL 1.0 [2020-07-03 00:27:42,50] [info] MaterializeWorkflowDescriptorActor [[38;5;2m5c8eec74[0m]: Call-to-Backend assignments: MultiBamExpressionQuantification.mergedStringtieTPMs -> Local, RNAseq.CPAT -> Local, GatkPreprocess.gatherBamFiles -> Local, GatkPreprocess.applyBqsr -> Local, MultiBamExpressionQuantification.mergedStringtieFPKMs -> Local, SampleWorkflow.umiDedup -> Local, QC.FastqcRead2 -> Local, SingleSampleCalling.callY -> Local, SingleSampleCalling.mergeSingleSampleVcf -> Local, CalculateRegions.intersectX -> Local, SampleWorkflow.star -> Local, SampleWorkflow.hisat2 -> Local, CalculateRegions.inverseBed -> Local, MultiBamExpressionQuantification.stringtieAssembly -> Local, MultiBamExpressionQuantification.stringtie -> Local, RNAseq.multiqcTask -> Local, SingleSampleCalling.Stats -> Local, RNAseq.gffreadTask -> Local, QC.FastqcRead1 -> Local, GatkPreprocess.splitNCigarReads -> Local, GatkPreprocess.gatherBqsr -> Local, BamMetrics.targetIntervalsLists -> Local, RNAseq.makeStarIndex -> Local, SingleSampleCalling.callX -> Local, MultiBamExpressionQuantification.htSeqCount -> Local, CalculateRegions.intersectAutosomalRegions -> Local, SingleSampleCalling.mergeSingleSampleGvcf -> Local, BamMetrics.rnaSeqMetrics -> Local, BamMetrics.Flagstat -> Local, SampleWorkflow.markDuplicates -> Local, BamMetrics.targetMetrics -> Local, CalculateRegions.scatterAutosomalRegions -> Local, QC.Cutadapt -> Local, MultiBamExpressionQuantification.mergedHTSeqFragmentsPerGenes -> Local, BamMetrics.ampliconIntervalsLists -> Local, RNAseq.GffCompare -> Local, RNAseq.scatterList -> Local, RNAseq.ConvertDockerTagsFile -> Local, QC.FastqcRead2After -> Local, CalculateRegions.intersectY -> Local, BamMetrics.picardMetrics -> Local, CalculateRegions.mergeBeds -> Local, RNAseq.ConvertSampleConfig -> Local, SingleSampleCalling.callAutosomal -> Local, QC.FastqcRead1After -> Local, MultiBamExpressionQuantification.mergeStringtieGtf -> Local, SampleWorkflow.postUmiDedupMarkDuplicates -> Local, GatkPreprocess.baseRecalibrator -> Local, SampleWorkflow.indexStarBam -> Local [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [cpu, memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [cpu, memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, cpu, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [cpu, memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [cpu, memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [cpu, time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [cpu, memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,63] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [cpu, memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [cpu, memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [cpu, memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [cpu, memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [cpu, memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [cpu, memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [time_minutes, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:42,64] [[38;5;220mwarn[0m] Local [[38;5;2m5c8eec74[0m]: Key/s [memory, time_minutes] is/are not supported by backend. Unsupported attributes will not be part of job executions. [2020-07-03 00:27:44,82] [info] WorkflowExecutionActor-5c8eec74-dace-4680-a79b-b5ca0d003def [[38;5;2m5c8eec74[0m]: Starting RNAseq.ConvertSampleConfig, RNAseq.ConvertDockerTagsFile [2020-07-03 00:27:44,98] [info] Not triggering log of token queue status. Effective log interval = None [2020-07-03 00:27:44,99] [info] Assigned new job execution tokens to the following groups: 5c8eec74: 2 [2020-07-03 00:27:46,66] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m5c8eec74[0mRNAseq.ConvertSampleConfig:NA:1]: Unrecognized runtime attribute keys: time_minutes, memory [2020-07-03 00:27:46,66] [[38;5;220mwarn[0m] BackgroundConfigAsyncJobExecutionActor [[38;5;2m5c8eec74[0mRNAseq.ConvertDockerTagsFile:NA:1]: Unrecognized runtime attribute keys: time_minutes, memory [2020-07-03 00:27:46,71] [info] BackgroundConfigAsyncJobExecutionActor [[38;5;2m5c8eec74[0mRNAseq.ConvertDockerTagsFile:NA:1]: [38;5;5mset -e mkdir -p "$(dirname ./dockerImages.json)" python <