Hello dear EGAPx team,
Recently I've pulled the recent 1.0.1 tag version but I've ran into a problem with the run_proteins_by_taxid subprocess.
ERROR ~ Error executing process > 'egapx:target_proteins_plane:target_proteins_plane:proteins_by_taxid:run
_proteins_by_taxid'
Caused by:
Process `egapx:target_proteins_plane:target_proteins_plane:proteins_by_taxid:run_proteins_by_taxid` term
inated with an error exit status (1)
Command executed:
mkdir -p output
mkdir -p tmp/asncache
#lds2_indexer -source indexed -db tmp/lds_index
products_by_taxid -count-threshold 0 -products align.tab -products-output output/@.ids -products-output-manifest output/@.mft -taxids-output output/taxid.list
rm -rf tmp
Command exit status:
1
Command output:
(empty)
Command error:
VmPin: 0 kB
VmHWM: 3072 kB
VmRSS: 3072 kB
VmData: 304 kB
VmStk: 132 kB
VmExe: 956 kB
VmLib: 1828 kB
VmPTE: 48 kB
VmSwap: 0 kB
voluntary_ctxt_switches: 17
nonvoluntary_ctxt_switches: 38'
+++ local 'x_peak=4328 3072 '
++++ awk -v rss=3072 -v mem_tot=1584443124 'BEGIN {printf "%.0f", rss/mem_tot*100*10}'
+++ local x_pmem=0
++++ awk '{print $2}'
USAGE
products_by_taxid [-h] [-help] [-xmlhelp] -products Products
-count-threshold CountThreshold
-identity-pct-threshold IdentityPctThreshold
[-relevant-product-types RelevantProductTypes] -taxids-output OutputFile
[-taxids-append] [-taxids-output-manifest OutputManifest]
[-taxids-destination-dir DestinationDirectory] [-taxids-manifest-append]
[-taxids-items-per-chunk ItemsPerChunk]
[-taxids-max-chunk-size MaxChunkSize]
[-taxids-min-chunk-size MinChunkSize]<!-- Failed to upload "EG11_test_run_ncRNA.yaml" -->
[-taxids-max-files-per-dir MaxFilesPerDirectory] [-taxids-allow-subdirs]
[-taxids-tolerate-failures] [-taxids-num-partitions NumberOfPartitions]
[-taxids-extension-mapping ExtensionMapping] [-products-output OutputFile]
[-products-append] [-products-output-manifest OutputManifest]
[-products-destination-dir DestinationDirectory]
[-products-manifest-append] [-products-items-per-chunk ItemsPerChunk]
[-products-max-chunk-size MaxChunkSize]
[-products-min-chunk-size MinChunkSize]
[-products-max-files-per-dir MaxFilesPerDirectory]
[-products-allow-subdirs] [-products-tolerate-failures]
[-products-num-partitions NumberOfPartitions]
[-products-extension-mapping ExtensionMapping] [-logfile File_Name]
[-conffile File_Name] [-version] [-version-full] [-version-full-xml]
[-version-full-json] [-dryrun]
DESCRIPTION
Classify aligned products by taxid
Use '-help' to print detailed descriptions of command line arguments
========================================================================
Error: Argument "identity-pct-threshold". Mandatory value is missing: `Integer'
Error: (CArgException::eNoArg) Argument "identity-pct-threshold". Mandatory value is missing: `Integer'
++++ grep '\bvoluntary_ctxt_switches'
++ kill 37
Up to my own research and daring attempts to solve this problem I suppose that the problem could be there: https://github.com/ncbi/egapx/blob/main/nf/subworkflows/ncbi/target_proteins/proteins_by_taxid/main.nf in the parameters expansion.
I'll try to investigate it further and do the pull request if I solve this problem successfully.
My configuration:
I'm using SLURM cluster with nextflow version 25.10.2. YAML file and full log are attached below.
Have a good day and thanks for your help!
EGAPx_ncRNA_test.log
EG11_test_run_ncRNA.txt
Hello dear EGAPx team,
Recently I've pulled the recent 1.0.1 tag version but I've ran into a problem with the run_proteins_by_taxid subprocess.
Up to my own research and daring attempts to solve this problem I suppose that the problem could be there: https://github.com/ncbi/egapx/blob/main/nf/subworkflows/ncbi/target_proteins/proteins_by_taxid/main.nf in the parameters expansion.
I'll try to investigate it further and do the pull request if I solve this problem successfully.
My configuration:
I'm using SLURM cluster with nextflow version 25.10.2. YAML file and full log are attached below.
Have a good day and thanks for your help!
EGAPx_ncRNA_test.log
EG11_test_run_ncRNA.txt