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util.out
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Loading required package: yaml
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
expand.grid, I, unname
Loading required package: BiocFileCache
Loading required package: dbplyr
Attaching package: ‘RcwlPipelines’
The following object is masked from ‘package:graphics’:
title
checking pl_alignMerge
[1;30mINFO[0m /projects/rpci/songliu/qhu/miniconda3/bin//cwltool 3.1.20240708091337
[1;30mINFO[0m Resolved '/tmp/RtmpTqjTO9/file26500c4cf99137/pl_alignMerge.cwl' to 'file:///tmp/RtmpTqjTO9/file26500c4cf99137/pl_alignMerge.cwl'
Rcwl/pl_alignMerge.R is validated
vep_plugin loaded
checking pl_AnnPhaseVcf
[1;30mINFO[0m /projects/rpci/songliu/qhu/miniconda3/bin//cwltool 3.1.20240708091337
[1;30mINFO[0m Resolved '/tmp/RtmpTqjTO9/file26500c4405eba2/pl_AnnPhaseVcf.cwl' to 'file:///tmp/RtmpTqjTO9/file26500c4405eba2/pl_AnnPhaseVcf.cwl'
../../../../../../../../tmp/RtmpTqjTO9/file26500c4405eba2/pl_AnnPhaseVcf.cwl:8:3: Warning: checking
item
Warning: Field
'class' contains
undefined reference
to
'http://commonwl.org/cwltool#LoadListingRequirement'
[1;30mWARNING[0m [33m../../../../../../../../tmp/RtmpTqjTO9/file26500c4405eba2/pl_AnnPhaseVcf.cwl:8:3: Warning: checking
item
Warning: Field
'class' contains
undefined reference
to
'http://commonwl.org/cwltool#LoadListingRequirement'[0m
URI prefix 'cwltool' of 'cwltool:LoadListingRequirement' not recognized, are you missing a $namespaces section?
[1;30mWARNING[0m [33mURI prefix 'cwltool' of 'cwltool:LoadListingRequirement' not recognized, are you missing a $namespaces section?[0m
../../../../../../../../tmp/RtmpTqjTO9/file26500c4405eba2/VCFvep.cwl:8:3: Warning: checking item
Warning: Unsupported
scheme 'cwltool' in url:
cwltool:LoadListingRequirement
[1;30mWARNING[0m [33m../../../../../../../../tmp/RtmpTqjTO9/file26500c4405eba2/VCFvep.cwl:8:3: Warning: checking item
Warning: Unsupported
scheme 'cwltool' in url:
cwltool:LoadListingRequirement[0m
[1;30mINFO[0m ../../../../../../../../tmp/RtmpTqjTO9/file26500c4405eba2/VCFvep.cwl:1:1: Unknown hint
cwltool:LoadListingRequirement
Rcwl/pl_AnnPhaseVcf.R is validated
arcasHLA_extract loaded
arcasHLA_genotype loaded
arcasHLA_partial loaded
checking pl_arcasHLA_pl
[1;30mINFO[0m /projects/rpci/songliu/qhu/miniconda3/bin//cwltool 3.1.20240708091337
[1;30mINFO[0m Resolved '/tmp/RtmpTqjTO9/file26500c37905f49/pl_arcasHLA_pl.cwl' to 'file:///tmp/RtmpTqjTO9/file26500c37905f49/pl_arcasHLA_pl.cwl'
Rcwl/pl_arcasHLA_pl.R is validated
STAR loaded
arriba loaded
Error in stepInputs(list(s1, s2)) : could not find function "stepInputs"
Calls: cwlLoad ... eval -> cwlWorkflow -> new -> initialize -> initialize
Execution halted