+ date=2019-10-01
+ data_source=data_sources
+ organism='Homo sapiens'
++ dirname ../prep/study_metadata_layout.sh
+ sdir=../prep
+ study=ERP110841
+ org=human
+ dsource=sra
+ preds_file=../prep/Human.SRA_curated_predict.meta.w_rids.rtypes.tsv
+ perl -e '$study="ERP110841"; $study=~/(..)$/; $lo=$1; `mkdir -p $lo/$study`; print "$lo/$study\n";'
++ cat ERP110841.dir
cat: ERP110841.dir: No such file or directory
+ dir=
+ cat ../prep/samples.tsv.header /dev/fd/63
++ fgrep '	ERP110841	' ../prep/samples.tsv
../prep/study_metadata_layout.sh: line 22: /samples.tsv.ERP110841: Permission denied
+ cut_cols=1-3
+ [[ human == \m\o\u\s\e ]]
+ [[ human == \h\u\m\a\n ]]
+ gzip
+ cut -f 1-41 /samples.tsv.ERP110841
../prep/study_metadata_layout.sh: line 34: /sra.sra.ERP110841.MD.gz: Permission denied
cut: /samples.tsv.ERP110841: No such file or directory
+ gzip
+ cut -f 1-3,42-150 /samples.tsv.ERP110841
../prep/study_metadata_layout.sh: line 36: /sra.recount_qc.ERP110841.MD.gz: Permission denied
cut: /samples.tsv.ERP110841: No such file or directory
+ [[ human == \g\t\e\x ]]
+ [[ human == \t\c\g\a ]]
+ proj_header='rail_id	external_id	study	project	organism	file_source	metadata_source	date_processed'
+ dsource_path=data_sources/sra
+ extra_proj_cols='Homo sapiens	data_sources/sra	data_sources/sra	2019-10-01'
+ gzip
++ echo 'rail_id	external_id	study	project	organism	file_source	metadata_source	date_processed'
+ cat /dev/fd/63 /dev/fd/62
++ tail -n+2 /samples.tsv.ERP110841
++ cut -f 1-3
++ perl -ne 'chomp; $f=$_; ($rid,$run,$study)=split(/\t/,$f); print "$f\t$study\tHomo sapiens	data_sources/sra	data_sources/sra	2019-10-01\n";'
../prep/study_metadata_layout.sh: line 60: /sra.recount_project.ERP110841.MD.gz: Permission denied
tail: cann++ perl -e '$s="ERP110841"; $s=~/(..)$/; $lo=$1; print "$lo\n";'
+ lo=41
+ gzip
+ cat /dev/fd/63 /dev/fd/62
++ head -1 ../prep/seqtk.w_study.tsv.cut
++ fgrep '	ERP110841	' ../prep/seqtk.w_study.tsv.cut
+ rm 41/ERP110841/samples.tsv.ERP110841
rm: cannot remove ‘41/ERP110841/samples.tsv.ERP110841’: No such file or directory
+ rm ERP110841.dir
rm: cannot remove ‘ERP110841.dir’: No such file or directory
rtypes.tsv
++ perl -e '$s="ERP110841"; $s=~/(..)$/; $lo=$1; print "$lo\n";'
+ lo=41
+ gzip
+ cat /dev/fd/63 /dev/fd/62
++ head -1 ../prep/seqtk.w_study.tsv.cut
++ fgrep '	ERP110841	' ../prep/seqtk.w_study.tsv.cut
+ rm /samples.tsv.ERP110841
rm: cannot remove ‘/samples.tsv.ERP110841’: No such file or directory
+ rm ERP110841.dir
rm: cannot remove ‘ERP110841.dir’: No such file or directory