+ date=2019-10-01
+ data_source=data_sources
+ organism='Homo sapiens'
++ dirname ../prep/study_metadata_layout.sh
+ sdir=../prep
+ study=SRP212755
+ org=human
+ dsource=sra
+ preds_file=../prep/Human.SRA_curated_predict.meta.w_rids.rtypes.tsv
+ perl -e '$study="SRP212755"; $study=~/(..)$/; $lo=$1; `mkdir -p $lo/$study`; print "$lo/$study\n";'
++ cat SRP212755.dir
cat: SRP212755.dir: No such file or directory
+ dir=
+ cat ../prep/samples.tsv.header /dev/fd/63
++ fgrep + cut_cols=1-3
+ [[ human == \m\o\u\s\e ]]
+ [[ human == \h\u\m\a\n ]]
+ gzip
+ cut -f 1-41 55/SRP212755/samples.tsv.SRP212755
cut: 55/SRP212755/samples.tsv.SRP212755: No such file or directory
+ gzip
+ cut -f 1-3,42-150 55/SRP212755/samples.tsv.SRP212755
cut: 55/SRP212755/samples.tsv.SRP212755: 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
+ cat /dev/fd/63 /dev/fd/62
++ echo 'rail_id	external_id	study	project	organism	file_source	metadata_source	date_processed'
++ tail -n+2 55/SRP212755/samples.tsv.SRP212755
++ 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";'
tail: cannot open ‘55/SRP212755/samples.tsv.SRP212755’ for reading: No such file or directory
+ [[ -n ../prep/Human.SRA_curated_predict.meta.w_rids.rtypes.tsv ]]
+ gzip
+ cat /dev/fd/63 /dev/fd/62
++ head -1 ../prep/Human.SRA_curated_predict.meta.w_rids.rtypes.tsv
++ fgrep '	SRP212755	' ../prep/Human.SRA_curated_predict.meta.w_rids.rtypes.tsv
++ perl -e '$s="SRP212755"; $s=~/(..)$/; $lo=$1; print "$lo\n";'
+ lo=55
+ gzip
+ cat /dev/fd/63 /dev/fd/62
++ head -1 ../prep/seqtk.w_study.tsv.cut
++ fgrep '	SRP212755	' ../prep/seqtk.w_study.tsv.cut
+ rm 55/SRP212755/samples.tsv.SRP212755
rm: cannot remove ‘55/SRP212755/samples.tsv.SRP212755’: No such file or directory
+ rm SRP212755.dir
rm: cannot remove ‘SRP212755.dir’: No such file or directory
ion denied
++ perl -e '$s="SRP212755"; $s=~/(..)$/; $lo=$1; print "$lo\n";'
+ lo=55
+ gzip
+ cat /dev/fd/63 /dev/fd/62
++ head -1 ../prep/seqtk.w_study.tsv.cut
++ fgrep '	SRP212755	' ../prep/seqtk.w_study.tsv.cut
+ rm /samples.tsv.SRP212755
rm: cannot remove ‘/samples.tsv.SRP212755’: No such file or directory
+ rm SRP212755.dir
rm: cannot remove ‘SRP212755.dir’: No such file or directory