+ date=2019-10-01
+ data_source=data_sources
+ organism='Homo sapiens'
++ dirname ../prep/study_metadata_layout.sh
+ sdir=../prep
+ study=SRP156888
+ org=mouse
+ dsource=sra
+ preds_file=../prep/Mouse.SRA_curated_predict.meta.w_rids.w_cell_types_nas.tsv
+ perl -e '$study="SRP156888"; $study=~/(..)$/; $lo=$1; `mkdir -p $lo/$study`; print "$lo/$study\n";'
++ cat SRP156888.dir
+ dir=88/SRP156888
+ cat ../prep/samples.tsv.header /dev/fd/63
++ fgrep '	SRP156888	' ../prep/samples.tsv
+ cut_cols=1-3
+ [[ mouse == \m\o\u\s\e ]]
+ organism='Mus musculus'
+ date=2020-01-01
+ gzip
+ cut -f 1-43 88/SRP156888/samples.tsv.SRP156888
+ cut -f 1-3,44-152 88/SRP156888/samples.tsv.SRP156888
+ gzip
+ [[ mouse == \h\u\m\a\n ]]
+ [[ mouse == \g\t\e\x ]]
+ [[ mouse == \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='Mus musculus	data_sources/sra	data_sources/sra	2020-01-01'
+ gzip
+ cat /dev/fd/63 /dev/fd/62
++ tail -n+2 88/SRP156888/samples.tsv.SRP156888
++ cut -f 1-3
++ echo 'rail_id	external_id	study	project	organism	file_source	metadata_source	date_processed'
++ perl -ne 'chomp; $f=$_; ($rid,$run,$study)=split(/\t/,$f); print "$f\t$study\tMus musculus	data_sources/sra	data_sources/sra	2020-01-01\n";'
+ [[ -n ../prep/Mouse.SRA_curated_predict.meta.w_rids.w_cell_types_nas.tsv ]]
+ gzip
+ cat /dev/fd/63 /dev/fd/62
++ head -1 ../prep/Mouse.SRA_curated_predict.meta.w_rids.w_cell_types_nas.tsv
++ fgrep '	SRP156888	' ../prep/Mouse.SRA_curated_predict.meta.w_rids.w_cell_types_nas.tsv
++ perl -e '$s="SRP156888"; $s=~/(..)$/; $lo=$1; print "$lo\n";'
+ lo=88
+ gzip
+ cat /dev/fd/63 /dev/fd/62
++ head -1 ../prep/seqtk.w_study.tsv.cut
++ fgrep '	SRP156888	' ../prep/seqtk.w_study.tsv.cut
+ rm 88/SRP156888/samples.tsv.SRP156888
+ rm SRP156888.dir