+ date=2019-10-01 + data_source=data_sources + organism='Homo sapiens' ++ dirname ../prep/study_metadata_layout.sh + sdir=../prep + study=SRP041471 + org=human + dsource=sra + preds_file=../prep/Human.SRA_curated_predict.meta.w_rids.rtypes.tsv + perl -e '$study="SRP041471"; $study=~/(..)$/; $lo=$1; `mkdir -p $lo/$study`; print "$lo/$study\n";' ++ cat SRP041471.dir + dir=7+ cat ../pre+ cat ../prep/samples.tsv.header /dev/fd/63 ++ fgrep ' SRP041471 ' ../prep/samples.tsv y_metadata_layout.sh: line 22: /samples.tsv.SRP041471: Permission denied + gzip + cut -f 1-3,42-150 71/SRP041471/samples.tsv.SRP041471../prep/study_metadata_layout.sh: line 34: /sra.sra.SRP041471.MD.gz: Permission denied cut: ] 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 date_processed' + dsource_path=data_sources/sra 019-10-01' + 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 71/SRP041471/samples.tsv.SRP041471 ++ 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";' ++ cut -f 1-3 dy\tHomo sapiens data_sources/sra data_sources/sra 2019-10-01\n";' + [[ -n ../prep/Human.SRA_curated_predict.meta.w_rids.rtypes.tsv ]] ; $f=$_; ($rid,$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.SRP041471.MD.gz: Permission denied tail: cannot open ‘/samples.tsv.SRP041471’ for reading: No such file or directory + [[ -n ../prep/Human.SRA_curated_predict.meta.w_rids.rtypes.tsv ]] SRA_curated_predict.meta.w_rids.rtypes.tsv ]] + gzip + cat /dev/fd/63 /dev/fd/62 ++ fgrep ' SRP041471 ' ../prep/Human.SRA_curated_predict.meta.w_rids++ fgrep ' SRP041471 ' ../prep/Human.SRA_curated_predict.meta.w_rids.rtypes.tsv ../prep/study_metadata_layout.sh: line 67: /sra.recount_pred.SRP041471.MD.gz: Permission denied + cat /dev/fd/63 /dev/fd/62 ++ head -1 ../prep/seqtk.w_study.tsv.cut ++ fgrep ' SRP041471 ' ../prep/seqtk.w_study.tsv.cut + rm /samples.tsv.SRP041471 rm: cannot remove + rm /samples.tsv.SRP041471 rm: such file or directory + rm SRP041471.dir