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epigen-UCSD / epigen_ucsd_django

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[10xATAC] not working #298

Closed biomystery closed 5 years ago

biomystery commented 5 years ago

http://epigenomics.sdsc.edu:8000/setqc/610/ clicking not generate qsub job wrong 10xprocessed in '.Set_580.txt' empty .Set_580_samplesheet.tsv

cat /projects/ps-epigen/outputs/setQCs/.Set_580.txt
Library ID      Genome  Library Name    Processed Or Not        Read Type       Sample Name     Species Experiment Type Machine Set Name        10xProcessed
MM_166  hg38    WT-D32  Yes     PE      WT-D32  human   10xATAC NextSeq550 Mid  beta cell aggregates test       Yes
MM_167  hg38    1B-D32  Yes     PE      1B-D32  human   10xATAC NextSeq550 Mid  beta cell aggregates test       Yes(scanpy) [zhc268@tscc-login2 RMM_317]$ cat /projects/ps-epigen/outputs/setQCs/.Set_580_samplesheet.tsv
(scanpy) [zhc268@tscc-login2 RMM_317]$
brandonGonzalez01 commented 5 years ago

https://github.com/epigen-UCSD/epigen_ucsd_django/commit/33681b7744ec5cbc0b378ee7e6ec4484987cc8f8

biomystery commented 5 years ago

Problem is still there: clicking not generate qsub job now submitedt the normal job but no 10x job wrong 10xprocessed in '.Set_580.txt' (shown TenX processed but not) empty .Set_580_samplesheet.tsv

brandonGonzalez01 commented 5 years ago

runsetqc.sh had a bad file path for when checking if the tenx .tsv file exists, should now submit job. https://github.com/epigen-UCSD/epigen_ucsd_django/commit/cd99d68c1815081a991c278da98ee5f3b3538a09

biomystery commented 5 years ago

https://github.com/epigen-UCSD/epigen_ucsd_django/commit/2ebd12e57a7134151bca02f2e8d83fd6ae350836