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databio / pepatac

A modular, containerized pipeline for ATAC-seq data processing
http://pepatac.databio.org
BSD 2-Clause "Simplified" License
54 stars 14 forks source link

Test run fails with this error: skewer (0.2.2): Can not read adapter sequences from FASTA file "tools/NexteraPE-PE.fa" #221

Closed ybukhman closed 2 years ago

ybukhman commented 2 years ago

PEPATAC_log.txt

ybukhman commented 2 years ago

tools/NexteraPE-PE.fa is present and I can access it when I am not in a pepatac crate. Once I activate the crate, some commands still work on this file while others do not. For example, I can list it but I can't cat it:

bash-4.2$ pwd
/mnt/isi5home/ybukhman/Software/PEPATAC/pepatac
bash-4.2$ 
bash-4.2$ cat tools/NexteraPE-PE.fa
>PrefixNX/1
AGATGTGTATAAGAGACAG
>PrefixNX/2
AGATGTGTATAAGAGACAG
>Trans1
TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
>Trans1_rc
CTGTCTCTTATACACATCTGACGCTGCCGACGA
>Trans2
GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
>Trans2_rc
CTGTCTCTTATACACATCTCCGAGCCCACGAGACbash-4.2$ 
bash-4.2$ 
bash-4.2$ 
bash-4.2$ bulker activate databio/pepatac:1.0.9
Activating bulker crate: databio/pepatac:1.0.9
databio/pepatac|/mnt/isi5home/ybukhman/Software/PEPATAC/pepatac$ 
databio/pepatac|/mnt/isi5home/ybukhman/Software/PEPATAC/pepatac$ ls -l tools/NexteraPE-PE.fa
-rw-rw-r-- 1 ybukhman domain users 239 Aug  1 16:14 tools/NexteraPE-PE.fa
databio/pepatac|/mnt/isi5home/ybukhman/Software/PEPATAC/pepatac$ 
databio/pepatac|/mnt/isi5home/ybukhman/Software/PEPATAC/pepatac$ cat tools/NexteraPE-PE.fa
cat: tools/NexteraPE-PE.fa: No such file or directory
ybukhman commented 2 years ago

Sorry, this was a problem with our file server.