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dib-lab / elvers

(formerly eelpond) an automated RNA-Seq workflow system
https://dib-lab.github.io/elvers/
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submodule 'databases' fails when `-t 6` specified #17

Closed ctb closed 5 years ago

ctb commented 5 years ago

see error output below.

without -t it works fine.

to rerun it, I just remove the 'databases' directory under eelpond/ and re-run eelpond.

Installing...
#### Run Tasks
- [ ] download:Pfam-A.hmm.gz:
    * Cmd: `curl -o Pfam-A.hmm.gz ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam28.0/Pfam-A.hmm.gz`
    * Python: function check_hash
- [ ] hmmpress:Pfam-A.hmm:
    * Cmd: `/home/titus/eelpond/.snakemake/conda/8b49a15e/bin/hmmpress /home/titus/eelpond/databases/Pfam-A.hmm`
TaskFailed - taskid:hmmpress:Pfam-A.hmm
Command failed: '/home/titus/eelpond/.snakemake/conda/8b49a15e/bin/hmmpress /home/titus/eelpond/databases/Pfam-A.hmm' returned 1

- [ ] download:Rfam.cm.gz:
    * Cmd: `curl -o Rfam.cm.gz ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.1/Rfam.cm.gz`
    * Python: function check_hash
- [ ] download:aa_seq_euk.fasta.gz:
    * Cmd: `curl -o aa_seq_euk.fasta.gz ftp://cegg.unige.ch/OrthoDB8/Eukaryotes/FASTA/aa_seq_euk.fasta.gz`
    * Python: function check_hash
- [ ] cmpress:Rfam.cm:
    * Cmd: `/home/titus/eelpond/.snakemake/conda/8b49a15e/bin/cmpress /home/titus/eelpond/databases/Rfam.cm`
- [ ] lastdb:aa_seq_euk.fasta:
    * Cmd: `/home/titus/eelpond/.snakemake/conda/8b49a15e/bin/lastdb -p -w3 /home/titus/eelpond/databases/aa_seq_euk.fasta /home/titus/eelpond/databases/aa_seq_euk.fasta`
TaskFailed - taskid:cmpress:Rfam.cm
Command failed: '/home/titus/eelpond/.snakemake/conda/8b49a15e/bin/cmpress /home/titus/eelpond/databases/Rfam.cm' returned 1

TaskFailed - taskid:lastdb:aa_seq_euk.fasta
Command failed: '/home/titus/eelpond/.snakemake/conda/8b49a15e/bin/lastdb -p -w3 /home/titus/eelpond/databases/aa_seq_euk.fasta /home/titus/eelpond/databases/aa_seq_euk.fasta' returned 1
ctb commented 5 years ago

I think this was fixed - but when?

bluegenes commented 5 years ago

shoot, should have closed this then - not sure which PR it was, bad labeling on my part. I solved it by removing threads from the databases command - haven't tracked down the underlying issue in dammit yet.

bluegenes commented 5 years ago

https://github.com/dib-lab/eelpond/commit/d173fb3a9ac15597a1fc59851515d4baa44d1622

ctb commented 5 years ago

(has issue been filed in dammit? issues link nicely in github :)

bluegenes commented 5 years ago

now filed!