dib-lab / dammit

just annotate it, dammit!
http://dib-lab.github.io/dammit/
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database install fails with n_threads #140

Open bluegenes opened 5 years ago

bluegenes commented 5 years ago

see dib-lab/eelpond/issues/17

dammit databases --install --database-dir /home/titus/eelpond/databases --busco-group metazoa --n_threads 4

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

works fine as: dammit databases --install --database-dir /home/titus/eelpond/databases --busco-group metazoa

camillescott commented 5 years ago

What an odd failure mode... I'll look into it.