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just annotate it, dammit!
http://dib-lab.github.io/dammit/
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TaskError - taskid:hmmscan:longest_orfs.pep.x.Pfam-A.hmm #194

Open sarah872 opened 4 years ago

sarah872 commented 4 years ago

Hi, I am getting the following error when running dammit:

dammit annotate ../trinity.fasta --busco-group nematoda --n_threads 4 --database-dir .
# dammit
## a tool for easy de novo transcriptome annotation

by Camille Scott

**v1.2**, 2018

## submodule: annotate
### Database Check
#### Info
* Database Directory: .
* Doit Database: ./databases.doit.db

*All database tasks up-to-date.*

### Annotation
#### Info
* Doit Database: /scratch/dammit/dammit_db/trinity.fasta.dammit/annotate.doit.db
* Input Transcriptome: /scratch/dammit/dammit_db/trinity.fasta.dammit/trinity.fasta

Some tasks out of date!

Out-of-date tasks:
* BUSCO-nematoda
* TransDecoder.LongOrfs
* TransDecoder.Predict
* annotate:fasta
* cmscan:Rfam
* gff3:OrthoDB
* gff3:Pfam-A
* gff3:Rfam
* gff3:merge-all
* gff3:sprot
* hmmscan:Pfam-A
* hmmscan:Pfam-A:remap
* lastal:OrthoDB
* lastal:best-hits:OrthoDB
* lastal:best-hits:sprot
* lastal:sprot
* rename-transcriptome
* transcriptome-stats

#### Run Tasks
- [ ] trinity.fasta:
    * Python: function get_rename_transcriptome_task.fix
- [ ] transcriptome_stats:trinity.fasta:
    * Python: function get_transcriptome_stats_task.cmd
- [ ] busco:trinity.fasta-nematoda_odb9:
    * Cmd: `python3 /apps/busco/3.0.2/scripts/run_BUSCO.py -i /scratch/dammit/dammit_db/trinity.fasta.dammit/trinity.fasta -f -o trinity.fasta.nematoda.busco.results -l ./busco2db/nematoda_odb9 -m tran -c 4`
- [ ] TransDecoder.LongOrfs:trinity.fasta:
    * Cmd: `/apps/transdecoder/5.5.0/TransDecoder.LongOrfs -t /scratch/dammit/dammit_db/trinity.fasta.dammit/trinity.fasta -m 80`
- [ ] hmmscan:longest_orfs.pep.x.Pfam-A.hmm:
    * Cmd: `cat /scratch/dammit/dammit_db/trinity.fasta.dammit/trinity.fasta.transdecoder_dir/longest_orfs.pep | /usr/bin/parallel --block `expr $(wc -c /scratch/dammit/dammit_db/trinity.fasta.dammit/trinity.fasta.transdecoder_dir/longest_orfs.pep | awk '{print $1}') / 4` --round-robin --pipe --recstart '>' --gnu -j 4 /apps/hmmer/3.1b2/bin/hmmscan --cpu 1 --domtblout /dev/stdout -E 1e-05 -o /scratch/dammit/dammit_db/trinity.fasta.dammit/trinity.fasta.transdecoder_dir/longest_orfs.pep.x.pfam.tbl.hmmscan.out ./Pfam-A.hmm /dev/stdin > /scratch/dammit/dammit_db/trinity.fasta.dammit/trinity.fasta.transdecoder_dir/longest_orfs.pep.x.pfam.tbl`
########################################
TaskError - taskid:hmmscan:longest_orfs.pep.x.Pfam-A.hmm
Command error: 'cat /scratch/dammit/dammit_db/trinity.fasta.dammit/trinity.fasta.transdecoder_dir/longest_orfs.pep | /usr/bin/parallel --block `expr $(wc -c /scratch/dammit/dammit_db/trinity.fasta.dammit/trinity.fasta.transdecoder_dir/longest_orfs.pep | awk '{print $1}') / 4` --round-robin --pipe --recstart '>' --gnu -j 4 /apps/hmmer/3.1b2/bin/hmmscan --cpu 1 --domtblout /dev/stdout -E 1e-05 -o /scratch/dammit/dammit_db/trinity.fasta.dammit/trinity.fasta.transdecoder_dir/longest_orfs.pep.x.pfam.tbl.hmmscan.out ./Pfam-A.hmm /dev/stdin > /scratch/dammit/dammit_db/trinity.fasta.dammit/trinity.fasta.transdecoder_dir/longest_orfs.pep.x.pfam.tbl' returned 141

when I run the last command cat ... outside of dammit, there's no error.