Open sarah872 opened 4 years ago
Hi, I am getting the following error when running dammit:
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* Input Transcriptome: /scratch/dammit/dammit_db/trinity.fasta.dammit/trinity.fasta Some tasks out of date! Out-of-date tasks: * BUSCO-nematoda * TransDecoder.LongOrfs * TransDecoder.Predict * annotate:fasta * cmscan:Rfam * gff3:OrthoDB * gff3:Pfam-A * gff3:Rfam * gff3:merge-all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.
cat ...
Hi, I am getting the following error when running
dammit
:when I run the last command
cat ...
outside of dammit, there's no error.