bbuchfink
segmentation fault
I'm getting segmentation faults thrown with one transcriptome, tried running both blastx and blastp and both fail. See here for the files: https://drive.google.com/file/d/1v2f7wH-6G4MvFERaaZ96aDeFJjTfRvqQ/view?usp=sharing https://drive.google.com/file/d/1pGxMq9GdbskZvgicWR79EmSCmwKOM7WA/view?usp=sharing
Is there a way I can fix this? Thanks!
Please provide the command line you used to run diamond and your version.
The command was:
diamond blastp --query /path/ncor_cdhit.fasta.transdecoder_dir/longest_orfs.pep \
--db /data2/ref_seq_June2024/refseq_vertebrate_other.protein.dmnd --max-target-seqs 1 \
--outfmt 6 --out ncor_cdhit_td_blast
diamond version 2.1.9
let me know if you can reproduce the error or you need more information. Thanks for your help!
These are not the files you provided. I ran diamond blastx of your ncor_cdhit.fasta against your ncor_cdhit.fasta.transdecoder.pep and it completed correctly.
Good point. When I go back to recreate the error, it occurred only when I was running diamond through EnTAP. Running diamond alone on the files completes correctly. Seems to be an error with EnTAP so I will post the issue there. Sorry for posting it in error here, I appreciate your follow up and help.
Hmm ok doing some more testing I was able to reproduce the error outside of EnTAP. The command is:
diamond blastx -p 8 -o /path/similarity_search/DIAMOND/blastx_ncor_cdhit_final_refseq_vertebrate_other.out --very-sensitive --max-target-seqs 3 --evalue 0.000010 -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp stitle --subject-cover 50.000000 --query-cover 50.000000 -q /path/transcriptomes/ncor_cdhit.fasta -d /data2/ref_seq_June2024/refseq_vertebrate_other.protein.dmnd
If you run these parameters with the ncor_cdhit.fasta file do you also get an error? It seems to occur with blastx and blastp; diamond runs just fine with this database with other queries.
I can reproduce this, it will be fixed in the next release. You can work around by not using a mutual coverage cutoff.
Great, thanks so much! Just for my reference, what's the argument for turning off the mutual coverage cutoff?
Use either --query-cover or --subject-cover, but not both. You can just filter the hits from the output file instead.