I have an issue of having no output after seemingly successful run of diamond blastp. Basically, i have a trinity file to be blasted and look for protein coding genes and their corresponding gene name, species of the organism that protein is derived from after performing transdecoder. The command is nohup diamond blastp --db /home/terance/diamond_DB/nr.dmnd --threads 30 --max-target-seqs 1 --mid-sensitive --evalue 1e-4 --outfmt 6 qseqid sseqid staxids sscinames pident length mismatch gapopen qstart qend sstart send evalue bitscore ppos qcovhsp --query scy_all_merged_trinity.Trinity.fasta.transdecoder.pep --out scy_merged_trinity_transdecoder_default_ORF_diamond_ncbi_nr_blastp.pep.outfmt6.merged &
Hi there,
I have an issue of having no output after seemingly successful run of diamond blastp. Basically, i have a trinity file to be blasted and look for protein coding genes and their corresponding gene name, species of the organism that protein is derived from after performing transdecoder. The command is nohup diamond blastp --db /home/terance/diamond_DB/nr.dmnd --threads 30 --max-target-seqs 1 --mid-sensitive --evalue 1e-4 --outfmt 6 qseqid sseqid staxids sscinames pident length mismatch gapopen qstart qend sstart send evalue bitscore ppos qcovhsp --query scy_all_merged_trinity.Trinity.fasta.transdecoder.pep --out scy_merged_trinity_transdecoder_default_ORF_diamond_ncbi_nr_blastp.pep.outfmt6.merged &
and the log file says Processing query block 1, reference block 118/118, shape 7/8. Building reference seed array... [0.292s] Building query seed array... [0.089s] Computing hash join... [0.075s] Searching alignments... [0.38s] Deallocating memory... [0s] Processing query block 1, reference block 118/118, shape 8/8. Building reference seed array... [0.295s] Building query seed array... [0.092s] Computing hash join... [0.075s] Searching alignments... [0.379s] Deallocating memory... [0s] Deallocating buffers... [0.048s] Clearing query masking... [0.006s] Opening temporary output file... [0s] Computing alignments... Loading trace points... [0.18s] Sorting trace points... [0.033s] Computing alignments... [7.224s] Deallocating buffers... [0.01s] Loading trace points... [0s] [7.503s] Deallocating reference... [0.019s] Loading reference sequences... [0.045s] Deallocating buffers... [0s] Joining output blocks... Loading dictionary... [1.165s] Joining output blocks... [38.159s] [39.325s] Deallocating queries... [0.165s] Loading query sequences... [0.011s] Closing the input file... [0s] Closing the output file... [0.005s] Closing the database... [0.409s] Cleaning up... [0s] Total time = 14536.2s Reported 61539 pairwise alignments, 61539 HSPs. 61539 queries aligned.
it seems it runs fine, but the output file is just empty.
I am looking forward to hearing from you soon, thanks a lot!
Best regards, Terance