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bbuchfink
Issues with --query-coverage --subject--coverage and --id for v 2.0.13
Hello I am currently using v2.0.13 and found that I was getting some errors on only a couple of cases, but when I use older version I get the correct results.
Using v0.9:
diamond blastp --query GN002461.0_query_fasta.fa --db GN088529.0_protein.faa.dmnd --out test.tsv --threads 1 --outfmt 6 --max-target-seqs 1 --max-hsps 1 --more-sensitive -e 0.00001 --query-cover 30 --subject-cover 30 --id 30
Results:
GN002461.00_010654-T1 GN088529.0_008499-T1 84.3 337 53 0 163 499 1 337 5.4e-173 603.6
GN002461.00_010691-T1 GN088529.0_008722-T1 80.5 457 86 1 1 454 1 457 4.6e-221 763.1
GN002461.00_010782-T1 GN088529.0_008908-T1 79.4 2500 403 19 50 2512 413 2838 0.0e+00 3930.6
Using v2.0.9:
diamond blastp --query GN002461.0_query_fasta.fa --db GN088529.0_protein.faa.dmnd --out test.tsv --threads 1 --outfmt 6 --max-target-seqs 1 --max-hsps 1 --more-sensitive -e 0.00001 --query-cover 30 --subject-cover 30 --id 30
Results:
GN002461.00_010654-T1 GN088529.0_008499-T1 84.3 337 53 0 163 499 1 337 1.36e-208 602
GN002461.00_010691-T1 GN088529.0_008722-T1 80.5 457 86 1 1 454 1 457 1.13e-278 759
GN002461.00_010782-T1 GN088529.0_008908-T1 79.4 2503 404 19 47 2512 410 2838 0.0 3921
Using v2.0.13:
diamond blastp --query GN002461.0_query_fasta.fa --db GN088529.0_protein.faa.dmnd --out test.tsv --threads 1 --outfmt 6 --max-target-seqs 1 --max-hsps 1 --more-sensitive -e 0.00001 --query-cover 30 --subject-cover 30 --id 30
Results:
Computing alignments... Error: generate_output: target with no hsps.
Using v2.0.13 (setting --query-cover, --subject-cover, --id to 0):
diamond blastp --query GN002461.0_query_fasta.fa --db GN088529.0_protein.faa.dmnd --out test.tsv --threads 1 --outfmt 6 --max-target-seqs 1 --max-hsps 1 --more-sensitive -e 0.00001 --query-cover 0 --subject-cover 0 --id 0
Results:
GN002461.00_010654-T1 GN088529.0_008499-T1 84.3 337 53 0 163 499 1 337 6.17e-207 598
GN002461.00_010691-T1 GN088529.0_008722-T1 80.5 457 86 1 1 454 1 457 1.31e-277 757
GN002461.00_010745-T1 GN088529.0_008908-T1 38.2 348 152 7 1 287 1 346 7.44e-56 193
GN002461.00_010782-T1 GN088529.0_008908-T1 79.4 2503 404 19 47 2512 410 2838 0.0 3911
Using v2.0.13 (setting --query-cover, --subject-cover, --id to 1):
diamond blastp --query GN002461.0_query_fasta.fa --db GN088529.0_protein.faa.dmnd --out test.tsv --threads 1 --outfmt 6 --max-target-seqs 1 --max-hsps 1 --more-sensitive -e 0.00001 --query-cover 1 --subject-cover 1 --id 1
Results:
Computing alignments... Error: generate_output: target with no hsps.
I believe the errors are also occurring on v2.0.12. Unfortunately I cannot provide the actual sequences due to proprietary information.
