Comments (4)
apetkau
commented on August 11, 2024
Thanks so much for reporting @bgruening . Your assessment makes sense. A better error message would be useful here 😄
I'll see if I can reproduce it.
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bgruening
commented on August 11, 2024
Thanks @apetkau!
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emarinier
commented on August 11, 2024
I can't seem to recreate this error in the newest version (38f24ad). Let me know if you want to me to try with the same data that gave you the error.
Example with BLAST Results:
rm -rf out-blast out-sum
staramr search --output-hits-dir out-blast --output-summary out-sum staramr/tests/integration/data/16S_gyrA_beta-lactam.fsa
Output Summary (out-sum):
Isolate ID Quality Module Genotype Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback
16S_gyrA_beta-lactam Failed blaIMP-42 ampicillin, amoxicillin/clavulanic acid, cefoxitin, ceftriaxone, meropenem None - - 5220 5220 1 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
BLAST Output (out-blast/resfinder_16S_gyrA_beta-lactam.fsa):
>blaIMP-42_1_AB753456 isolate: 16S_gyrA_beta-lactam, contig: 16S_rrsD, contig_start: 4381, contig_end: 5121, database_gene_start: 1, database_gene_end: 741, hsp/length: 741/741, pid: 99.73%, plength: 100.00%
ATGAGCAAGTTATCTGCATTCTTTATATTTTTGTTTTGCAGCATTGATACCGCAGCAGAG
TCTTTGCCAGATTTAAAAATTGAAAAGCTTGATGAAGGCGTTTATGTTCATACTTCGTTT
GAAGAAGTTAACAGGTGGGGCGTTGTTCCTAAACATGGTTTGGTGGTTCTTGTAAATGCT
GAGGCTTACCTAATTGACACTCCATTTACGGCTAAAGATACTGAAAAGTTAGTCACTTGG
TTTGTGGAGCGTGGCTATAAAATAAAAGGCAGCATTTCCTCTCATTTTCATAGCGACAGC
ACGGGCGGAATAGAGTGGCTTAATTCTCGATCTATCCCCACGTATGCATCTGAATTAACA
AATGAACTGCTTAAAAAAGACGGTAAGGTTCAAGCCACAAATTCATTTAGCGGAGTTAAC
TATTGGCTAGTTAAAAATAAAATTGAAGTTTTTTATCCAGGCCCGGGACACACTCCAGAT
AACGTAGTGGTTTGGTTGCCTGAAAGGAAAATATTATTCGGTGGTTGTTTTATTAAACCG
TACGGTTTAGGCAATTTGGGTGACGCAAATATAGAAGCTTGGCCAAAGTCCGCCAAATTA
TTAAAGTCCAAATATGGTAAGGCAAAACTGGTTGTTCCAAGTCACAGTGAAGTTGGAGAC
GCATCACTCTTGAAACTTACATTAGAGCAGGCGGTTAAAGGGTTAAACGAAAGTAAAAAA
CCATCAAAACCAAGCAACTAA
Example with NO BLAST Results:
too-short.fsa:
>SHORT
A
rm -rf out-blast out-sum
staramr search --output-hits-dir out-blast --output-summary out-sum too-short.fsa
Output Summary (out-sum):
Isolate ID Quality Module Genotype Predicted Phenotype Plasmid Scheme Sequence Type Genome Length N50 value Number of Contigs Greater Than Or Equal To 300 bp Quality Module Feedback
too-short Failed None Sensitive None - - 1 1 0 Genome length is not within the acceptable length range [4000000,6000000] ; N50 value is not greater than the specified minimum value [10000]
BLAST Output (out-blast/):
ls -l out-blast/
total 0
And there was no error message.
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apetkau
commented on August 11, 2024
Fixed in #160
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Related Issues (20)
- cant run staramr HOT 3
- an unexpected keyword argument "inplace" and can't out the "results.xlxs" HOT 3
- Update Plasmidfinder DB HOT 1
- Update StarAMR documentation HOT 1
- Add PointFinder "Required_mut" column to pointfinder.tsv results HOT 1
- Add option to specify database path HOT 4
- different percent identity/alignment length for identical sequences on opposite strands HOT 5
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- Update MLST references in README
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- CGE phenotype not populated for E. faecium pbp5 when all essential mutations are present HOT 1
- Add to GRDI-AMR.com HOT 2
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