ignore artic-medaka fails with exit status 20#288
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- when no reads map to the reference, ARTIC medaka fails with a segfault while reading an empty VCF file (see vcfcheck.log in workdir) - I would have liked to catch such samples before the ARTIC step, however Kraken2 classifies some reads as SC2, however no reads map in the end
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can you provide me with the sequences to reproduce this error? core dumped usually is a hardware issue thats why iam a bit curious |
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I would have liked to catch such samples before the ARTIC step, however Kraken2 classifies some reads as SC2, which do not map in the end
Let me know it it makes sense or you have a good idea for a solution!