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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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collapse error - im tag missing #604

Closed Ollipolli1909 closed 1 year ago

Ollipolli1909 commented 1 year ago

Hi, issues was already reported before - suggested solution was update to Isoseq 3.8 - I am running 4.0.0 but still get this error:

|> 20230823 05:56:18.093 -|- WARN -|- BamRecordIsGood -|- 0x7f42fa455d40|| -|- Read transcript/563 does not have tag im or is. Reads without im or is will be assumed to be a single molecule.

  1. ran cluster on service provider supplied hifi bam
  2. mapped to genome using minimap2
  3. ran cluster, getting above error message
armintoepfer commented 1 year ago

You need to use pbmm2 to align reads. We do not recommend pure minimap2, as it won't forward custom BAM tag.