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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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pbmm2 single read align error #573

Closed yueqitaoo closed 1 year ago

yueqitaoo commented 1 year ago

Hi,

my script: pbmm2 align 4063682.fa 4063682.bam 4063682.aligned.bam log file: ERROR version: 1.10.0

Since I would detect base modification of one unmapped HiFi read, the input I used is the bam file of the read and the fasta file of the read itself. The log file didn't have detailed error description. I'm wondering if pbmm2 not support self-align or what I should modify for my script?

Thanks!

armintoepfer commented 1 year ago

Could you provide said files? There are instructions in the readme, where to upload if it's sensitive data.

yueqitaoo @.***> schrieb am Mi., 15. März 2023, 20:12:

Hi,

my script: pbmm2 align 4063682.fa 4063682.bam 4063682.aligned.bam log file: ERROR version: 1.10.0

Since I would detect base modification of one unmapped HiFi read, the input I used is the bam file of the read and the fasta file of the read itself. The log file didn't have detailed error description. I'm wondering if pbmm2 not support self-align or what I should modify for my script?

Thanks!

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armintoepfer commented 1 year ago

Closing due to lack of activity.