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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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pbfusion::bam_scanner unknown data type in input #655

Closed shizhuoxing closed 4 months ago

shizhuoxing commented 5 months ago

Dear developers,

I've been using pbfusion for fusion gene detection, and I encountered an issue with version v0.4.0. The error message is: [2024-02-18T09:44:19.827Z ERROR pbfusion::bam_scanner] Unknown data type in input ["s1.hifi.Transcript.fastq.bam"]

Here are the commands I used: pbmm2 align genome.fa s1.hifi.Transcript.fastq.gz s1.hifi.Transcript.fastq.bam --preset ISOSEQ --sort -j 40 -J 40 pbfusion discover --gtf refdata-gex-GRCh38-2020-A.gtf.bin --output-prefix s1.hifi --threads 40 -b s1.hifi.Transcript.fastq.bam

Thank you and look foward to your reply.

velociroger-pb commented 5 months ago

Can you post the output of samtools view -H s1.hifi.Transcript.fastq.bam please?

shizhuoxing commented 5 months ago

The simplifyed output of samtools view -H s1.hifi.Transcript.fastq.bam was list at below:

image image

velociroger-pb commented 5 months ago

Can you post a couple of reads for us to check?

shizhuoxing commented 4 months ago

Sure, i have upload a test file on here. test.sam.gz

velociroger-pb commented 4 months ago

To me it looks like the read type is incorrect and that your bam file is malformatted. You can read about our bam spec here