Closed cyriltata closed 2 years ago
Sounds like an issue with the input subreads bam file. See https://github.com/PacificBiosciences/pbbioconda/issues/432#issuecomment-913427865.
@jemunro I have bam files that have not been demultiplexed. What can I do to generate bam reads with pw and ip tags?
The pipeline is designed for Sequel subreads output - can you run:
samtools view <input.bam> | cut -f1,12- | head -1
and share the ouput to confirm the format of the pacbio reads?
Are able to get raw subreads output file and try that? (i.e. the file output from the sequel run).
Running samtools gives this output
/bam > samtools view demultiplex.M13_bc1001_F--M13_bc1049_R.bam | cut -f1,12- | head -1
m64187e_220214_111831/461574/ccs bx:B:i,37,36 ec:f:55 np:i:55 rq:f:1 sn:B:f,9.69447,14.7193,3.3817,6.14301 we:i:9056538 ws:i:339056 zm:i:461574 qs:i:37 qe:i:114 bc:B:S,0,32 bq:i:93 cx:i:12 bl:Z:GGTAGACACGTGTGCTCTCTCCGGAAACAGCTATGAC bt:Z:ACTGGCCGTCGTTTTACCGCACTCTGATATGTGCTA ql:Z:~~~~~~~~~~~~~~~~~~~~~~U~~~~~~~~~~~~~~ qt:Z:~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ RG:Z:34e88679/0--32
Hi Cyril,
Your input file contains CCS reads not subreads, which unfortunately is not a compatible with the pipeline. You will need to obtain the original subreads BAM file in order to use the pipeline.
After successfully running with the test configuration, I now tried running pre-processing with my own config and bam files and I get this fatal error
any ideas why this is?