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EOF markers absent #34

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pdimens opened this issue Mar 27, 2021 · 0 comments
Open

EOF markers absent #34

pdimens opened this issue Mar 27, 2021 · 0 comments

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@pdimens
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pdimens commented Mar 27, 2021

Hello, I'm trying to use gencore as described with the simple examples in the README, and some of the resulting files get the error

[W::bam_hdr_read] EOF marker is absent. The input is probably truncated

when trying to run samtools sort on them.

The process to create the input alignment files for gencore has been:

  1. fastp
  2. bwa mem
  3. samtools sort
  4. samtools index

Some of the files do have a UMI read mismatch in the gencore output. What could be causing that, and do you think that it related to the issue?
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