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10XGenomics / bamtofastq

Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
MIT License
59 stars 6 forks source link

Is there a way to skip the error and continue converting? #100

Open wangyiqing50 opened 2 years ago

wangyiqing50 commented 2 years ago

Hi,

I am running it on a bam file but the error message told me it could be truncated. I am seeking a way how to skip these errors. Slight data loss is acceptable.

`[W::bam_hdr_read] EOF marker is absent. The input is probably truncated [E::bgzf_read_block] Invalid BGZF header at offset 295634318 [E::bgzf_read] Read block operation failed with error 6 after 0 of 4 bytes bamtofastq error: IO Error reading BAM file. Your BAM file may be corrupt

If this error is unexpected, contact support@10xgenomics.com for assistance. Please re-run with --traceback and include stack trace with an error report see below for more details:

IO Error reading BAM file. Your BAM file may be corrupt 0: anyhow::backtrace::capture::Backtrace::capture 1: bamtofastq::inner 2: bamtofastq::main 3: std::sys_common::backtrace::__rust_begin_short_backtrace 4: _main `

lisafournier commented 2 years ago

Hi, I am getting the same problem. Did you find a solution to resolve/skip this error ?