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GuoliangLi-HZAU / BatMeth2

BS-seq analysis pipeline
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samtools sort truncated file #19

Open paulstretenowich opened 4 years ago

paulstretenowich commented 4 years ago

Hi,

I'm running BatMeth2 doing: BatMeth2 align -1 R1.fastq.gz -2 R2.fastq.gz -g reference.fa -of BAM -o pwet -p 30 and I have the following issue: [E::sam_parse1] numeric value out of allowed range samtools sort: truncated file. Aborting

Thanks in advance for the help, Paul

ZhouQiangwei commented 3 years ago

I'm very sorry, this is a bug in the software. We fixed the bug in the updated software. Please download the latest version and try it?

paulstretenowich commented 3 years ago

Hi @ZhouQiangwei the latest release matches with the version I used. Do you want me to try a specific branch of your repo or will you do a new release?

Thanks, Paul

ZhouQiangwei commented 3 years ago

Hi Paul, are you downloading the release version or the latest version of git clone? Is it convenient for you to tell us what species your data are, or to provide data sources for me to test?

paulstretenowich commented 3 years ago

Hi @ZhouQiangwei, I used the release and not the clone. As far as I remember I used human genome as reference and it was WGBS reads. Let me try again one more time and I'll be back to you.

ZhouQiangwei commented 3 years ago

Hi Paul, please download the latest version of the software through git clone. The release version has not been updated for a long time. I'm very sorry. If there are still problems with the new version of the software, please feel free to contact us.

FAFUshiyan commented 3 years ago

[W::sam_read1] parse error at line 1 [bam_sort_core] truncated file. Aborting. I used the latest version of the software.