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smithlabcode / methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.
http://smithlabresearch.org/methpipe
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to-mr cannot transform successfully instead of generating a null .mr file #173

Closed xxzzwan closed 3 years ago

xxzzwan commented 3 years ago

Hi, I met a problem with to-mr transforming bam file to .mr file on centos server. I've set up all the environment the methpipe needs and installed methpipe successfully on the server. However when I used "to-mr -o /path/name.mr -m bismark /path/mybam.bam" command, it only run 3 minutes and wrote a null .mr file as output. -rw-rw-r--. 1 zx zx 0 3月 4 23:27 lz1895n.mr My bam file path was correct and methpipe was also in my path. Insterestingly, when I used the same command and same bam file on my mac, it went well and generated a normal output. So why it cannot work on linux system or just centos? Hope somebody could help! Thanks a lot.

xxzzwan commented 3 years ago

Also, the g++ version on my centos server is 5.3.0. On my macos system, the g++ version shows as follows. 

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.0 (clang-1100.0.33.17)
Target: x86_64-apple-darwin19.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
weishwu commented 3 years ago

Did you figure it out? I'm having the same problem. There is no error message but the output *.mr file is empty.

xxzzwan commented 3 years ago

With version 4.1.1, no. I've downloaded the pre-release version 4.1.2 and used format_reads instead and it worked. Guess it's the bug inside the pipeline and they fixed. Hope it could help!

guilhermesena1 commented 3 years ago

Thank you for reporting this. We are on the process of merging version 4.1.2 alpha to a full release in which the mr file format will no longer be necessary. I will close this issue since to-mr will no longer exist but we'll be happy to assist if other problems may arise with SAM outputs in the next releases.