bs_seeker2-call_methylation.py error report

[Shicheng-Guo]

Hi,

I met such problems for bs_seeker2-call_methylation.py. I am appreciated to get some help. Thanks.

[shg047@tscc-login2 fastq]$ python /home/shg047/software/BSseeker2/bs_seeker2-call_methylation.py -x -r 5 --rm-CCGG -i T19.bam -o T19.mr --txt

 BS-Seeker2 v2.0.10 - Nov 5, 2015

[2016-11-10 22:22:03] sorting BS-Seeker alignments Traceback (most recent call last): File "/home/shg047/software/BSseeker2/bs_seeker2-call_methylation.py", line 106, in pysam.sort(options.infilename, sorted_input_filename) File "/home/shg047/anaconda2/lib/python2.7/site-packages/pysam/utils.py", line 75, in call stderr)) pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files\nUsage: samtools sort [options...] [in.bam]\nOptions:\n -l INT Set compression level, from 0 (uncompressed) to 9 (best)\n -m INT Set maximum memory per thread; suffix K/M/G recognized [768M]\n -n Sort by read name\n -o FILE Write final output to FILE rather than standard output\n -T PREFIX Write temporary files to PREFIX.nnnn.bam\n -@, --threads INT\n Set number of sorting and compression threads [1]\n --input-fmt-option OPT[=VAL]\n Specify a single input file format option in the form\n of OPTION or OPTION=VALUE\n -O, --output-fmt FORMAT[,OPT[=VAL]]...\n Specify output format (SAM, BAM, CRAM)\n --output-fmt-option OPT[=VAL]\n Specify a single output file format option in the form\n of OPTION or OPTION=VALUE\n --reference FILE\n Reference sequence FASTA FILE [null]\n'

Regards,

[guoweilong]

Hi Shicheng,

Thanks for writting to me the issue.

It seems to related with pysam. The samtools command parameters for sorting seems changed. And I might take some time to validate it on multiple versions of pysam before fix it.

Two ways you can try currently:

1. You can try to install a local version of python and pysam (v0.6+) would be help https://github.com/BSSeeker/BSseeker2#qa31
2. You can follow markmcdowall's suggestions and change the BS-Seeker2 code locally.

https://github.com/BSSeeker/BSseeker2/issues/9

Best, Weilong

[Shicheng-Guo]

Eventually, I made it. It seems BSSeeker2 dependent on the version strongly. The current verison could run:

BS-Seeker2 v2.0.9 - Dec 30, 2014 Python-2.7.4 pysam-0.6

Hope it is helpful for others.

[guoweilong]

Thanks Shicheng. Indeed it is. BS-Seeker2 was developed when pysam v0.6, while the new versions of pysam seems have changed a lot. Hopefully more people could involved in improving the version support.

Weilong

At 2016-11-15 10:24:41, "Shicheng Guo" notifications@github.com wrote:

Eventually, I made it. It seems BSSeeker2 dependent on the version strongly. The current verison could run:

BS-Seeker2 v2.0.9 - Dec 30, 2014 Python-2.7.4 pysam-0.6

Hope it is helpful for others.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[Shicheng-Guo]

I see. but I am not python user. I like bismark since I know how to change it because it is completed with Perl. However, there are too many great features of BSSeeker2, that's why I want to make a try, but actually, BSSeeker spend me lots of time to install, for example, python 2 vs python 3 and pysam versions and so on.

I am lucky. Now I can use it.

[guoweilong]

Thanks for your comments. I'll try to update it to be more convenient recently.

Weilong

At 2016-11-15 10:56:40, "Shicheng Guo" notifications@github.com wrote:

I see. but I am not python user. I like bismark since I know how to change it since it is completed with perl. but there are two many great features of BSSeeker2, that's why I want to make a try, but actually, BSSeeker spend me lots of time to install, for example, python 2 vs python 3 and pysam versions and so on.

I am lucky. Now I can use it.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[guoweilong]

Hi ShiCheng,

Thanks for your comments. And I have updated BS-Seeker2 to v2.1.0. The new version should work with pysam new versions.

Do let me know if you have any problem/comments/suggestion with BS-Seeker2.

Thanks and best, Weilong

[DarrellL]

Hi Weilong,

I'm seeing the same error mentioned by OP. I'm running BS-Seeker2 v2.1.0 & pysam v 0.9. Can you tell me which version(s) of pysam you validated the latest B-Seeker2 release with?

Thanks, Darrell

[guoweilong]

Hi Darrell,

Thanks for your feedback. It seems not fully commit the changes to the github. Currently, additional modificaitons are made here. You can try the new version v2.1.1.

Tip: Whenever update the BS_Seeker2 to newer version, just mv the bs_utils/reference_genome folder to your new BS-Seeker2 location, instead of re-building the new indexes.

Let me know if you have further question.

Thanks and best, Weilong

[DarrellL]

Thanks very much for the quick fix Weilong, it seems to be working fine now,

Cheers, Darrell

On 13/03/2017, at 4:27 PM, Weilong Guo notifications@github.com wrote:

Hi Darrell,

Thanks for your feedback. It seems not fully commit the changes to the github. Currently, additional modificaitons are made here. You can try the new version v2.1.1 https://github.com/BSSeeker/BSseeker2/releases/tag/v2.1.1.

Tip: Whenever update the BS_Seeker2 to newer version, just mv the bs_utils/reference_genome folder to your new BS-Seeker2 location, instead of re-building the new indexes.

Let me know if you have further question.

Thanks and best, Weilong

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BSSeeker/BSseeker2/issues/11#issuecomment-286007555, or mute the thread https://github.com/notifications/unsubscribe-auth/AICtZBWVqMnBbw_LrZan8diFHLKuNlNVks5rlLeRgaJpZM4Kvdku.