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xie186 / ViewBS

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
GNU General Public License v3.0
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cannot recognize ref and samples #4

Closed cherrypath closed 7 years ago

cherrypath commented 7 years ago

When I tried the first TOP command, it reported error as bellow:

Unknown option: reference Subcommand: MethCoverage Please provide --sample! Sample(s): Please provide --reference! Output directory is: /Users/Yirong/Documents/Software/ViewBS-master Default output prefix is used: MethCoverage

However, I did provided refenence and samples. Here is my cmd: ./ViewBS MethCoverage --reference /Users/Documents/RRBS/ViewBSinput/ucsc.hg38.fa --sample /Users/Documents/RRBS/ViewBSinput/VBS_inputWT.tab.gz,WT --sample /Users/Documents/RRBS/ViewBSinput/VBS_input14.tab.gz,s14 --outdir methCoverage --prefix LJ_proj_met

readbio commented 7 years ago

Could you provide me some more information about your experiences using ViewBS: 1) Which version of perl did you use? Also the version of packages you were using. You can use cpan -D Getopt::Long::Subcommand to get the version information of perl packages. 2) Did you have problem using other sub commands? 3) Can you give a test dataset that can repeat the error message? Thanks.

cherrypath commented 7 years ago

I used perl 5, version 18, subversion 2 (v5.18.2). And I had the same problem using other sub commands. When I run test dataset (download from https://zenodo.org/record/58470#.V_UR-E0rJhE) it also reported the same error.

2016-12-20 4:49 GMT+08:00 readbio notifications@github.com:

Could you provide me some more information about your experiences using ViewBS:

  1. Which version of perl did you use? 2 ) Did you have problem using other sub commands?
  2. Can you give a test dataset that can repeat the error message? Thanks.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/readbio/ViewBS/issues/4#issuecomment-268074307, or mute the thread https://github.com/notifications/unsubscribe-auth/AXctFh52rPrf6o2KB1K17YPZwUPfdoAzks5rJu3WgaJpZM4LQqvV .

-- Yirong Wang Ph.D candidate Laboratory of Population and Evolutionary Genomics Center of Life Sciences, Peking University Academy for Advanced Interdisciplinary Studies, Peking University Beijing, 100871 China

readbio commented 7 years ago

Could you send your code (ViewBS code, including the lib directory) to me? Thanks. Here is my email: read2bio@foxmail.com

xie186 commented 7 years ago

Do you still have the problem?

cherrypath commented 7 years ago

Sorry, I've got the results by using Perl and R already. Thanks for your help~

2016-12-24 11:29 GMT+08:00 Shaojun Xie notifications@github.com:

Do you still have the problem?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/readbio/ViewBS/issues/4#issuecomment-269066852, or mute the thread https://github.com/notifications/unsubscribe-auth/AXctFgIXcFZI_6W-G-er9umTrenUrRv2ks5rLJG1gaJpZM4LQqvV .

-- Yirong Wang Ph.D candidate Laboratory of Population and Evolutionary Genomics Center of Life Sciences, Peking University Academy for Advanced Interdisciplinary Studies, Peking University Beijing, 100871 China