关于在运行ViewBS MethCoverage时候报错

[qliugithub]

我在testdata目录下运行manual中的命令如下： ../../ViewBS MethCoverage --reference TAIR10_chr_all.fasta --sample bis_WT.tab.gz,WT --sample bis_cmt23.tab.gz,cmt23 --sample bis_cmt2-3.tab.gz,cmt2-3 --sample bis_drm12cmt23.tab.gz,drm12cmt12 --sample bis_drm12cmt2.tab.gz,drm12cmt2 --outdir methCoverage --prefix cmt2_proj_allsam 但是程序报错了 Subcommand: MethCoverage Please provide --sample! Sample(s): Please provide --reference! ARRAY(0x9e4a70) ne BisNonConvRate 但是我使用sh test_ViewBS.sh 运行时候没有报错，请问一下改如何解决呢？困扰了一天了。 谢谢了！

[xie186]

Are you using the latest version (https://github.com/xie186/ViewBS/releases/tag/ViewBS_v0.1.3)? If not, please use the latest version. I tried your command line and didn't get the error message you got. If you are using the latest version, could you please give a screenshot of your command line?

[qliugithub]

Thanks ! I had solved . I was used ViewBS instead of ../../ViewBS, and then can run , It's just so magic. but I didn't find why use ../../ViewBS can't run. I find some mistake in running MethLevDist , It's should be ViewBS rather than ViewBS,pl. just a a slip of a pen. Finally I offered my appreciation to your answer and forgive my poor English.

[xie186]

Glad you already solved this problem. Please let us know if you have any problem in the future. Best, Shaojun

[ryys1122]

In some version of perl or Getopt::Long::Subcommand, the following code does't work correctly 'sample:s' => \@{$opts_subcmd{sample}}, the following one works well 'sample=s' => \@{$opts_subcmd{sample}},

[xie186]

@ryys1122 could you please let me know the version you tried? Thanks for reporting this.

[ryys1122]

Getopt::Long::Subcommand 0.102, Perl 5.22.1 Getopt::Long::Subcommand 0.102, Perl 5.26.1

[xie186]

Got it. Thanks. We'll test this shortly.

[AbRawoof]

Hello every one, u@u:~/Downloads/ViewBS-ViewBS_v0.1.3$perl ViewBS MethCoverage --reference GCF_0007108_genomic.fasta --sample S1_cov10x_CX_report.txt.gz,S1 --sample S2_cov10x_CX_report.txt.gz,S2 --sample S3_cov10x_CX_report.txt.gz,S3 --sample S4_cov10x_CX_report.txt.gz,S4 --outdir myCoverage

Error Message: Subcommand: MethCoverage Please provide --sample! Sample(s): Please provide --reference! ARRAY(0x559bf30de220) ne BisNonConvRate

############# My files are bismark methylation extraction output files and I have followed bgzip for zipping file and tabix for indexcing. Please let me where I am going wrong. Thanks

[xie186]

Could you please tell the which version you're using?

[AbRawoof]

I am using perl-5.24.1, Bio-DB-HTS-2.9 and Getopt-Long-Subcommand-0.102 and ViewBS-v0.1.3 version. I am puzzled about the message given as it is not taking input for samples as well as reference.

[AbRawoof]

Hello.. Please help me out. Where I am going wrong. I have done proper installation and have all packages as mentioned in your installation guide. Do I need to make some changes in any script.. Thanks,

[xie186]

​Sorry for the late response. I was out of town. I’ll help you out today.

---

From: AbRawoof notifications@github.com Sent: Monday, February 12, 2018 11:12 PM To: xie186/ViewBS Cc: Xie, Shaojun; State change Subject: Re: [xie186/ViewBS] 关于在运行ViewBS MethCoverage时候报错 (#13)

Hello.. cd Do I need to make some changes in any script.. Thanks,

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHubhttps://github.com/xie186/ViewBS/issues/13#issuecomment-365145584, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AT8Ot3rLZzNm2b2Hp0mgukjQikiojqdFks5tUQurgaJpZM4QKVxg.

[xie186]

Hi @AbRawoof, I didn't see anything wrong with the command line. Is it possible you can provide me the files you are using? I couldn't get the same error you got. Thanks.

[AbRawoof]

Hi @xie186 . I have tried in other system having same configuration but ubuntu version is different 17.10 instead of 17.02. The program is working fine in that system.

I think I might have missed some library. Will work on that.

Thanks.

[xie186]

I tested ViewBS in Ubuntu 16.04. It works fine,

Is it possible that I can get access to 17.02 of yours to see whether I can fix this if it's a bug? Thanks.

[AbRawoof]

Hello @xie186 .. Sorry for late response..I have installed kubuntu 17.10 and now the problem is sorted out. Thanks for your response.

Best, Abdul