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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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Problem to run test data #25

Closed davidries84 closed 5 years ago

davidries84 commented 5 years ago

Hi, I cloned https://gitlab.com/BS-seq/ViewBS_testdata im my ViewBS folder. But when running sh test_ViewBS.sh I get ...

Subcommand: BisNonConvRate Sample list: Please provide --sample!

Error: Please provide --chrom for the chromosome IDs that you want to use to estimate the non-conversion rate!

Maybe you could fix the script for your test data?

Best,

David

xie186 commented 5 years ago

Hi David,

Could you please share me with your configuration? E.g. Perl version, the command line of BisNonConvRate in test_ViewBS.sh. I'm fine running the command line.

Best, Shaojun

davidries84 commented 5 years ago

Hi Shaojun,

perl --version This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi

./memusg perl $Path2ViewBS/ViewBS BisNonConvRate --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,drm12cmt23 --sample bis_drm12cmt2.tab.gz,drm12cmt2 --outdir BisNonConvRate --prefix cmt2_proj_allsam --chr chrC --height 10 --width 14

If I run it like this from the command line, it runs:

perl ../../ViewBS BisNonConvRate --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,drm12cmt23 --sample bis_drm12cmt2.tab.gz,drm12cmt2 --outdir BisNonConvRate --prefix cmt2_proj_allsam --chr chrC --height 10 --width 14

Best, David

lileiting commented 5 years ago

Hi David,

I also encountered this problem. I found that ViewBS was not working with perl-v5.26.1 (v5.26.2 in your case), but working with perl-v5.16.3 and perl-v5.18.2. I didn't figure out why, but you may try perl-v5.16 or perl-v.18.

Best, Leiting

davidries84 commented 5 years ago

Hi Leiting,

thank you for the suggestion. Did you encounter any further problems using the wrong perl version?

Best,

David

xie186 commented 5 years ago

Hi @davidries84,

Thanks for your information. I'll enable ViewBS to be able install using Conda during the holiday. That way you don't need to worry about the configuration. I'll let you know when it's ready. Currently I think the best way is to use the version @lileiting mentioned.

Best, Shaojun

anupambh commented 5 years ago

Hi, I am trying to run the testdata and use the commands in your tutorial. But I got the following error:

Subcommand: MethCoverage Please provide --sample! Sample(s): Please provide --reference!

command:

/opt/ViewBS-0.1.6/ViewBS MethCoverage --reference TAIR10_chr_all.fasta --sample bis_WT.tab.gz,WT --sample bis_cmt23.tab.gz,cmt2-3 --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

I am having the following perl version installed:

perl --version

This is perl 5, version 24, subversion 1 (v5.24.1) built for x86_64-linux-thread-multi (with 79 registered patches, see perl -V for more detail)

Any suggestions would be very helpful for me.

Regards; Anupam

xie186 commented 5 years ago

Hi Anupam, Thanks for using ViewBS. Could you please ls the folder you ran the command line? Best, Shaojun

anupambh commented 5 years ago

Hi, Here is the content of the test folder.

bis_cmt2-3.tab bis_cmt23.tab.gz bis_cmt2-3.tab.gz.tbi bis_cmt23.tab.gz.tbi bis_drm12cmt23.tab.gz bis_drm12cmt23.tab.gz.tbi bis_drm12cmt2.tab.gz bis_drm12cmt2.tab.gz.tbi bis_WT.tab.gz bis_WT.tab.gz.tbi CHG_hypo_DMR_drm12cmt23_to_WT.txt memusg methCoverage sampl_info_tab.txt TAIR10_chr_all.fasta TAIR10_chr_all.fasta.fai TAIR10_GFF3_genes.bed TAIR10_GFF3_genes_chr1.bed TAIR10_GFF3_genes_prot.bed TAIR10_GFF3_genes.WT.rank1.tab TAIR10_GFF3_genes.WT.rank2.tab TAIR10_GFF3_genes.WT.rank3.tab TAIR10_GFF3_genes.WT.rank4.tab TAIR10_GFF3_genes.WT.rank5.tab TAIR10_Transposable_Elements.chr1.bed TAIR10_Transposable_Elements.sim_xie.bed test_ViewBS.sh

Regards; Anupam

xie186 commented 5 years ago

Thanks. I'll look into this and get back to you.

xie186 commented 5 years ago

Hi Anupam,

Currently I'm still working on this. I already repeated the error you encountered. It may spend some time for debugging. But you can use other versions of Perl.

The versions I have tested are: perl-v5.14.4 perl-v5.16.3 perl-v5.18.2 perl-v5.22.1

The versions don't work: v5.24.1 v5.26.*

I suggest you use conda to install ViewBS: https://github.com/xie186/ViewBS/wiki/Install-ViewBS-using-conda

Best, Shaojun

anupambh commented 5 years ago

Hi, I have installed ViewBS by using conda. Installation is successful and the testdata is working fine.

Thank you very much for the support.

Regards; Anupam

xie186 commented 5 years ago

As shown here:, the problem is because:

Getopt::Long::Subcommand relies on Getopt::Long, but it's incompatible with Getopt::Long 2.43 (inclusive) to 2.50 (exclusive). The simple solution is to upgrade to the latest version of Getopt::Long.

I tried upgrading Getopt::Long to version 2.50 by using cpanm Getopt::Long in perl-v5.24.1. As of 2/26/2019, version 2.5 was installed. Everything ran fine.