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xie186 / ViewBS

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
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Error in MethOneRegion #22

Closed avdanurag closed 5 years ago

avdanurag commented 5 years ago

Hello Dr. Shaojun, When I am trying run MethOneRegion, I am getting following error although gzipped, tabixed bedfile is present in the working directory. What could be the possible cause?

error: Tabix region lookup requires a gzipped, tabixed bedfile at /home/anurag/anaconda3/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi/Bio/DB/HTS/Tabix.pm line 40

xie186 commented 5 years ago

Could you please provide me some more information? Thanks.

  1. Did you successfully run the test data.
  2. Command line you were using.
avdanurag commented 5 years ago

Yes I could successfully run the test data and I used the following command.

perl ViewBS MethOneRegion --region NC_021160.1:26032601-26032700 --sample Viewbs/LIB19570_LBS-1_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.g,ICC5590 --sample Viewbs/LIB19572_LBS-4_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.g,ICC8155 --sample Viewbs/LIB19573_VBS-1_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,ICC4958 --sample Viewbs/LIB19574_VBS-3_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,ICC8261 --sample Viewbs/LIB19575_VBS-4_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,ICC17160 --prefix Dbxref=GeneID:101503890 --context CG

Subcommand: MethOneRegion Viewbs/LIB19570_LBS-1_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.g,ICC5590 Viewbs/LIB19572_LBS-4_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.g,ICC8155 Viewbs/LIB19573_VBS-1_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,ICC4958 Viewbs/LIB19574_VBS-3_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,ICC8261 Viewbs/LIB19575_VBS-4_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,ICC17160 NC_021160.1:26032601-26032700 Output directory is: /home/anurag/Downloads/ViewBS-ViewBS_v0.1.4 Output prefix: Dbxref=GeneID:101503890 Start calculate methylation information for target context CG Tabix region lookup requires a gzipped, tabixed bedfile at /home/anurag/anaconda3/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi/Bio/DB/HTS/Tabix.pm line 40.

On Sat, Sep 29, 2018 at 5:24 AM Shaojun Xie notifications@github.com wrote:

Could you please provide me some more information? Thanks.

  1. Did you successfully run the test data.
  2. Command line you were using.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xie186/ViewBS/issues/22#issuecomment-425640991, or mute the thread https://github.com/notifications/unsubscribe-auth/AfRjny-rJFlKbK_5ek4xR1g2aapTMOVEks5uf2ZjgaJpZM4XAV5S .

-- With Regards, Anurag Daware PhD Scholar National Institute of Plant Genome Research, New Delhi (India)-10067

avdanurag commented 5 years ago

Here I am attaching my bed file. I hope this is fine.

On Sun, Sep 30, 2018 at 7:03 PM Anurag Daware avd.anurag@gmail.com wrote:

Yes I could successfully run the test data and I used the following command.

perl ViewBS MethOneRegion --region NC_021160.1:26032601-26032700 --sample Viewbs/LIB19570_LBS-1_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.g,ICC5590 --sample Viewbs/LIB19572_LBS-4_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.g,ICC8155 --sample Viewbs/LIB19573_VBS-1_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,ICC4958 --sample Viewbs/LIB19574_VBS-3_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,ICC8261 --sample Viewbs/LIB19575_VBS-4_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,ICC17160 --prefix Dbxref=GeneID:101503890 --context CG

Subcommand: MethOneRegion Viewbs/LIB19570_LBS-1_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.g,ICC5590 Viewbs/LIB19572_LBS-4_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.g,ICC8155 Viewbs/LIB19573_VBS-1_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,ICC4958 Viewbs/LIB19574_VBS-3_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,ICC8261 Viewbs/LIB19575_VBS-4_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,ICC17160 NC_021160.1:26032601-26032700 Output directory is: /home/anurag/Downloads/ViewBS-ViewBS_v0.1.4 Output prefix: Dbxref=GeneID:101503890 Start calculate methylation information for target context CG Tabix region lookup requires a gzipped, tabixed bedfile at /home/anurag/anaconda3/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi/Bio/DB/HTS/Tabix.pm line 40.

On Sat, Sep 29, 2018 at 5:24 AM Shaojun Xie notifications@github.com wrote:

Could you please provide me some more information? Thanks.

  1. Did you successfully run the test data.
  2. Command line you were using.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xie186/ViewBS/issues/22#issuecomment-425640991, or mute the thread https://github.com/notifications/unsubscribe-auth/AfRjny-rJFlKbK_5ek4xR1g2aapTMOVEks5uf2ZjgaJpZM4XAV5S .

-- With Regards, Anurag Daware PhD Scholar National Institute of Plant Genome Research, New Delhi (India)-10067

-- With Regards, Anurag Daware PhD Scholar National Institute of Plant Genome Research, New Delhi (India)-10067

xie186 commented 5 years ago

Is it because you didn't give the correct file name? Viewbs/LIB19570_LBS-1_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.g, should be Viewbs/LIB19570_LBS-1_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,?

avdanurag commented 5 years ago

I did make a silly mistake, its working fine now. Thanks a lot for your help.

On Mon, Oct 1, 2018 at 7:14 AM Shaojun Xie notifications@github.com wrote:

Is it because you didn't give the correct file name?

Viewbs/LIB19570_LBS-1_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.g, should be Viewbs/LIB19570_LBS-1_R1_val_1_bismark_bt2_pe.deduplicated.CX_report.txt.CX_report.txt.gz,

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xie186/ViewBS/issues/22#issuecomment-425923368, or mute the thread https://github.com/notifications/unsubscribe-auth/AfRjn_wJ8tnlPhcY7gGEEengtztqajJ2ks5ugiMzgaJpZM4XAV5S .

-- With Regards, Anurag Daware PhD Scholar National Institute of Plant Genome Research, New Delhi (India)-10067