gdtool error

[roshanbernard]

Hi,

I am not able to run the gdtools. I got the below error msg. Any solutions?...

thanks

Rosh

$ gdtools COMPARE -o compare.html -r GCF_000240185.1_ASM24018v2_genomic.gbff Ctrl.gd Sample.gd

breseq 0.30.2 http://barricklab.org/breseq

Active Developers: Barrick JE, Deatherage DE Contact: jeffrey.e.barrick@gmail.com

breseq is free software; you can redistribute it and/or modify it under the terms the GNU General Public License as published by the Free Software Foundation; either version 2, or (at your option) any later version.

Copyright (c) 2008-2010 Michigan State University Copyright (c) 2011-2016 The University of Texas at Austin

If you use breseq in your research, please cite:

Deatherage, D.E., Barrick, J.E. (2014) Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151: 165–188.

If you use structural variation (junction) predictions, please cite

Barrick, J.E., Colburn, G., Deatherage D.E., Traverse, C.C., Strand, M.D., Borges, J.J., Knoester, D.B., Reba, A., Meyer, A.G. (2014) Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics 15:1039.

** Begin ANNOTATE/COMPARE

Reading input reference sequence files
    GCF_000240185.1_ASM24018v2_genomic.gbff

Reading input GD file: Ctrl.gd

Error(s) in GenomeDiff format. FILE: Ctrl.gd <<< ERROR: Expected positive integral value for field 5: [position] instead of [-32177]. LINE: 15 DEL3208NC_016839-32177105974 ERROR: Expected positive integral value for field 5: [position] instead of [-4087851]. LINE: 19 DEL7211NC_016845-40878515333942

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> FATAL ERROR <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Parse errors in loading GenomeDiff File. Not safe to continue FILE: genome_diff.cpp LINE: 1851 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!> STACK TRACE <!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Backtrace with 8 stack frames. gdtools() [0x457bfe] gdtools() [0x4b86a8] gdtools() [0x4b8edf] gdtools() [0x4439a1] gdtools() [0x445f8c] gdtools() [0x408994] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x7f7d2a775830] gdtools() [0x4161d9] !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!**

[jeffreybarrick]

Hi, thanks for the bug report,

This command is failing because one of the lines in your input GenomeDiff file has a negative position in the genome which shouldn't be allowed. Was that GenomeDiff file generated by a breseq run or manually edited?

If it's from breseq I will probably need to look at your reference file or know how it was downloaded/generated to figure out what is going on. My first thought is that something is off with some of the features there. You can email me at the address in the breseq header if you want to followup by sending a file.

Thanks!

[rohanmaddamsetti]

Hi Jeff,

I'm now getting a similar error in one of my breseq runs.

breseq now erroneously calls the entire F plasmid as a deletion, and assigns a negative start position to the deletion (something like –50000). I've run these data before without problems, in the past breseq has correctly called the presence of the F plasmid in this Hfr K-12 strain.

Can you take a look when you get the chance? I've uploaded the read data to the same Box folder as before.

Thanks for your help! Rohan

[jeffreybarrick]

Are you using the most up-to-date code? I fixed this particular issue.

[rohanmaddamsetti]

I got this message running breseq/0.30.2 with the coverage_distribution.R bug fix on our computing cluster.

I see that this fix is described in the ChangeLog, but that 0.30.3 is not yet listed in the Releases on github.

Should I wait for 0.30.3 to go live or should I ask IT to install breseq on the cluster from the master branch?

On Tue, Aug 15, 2017 at 9:54 PM, Jeffrey Barrick notifications@github.com wrote:

Are you using the most up-to-date code? I fixed this particular issue.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/barricklab/breseq/issues/129#issuecomment-322641029, or mute the thread https://github.com/notifications/unsubscribe-auth/AGGvLMpUol73RJ7H1wjpxRmCjdFRre8-ks5sYkvdgaJpZM4OjTj4 .

[jeffreybarrick]

Let me verify that it runs your current data and then I can release a v0.30.3.

[rohanmaddamsetti]

Awesome, thanks!

On Tue, Aug 15, 2017 at 10:06 PM, Jeffrey Barrick notifications@github.com wrote:

Let me verify that it runs your current data and then I can release a v0.30.3.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/barricklab/breseq/issues/129#issuecomment-322643260, or mute the thread https://github.com/notifications/unsubscribe-auth/AGGvLInNk9PQEHh7r_BM0YEirCejG-dbks5sYk6egaJpZM4OjTj4 .

[jeffreybarrick]

Released v0.31.0 fixes.