bedpe ann error

[gbnci]

Good Morning:
I am trying to use brass.pl recently but unfortunately got error at adding annotation step to the bedpe file. Here is the error I got:

$ more Sanger_CGP_Brass_Implement_grass.0.err
+ bash -c 'set -o pipefail; (cat /scratch/wangyong/dis/0A4HY5/tmpBrass/assemble/bedpe.* | sort -k1,1 -k 2,2n > /scratch/wangyong/dis/0A4HY5/0A4HY5_Tumor_vs_0A4
HY5_Normal.assembled.bedpe)'
+ /usr/bin/perl /opt/wtsi-cgp/bin/grass.pl -genome_cache /data/CCRBioinfo/wangyh/brass_file/chr_vagrent.human.GRCh37.homo_sapiens_91_37.cache -ref /data/CCRBio
info/wangyh/chr_genome.fa -species human -assembly GRCh37 -platform ILLUMINA -protocol WXS -tumour 0A4HY5_Tumor -normal 0A4HY5_Normal -file /scratch/wangyong/d
is/0A4HY5/0A4HY5_Tumor_vs_0A4HY5_Normal.assembled.bedpe -add_header brassVersion=6.1.2
+ /usr/bin/perl /opt/wtsi-cgp/bin/grass.pl -genome_cache /data/CCRBioinfo/wangyh/brass_file/chr_vagrent.human.GRCh37.homo_sapiens_91_37.cache -ref /data/CCRBio
info/wangyh/chr_genome.fa -species human -assembly GRCh37 -platform ILLUMINA -protocol WXS -tumour 0A4HY5_Tumor -normal 0A4HY5_Normal -file /scratch/wangyong/d
is/0A4HY5/0A4HY5_Tumor_vs_0A4HY5_Normal.groups.clean.bedpe -add_header brassVersion=6.1.2
+ /usr/bin/perl /opt/wtsi-cgp/bin/combineResults.pl /scratch/wangyong/dis/0A4HY5/0A4HY5_Tumor_vs_0A4HY5_Normal_ann.groups.clean /scratch/wangyong/dis/0A4HY5/0A
4HY5_Tumor_vs_0A4HY5_Normal_ann.assembled /scratch/wangyong/dis/0A4HY5/0A4HY5_Tumor_vs_0A4HY5_Normal.annot 2 0.75 DEFAULT
Can't open '/scratch/wangyong/dis/0A4HY5/0A4HY5_Tumor_vs_0A4HY5_Normal_ann.assembled.bedpe' for reading: 'No such file or directory' at /opt/wtsi-cgp/bin/combi
neResults.pl line 178
Command exited with non-zero status 255
0.39user 0.10system 0:00.53elapsed 93%CPU (0avgtext+0avgdata 27544maxresident)k
530inputs+296outputs (1major+17427minor)pagefaults 0swaps  

The command line I used is:

brass.pl -o 0A4HY5 -t 0A4HY5_Tumor.realigned.md.bam -n 0A4HY5_Normal.realigned.md.bam -d /data/CCRBioinfo/wangyh/brass_file/depth_final.bed -g /data/CCRBioinfo/wangyh/chr_genome.fa -s human -as GRCh37 -pr WXS -gc /data/CCRBioinfo/wangyh/brass_file/chr_vagrent.human.GRCh37.homo_sapiens_91_37.cache -vi /data/CCRBioinfo/wangyh/brass_file/viral.genomic.fa -mi /data/CCRBioinfo/wangyh/brass_file/all_bacteria.fa -b /data/CCRBioinfo/wangyh/brass_file/re_gcBins.bed.gz -cb /data/CCRBioinfo/wangyh/brass_file/cytoband.txt -ct /data/CCRBioinfo/wangyh/brass_file/chr_centTelo.tsv 

All the files listed under 0A4HY5 folder are:

0A4HY5_Tumor.insert_size_distr                                0A4HY5_Tumor_vs_0A4HY5_Normal.ngscn.abs_cn.bg
0A4HY5_Tumor_vs_0A4HY5_Normal.assembled.bedpe                 0A4HY5_Tumor_vs_0A4HY5_Normal.ngscn.abs_cn.bg.rg_cns
0A4HY5_Tumor_vs_0A4HY5_Normal.cn_filtered                     0A4HY5_Tumor_vs_0A4HY5_Normal.ngscn.segments.abs_cn.bg
0A4HY5_Tumor_vs_0A4HY5_Normal.groups                          0A4HY5_Tumor_vs_0A4HY5_Normal.r2
0A4HY5_Tumor_vs_0A4HY5_Normal.groups.clean.bedpe              0A4HY5_Tumor_vs_0A4HY5_Normal.r3
0A4HY5_Tumor_vs_0A4HY5_Normal.groups.filtered.bedpe           0A4HY5_Tumor_vs_0A4HY5_Normal.r4
0A4HY5_Tumor_vs_0A4HY5_Normal.groups.filtered.bedpenohead     0A4HY5_Tumor_vs_0A4HY5_Normal.r5
0A4HY5_Tumor_vs_0A4HY5_Normal.groups.filtered.bedpe.preclean  0A4HY5_Tumor_vs_0A4HY5_Normal.r5.scores
0A4HY5_Tumor_vs_0A4HY5_Normal.inversions.pdf                  0A4HY5_Tumor_vs_0A4HY5_Normal.r6
0A4HY5_Tumor_vs_0A4HY5_Normal.is_fb_artefact.txt              tmpBrass 

Seems to me the program failed to add annotation information to the bedpe file so could not generate the "ann.assembled.bedpe" file. Would you please let me know why this happens and how to address the problem? Any suggestions would be very appreciated.
Best
Yonghong

[udvzol]

I have the same problem. Did you or anyone found a resolution?

[gbnci]

no From: Zoltán Udvarnoki <notifications@github.com> Reply-To: cancerit/BRASS <reply@reply.github.com> Date: Thursday, March 26, 2020 at 12:32 PM To: cancerit/BRASS <BRASS@noreply.github.com> Cc: "Wang, Yonghong (NIH/NCI) [E]" <wangyong@mail.nih.gov>, State change <state_change@noreply.github.com> Subject: Re: [cancerit/BRASS] bedpe ann error (#77) I have the same problem. Did you or anyone found a resolution? — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub<#77 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AI62R6EC7G2JZRS4NDFSAFTRJN7QZANCNFSM4FTMFK6A>.

[keiranmraine]

We haven't looked at this as the requestor closed the issue.

How many lines of output (not header) are in the file:

0A4HY5_Tumor_vs_0A4HY5_Normal.assembled.bedpe

I suspect there are no events.

[udvzol]

Thank you for the fast reply.
Yes, you are right there are no lines in that file. What does that mean?

[gbnci]

In my case, I did have event, but could not get annotation information (for instance genes). My work around is simply adding gene information by myself. From: Keiran Raine <notifications@github.com> Reply-To: cancerit/BRASS <reply@reply.github.com> Date: Thursday, March 26, 2020 at 12:37 PM To: cancerit/BRASS <BRASS@noreply.github.com> Cc: "Wang, Yonghong (NIH/NCI) [E]" <wangyong@mail.nih.gov>, State change <state_change@noreply.github.com> Subject: Re: [cancerit/BRASS] bedpe ann error (#77) We haven't looked at this as the requestor closed the issue. How many lines of output (not header) are in the file: 0A4HY5_Tumor_vs_0A4HY5_Normal.assembled.bedpe I suspect there are no events. — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub<#77 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AI62R6FXDH4SPR7XPBE3JW3RJOADPANCNFSM4FTMFK6A>.

[keiranmraine]

@udvzol this means that the filtering has removed all events leaving nothing to report, I expect the following will show the gradual decrease in events (if files were ordered by last modified)

wc -l Tumor_vs_Normal.groups*

This is a very rare occurrence, but does occur, especially if the input data is low depth.... and the code should handle it better.

[udvzol]

The number of events is decreasing, but there are still some in all of them. Also, I have a .annot.bedpe file which is also not empty.
Could this still mean that all events were removed? I try to work with WXS, it could be also a challenge, I suppose.

[keiranmraine]

BRASS is not intended for use on Exomes, only wholegenome sequencing. We cannot support this use case.

[udvzol]

I completely understand, but here is such an option: -protocol -pr Sequencing protocol (WGS|WXS|RNA) in the command line. Is this only the remains of a planned feature?
Thank you anyway for your help!

[keiranmraine]

@udvzol that is just to pass the value through to the final VCF file header. I suspect it was copied from a different tool without too much thought, I'll raise an issue to remove it.