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cancerit / BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
GNU Affero General Public License v3.0
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bedpe ann error #77

Closed gbnci closed 5 years ago

gbnci commented 6 years ago

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 commented 4 years ago

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

gbnci commented 4 years ago

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 GitHubhttps://github.com/cancerit/BRASS/issues/77#issuecomment-604532807, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AI62R6EC7G2JZRS4NDFSAFTRJN7QZANCNFSM4FTMFK6A.

keiranmraine commented 4 years ago

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 commented 4 years ago

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

gbnci commented 4 years ago

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 GitHubhttps://github.com/cancerit/BRASS/issues/77#issuecomment-604535555, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AI62R6FXDH4SPR7XPBE3JW3RJOADPANCNFSM4FTMFK6A.

keiranmraine commented 4 years ago

@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 commented 4 years ago

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 commented 4 years ago

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

udvzol commented 4 years ago

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 commented 4 years ago

@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.