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ccgd-profile / BreaKmer

A method to identify structural variation from sequencing data in target regions
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Translocations not called? #29

Closed signy-chow closed 8 years ago

signy-chow commented 8 years ago

Hello,

After running breakmer with a sample with known translocations, I have and output folder with a subfolder for each exon, which contains sorted reads in bam files, (tree below):

├── TRAF3_EXON_12 │   ├── TRAF3_EXON_12_contig89_reads.bam │   ├── TRAF3_EXON_12_contig89_reads.sorted.bam │   ├── TRAF3_EXON_12_contig89_reads.sorted.bam.bai │   ├── TRAF3_EXON_12_contig89_svs.out │   ├── TRAF3_EXON_12_discreads.out │   └── TRAF3_EXON_12_svs.out ├── TRAF3_EXON_3 │   └── TRAF3_EXON_3_discreads.out ├── TRAF3_EXON_6 │   └── TRAF3_EXON_6_discreads.out

Each of the _svs.out files gives the coordinates of indels which look like they can be found in the bam files. It seems that the _discreads.out files contain the structural variants (large inserts and translocations) that I am looking for but there is no sorted bam file to go with these.

The documentation seems to indicate that there should be a bam file output as well as a folder for each variant - is this correct? If so, what is preventing these from being generated?

I have no error messages in my log -- it seems to complete properly (below):

breakmer.assembly.assembler - INFO - Initiating kmer xxxxxxxxxxxx, found in 16 reads breakmer.assembly.contig - DEBUG - 0 kmers left to check breakmer.assembly.contig - INFO - Contig done with contig seq xxxxxxx Supported by 2 read(s). breakmer.assembly.contig - INFO - Read IDs: xxxxxxxxxxxxxxxx breakmer.assembly.assembler - INFO - Contig did not meet the read count threshold 2, with 2 or contig length (151) < readLen (151) breakmer.processor.target - INFO - Resolving structural variants from 0 kmer clusters breakmer.processor.target - INFO - Writing TRAF3_EXON_9 discordant read cluster result file /mnt/work1/users/xxxxxxxxxxxxxxxxxxxx breakmer.processor.analysis - INFO - Writing "Breakmer.JJN3.14Jun16_onlyMAX.NF.TRAF" aggregated results files: all result - xxxxxxxxxxx"_svs.all.out and filtered results - /mnt/work1/users/xxxxxxxxxxxxxxxxxxxxxx_svs.out breakmer.processor.analysis - INFO - Writing "xxxxxxxxxxxxx" aggregated results file /mnt/work1/users/xxxxxxxxxxxxxxx_discreads.out breakmer.processor.analysis - INFO - Analysis complete in 2489.59

Thanks for any insights!

mducar commented 8 years ago

Hi, It looks like you are using the unstable code in the master branch or one of the prototype releases. We've identified several issues with this code and recommend everyone use the release 0.0.6 version of BreaKmer.

signy-chow commented 8 years ago

Hi, Matt,

Thank you for your quick response. I have a couple of additional questions. I downloaded again the 0.0.6 version, which has the sv_assembly_mm2.py sv_assembly_py sv_caller.py sv_processor.py utils.py breakmer.py

all in the root directory, with a drawimage folder with a draw_trl_plot.R file.

The documentation for this here: http://ryanabo.github.io/BreaKmer/ does not seem to apply in the same way.

When I put in the command python breakmer.py prepare_reference_data -c /path/to/config/file/kmer_region.config

I get the following error

Usage: breakmer.py [options]

breakmer.py: error: option -c: invalid integer value:

when I look at python breakmer.py --help

informs me that the -c option is to specify translocation threshold, not to take a config file:

-c TRL_SR_THRESH, --trl_sr_thresh=TRL_SR_THRESH

                    Split read support threshold for translocations

                    [default: 2]

I attempted to drop the "-c", to put the relative path instead of the absolute path, but this does not seem to work. (and I get different errors)

Thanks for your help,

Signy

On Wed, Jun 15, 2016 at 7:27 AM, Matt Ducar notifications@github.com wrote:

Hi, It looks like you are using the unstable code in the master branch or one of the prototype releases. We've identified several issues with this code and recommend everyone use the release 0.0.6 version of BreaKmer.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ccgd-profile/BreaKmer/issues/29#issuecomment-226160357, or mute the thread https://github.com/notifications/unsubscribe/AR0PsMkEyg5AY2sxZDuiPQWuA50HSnVsks5qL-GOgaJpZM4I11Jf .

signy-chow commented 8 years ago

I also tried using the breakmer.cfg ( prepare_reference_data --c /path/to/config/breakmer.cfg) from the B2M example data set from the previous version, which it will still not take

Also, do you have an example data file I can try this on?

Thank you! Signy

Thanks!

On Wed, Jun 15, 2016 at 4:56 PM, Signy Chow signy@ualberta.ca wrote:

Hi, Matt,

Thank you for your quick response. I have a couple of additional questions. I downloaded again the 0.0.6 version, which has the sv_assembly_mm2.py sv_assembly_py sv_caller.py sv_processor.py utils.py breakmer.py

all in the root directory, with a drawimage folder with a draw_trl_plot.R file.

The documentation for this here: http://ryanabo.github.io/BreaKmer/ does not seem to apply in the same way.

When I put in the command python breakmer.py prepare_reference_data -c /path/to/config/file/kmer_region.config

I get the following error

Usage: breakmer.py [options]

breakmer.py: error: option -c: invalid integer value:

when I look at python breakmer.py --help

informs me that the -c option is to specify translocation threshold, not to take a config file:

-c TRL_SR_THRESH, --trl_sr_thresh=TRL_SR_THRESH

                    Split read support threshold for translocations

                    [default: 2]

I attempted to drop the "-c", to put the relative path instead of the absolute path, but this does not seem to work. (and I get different errors)

Thanks for your help,

Signy

On Wed, Jun 15, 2016 at 7:27 AM, Matt Ducar notifications@github.com wrote:

Hi, It looks like you are using the unstable code in the master branch or one of the prototype releases. We've identified several issues with this code and recommend everyone use the release 0.0.6 version of BreaKmer.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ccgd-profile/BreaKmer/issues/29#issuecomment-226160357, or mute the thread https://github.com/notifications/unsubscribe/AR0PsMkEyg5AY2sxZDuiPQWuA50HSnVsks5qL-GOgaJpZM4I11Jf .

signy-chow commented 8 years ago

Hi, again, Matt,

Are you able to clarify for me which version of breakmer I should be using? Again, the 0.0.6b version, which has the sv_assembly_mm2.py sv_assembly_py sv_caller.py sv_processor.py utils.py breakmer.py

all in the root directory, with a drawimage folder with a draw_trl_plot.R file. and runs everything at once

whereas the 0.0.6-ccgd version has these modularlized in separate folders with the need to put in the prepare_reference_data, the start_blat_server and the run commands separately.

I cannot get either of these versions to output a bamfile for the translocation events for me.

Thanks, Signy

On Wed, Jun 15, 2016 at 4:56 PM, Signy Chow signy@ualberta.ca wrote:

Hi, Matt,

Thank you for your quick response. I have a couple of additional questions. I downloaded again the 0.0.6 version, which has the sv_assembly_mm2.py sv_assembly_py sv_caller.py sv_processor.py utils.py breakmer.py

all in the root directory, with a drawimage folder with a draw_trl_plot.R file.

The documentation for this here: http://ryanabo.github.io/BreaKmer/ does not seem to apply in the same way.

When I put in the command python breakmer.py prepare_reference_data -c /path/to/config/file/kmer_region.config

I get the following error

Usage: breakmer.py [options]

breakmer.py: error: option -c: invalid integer value:

when I look at python breakmer.py --help

informs me that the -c option is to specify translocation threshold, not to take a config file:

-c TRL_SR_THRESH, --trl_sr_thresh=TRL_SR_THRESH

                    Split read support threshold for translocations

                    [default: 2]

I attempted to drop the "-c", to put the relative path instead of the absolute path, but this does not seem to work. (and I get different errors)

Thanks for your help,

Signy

On Wed, Jun 15, 2016 at 7:27 AM, Matt Ducar notifications@github.com wrote:

Hi, It looks like you are using the unstable code in the master branch or one of the prototype releases. We've identified several issues with this code and recommend everyone use the release 0.0.6 version of BreaKmer.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ccgd-profile/BreaKmer/issues/29#issuecomment-226160357, or mute the thread https://github.com/notifications/unsubscribe/AR0PsMkEyg5AY2sxZDuiPQWuA50HSnVsks5qL-GOgaJpZM4I11Jf .

mducar commented 8 years ago

Hi Signy,

The version of Breakmer you should use is under the "Releases" section. You should use the latest release v0.0.6 called "CCGD_Profile_Production". It sounds like you are cloning the repo and trying to run from there.

Thanks for pointing out the issue with the documentation. The description at http://ryanabo.github.io/BreaKmer/ wasn't set up by our team and doesn't apply to the latest release. We need to improve the documentation, but won't have the opportunity for a while.

-Matt