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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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Values for optional field not being handled #42

Closed keiranmraine closed 7 years ago

keiranmraine commented 8 years ago

Need to handle absence of sample stats file from ascatNgs:

        -sampstat  -ss  ASCAT sample statistics file or file containing
                          NormalContamination 0.XXXXX [0.25]
                          Ploidy X.XXX [2.0]

If absent should apply the indicated default values.

keiranmraine commented 8 years ago

Info copied from unrelated item:

Below is another bug I found here:

Use of uninitialized value in -e at /risapps/rhel6/brass/5.0.0/bin/brass.pl line 180

"copy($options->{'ascat_summary'}, $intdir) if(-e $options->{'ascat_summary'});"

Could you please let me know why?

keiranmraine commented 8 years ago

@mailllonely, Please upgrade to the current release, 5.0.0 is not a release just a tag.

The option '-samplestat' is not being handled correctly when absent. You can work around this by creating a file as follows:

NormalContamination 0.25
Ploidy 2.0

If you have any information that could give you more accurate values please use them. This is ideally generated by ascatNgs as indicated at the start of this ticket.

mailllonely commented 8 years ago

The sample statistical file from ASCAT is absent, and I just created a file called "ascat.txt" including the following:

NormalContamination 0.25 Ploidy 2.0

then run the command:

/risapps/rhel6/brass/5.0.0/bin/brass.pl -o /rsrch2/genomic_med/jli19/brass/ -t del/IPCT-FC117-MS16-Cap-889-8-ID40_160609-STJ00106-0174-BHCLC7BBXX-8-CTCAGA.bwa_recalibed.bam -n del/IPCT-FC117-TDEV0004-Cap-888-8-ID39_160609-STJ00106-0174-BHCLC7BBXX-7-CTATAC.bwa_recalibed.bam -d /rsrch2/iacs/data/BRASS/ucscHiDepth_0.01_mrg1000_no_exon_coreChrs.bed.gz -g /scratch/rists/hpcapps/reference/human/broad_hg19/fastas/Homo_sapiens_assembly19.fasta -s human -as hg19 -pr WXS -gc /rsrch2/iacs/data/BRASS/Homo_sapiens.GRCh37.75.vagrent.cache.gz -vi /rsrch2/iacs/data/BRASS/viral.1.1.genomic.fa -mi /rsrch2/iacs/data/BRASS/all_ncbi_bacteria.20150703 -b /rsrch2/iacs/data/BRASS/hs37d5_500bp_windows.gc.bed.gz -ct /rsrch2/iacs/data/BRASS/Human.GRCh37.CentTelo.tsv.txt -sampstat -ss ascat.txt

it show the error below: Option 'ascat_summary' (-ss) should be an existing file.

then I removed the parameter "-sampstat", it throw an error:

Failed to find 'NormalContamination' in /rsrch2/genomic_med/jli19/brass/ascat.txt

keiranmraine commented 8 years ago

Apologies it appears that the expected key for normal contamination is rho. Change NormalContamination to rho and retry. I'll create an issue to get the command line option corrected.

FYI: -ss and -sampstat are the same option so you should only define one.

anoronh4 commented 3 years ago

i am having a similar issue. in the dockstore-cgpwgs git, we can supposedly run the input and cover steps without ascat results. however when using the latest dedicated BRASS docker: quay.io/wtsicgp/brass:v6.3.4 you have to provide it, even when only running one of those two steps.

has BRASS changed to require ascat for the previous steps as well? does it make sense to run those two steps in parallel with ascat, before running the remaining steps?