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cancerit / BRASS

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements in whole genome sequencing data.
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unused argument (cytoband_file = cytoband_file) - caused by Rlib - gam incompatibility #91

Open podro182 opened 4 years ago

podro182 commented 4 years ago

Hi,

I'm getting the following error in normalise_cn_by_gc_and_fb_reads.R: Error in pcf(data_for_pcf, gamma = 200, assembly = ".", cytoband_file = cytoband_file) : unused argument (cytoband_file = cytoband_file)

The cytoband file is provided as an argument in the function call: /services/tools/brass/6.2.1/bin/Rscript /services/tools/brass/6.2.1/lib/perl5/auto/share/module/Sanger-CGP-Brass-Implement/Rscripts/normalise_cn_by_gc_and_fb_reads.R brass_out/tmpBrass/cover/tumor.ngscn.fb_reads.bed.gz brass_out/tmpBrass/cover/blood.ngscn.fb_reads.bed.gz 2 0.75 brass_out/tmpBrass/cover/tumor_vs_blood.ngscn Human.GRCh37.CentTelo.tsv cytoband.txt

Do you have any idea on what might be wrong?

Thanks!

keiranmraine commented 4 years ago

Looks like one of the required parameters isn't defined (and the wrapper isn't checking it):

brass.pl [options]
  Required parameters:
...
    -cytoband    -cb  Cytoband file for a species build (can be obtained from UCSC)
keiranmraine commented 4 years ago

Don't think the above was as first thought. The code is checking these options. Would need the brass.pl command to understand more.

podro182 commented 4 years ago

Thanks for getting back to me.

The brass.pl command is the following:

brass.pl
    -o output/
    -t input/tumor.bam
    -n input/normal.bam
    -d coverage_profile.bed.gz
    -g hs37d5.fa
    -s Human
    -as GRCh37
    -pr WGS
    -b gcBins.bed.gz
    -vi 2bit/viral.genomic.merged.fa.2bit
    -mi 2bit/all_ncbi_bacteria
    -gc vagrent.Human.GRCh37.homo_sapiens_core_85_37.cache.gz
    -cb cytoband.txt
    -ct Human.GRCh37.CentTelo.tsv
    -c 1

The cytoband file looks like that:

$ head cytoband.txt
#chrom  chromStart      chromEnd        name    gieStain
1       0       2300000 p36.33  gneg
1       2300000 5400000 p36.32  gpos25
1       5400000 7200000 p36.31  gneg
1       7200000 9200000 p36.23  gpos25
1       9200000 12700000        p36.22  gneg
1       12700000        16200000        p36.21  gpos50
1       16200000        20400000        p36.13  gneg
1       20400000        23900000        p36.12  gpos25
1       23900000        28000000        p36.11  gneg

I'm using the following modules:

$ module list
Currently Loaded Modulefiles:
 1) cgpbigwig/1.0.1   3) cgpvcf/2.0.4    5) grass/2.0.0   7) intel/perflibs/2019_update5   9) R/3.2.5      11) bedtools/2.28.0
 2) pcap-core/3.5.0   4) vagrent/3.2.1   6) gcc/8.2.0     8) hdf5/1.10.1                  10) perl/5.20.2  12) brass/5.4.1
keiranmraine commented 4 years ago

You are using a very old version of brass. We discovered that the current GAM package used to generate the data_for_pcf1 variable is incompatible during the migration to a new image base. I this is fixed in v6.3.4.

There are docker images available from v6.3.0 onwards, all known to work with singularity.

If you specifically need that old version, you will need to downgrade the GAM R lib:

install.packages("devtools", lib=instLib)
library(devtools)
options(download.file.method = "auto")
install_github("cran/gam", ref="1.16.1")