ascat error inside of cgpwgs docker file

[leehs96]

i can't figure it out that error message i mapped my bam file use cgpmap and my ref files are coordinated hg38

my bam, ref are matched with prifix 'chr'

here is my whole command and error message

cgpmap command

'sample=$1

docker run \
--tmpfs /tmp \
-v /users/hslee/ref/hg38:/var/spool/ref:ro \
-v /users/data/CancerEvolution_WGS/fastq:/var/spool/data:ro \
-v /users/hslee/cancer/WGS_hg38/cgpmap_bam:/home/ubuntu  \
quay.io/wtsicgp/dockstore-cgpmap:3.1.4 \
ds-cgpmap.pl \
-r /var/spool/ref/core_ref_GRCh38_hla_decoy_ebv.tar.gz \
-i /var/spool/ref/bwa_idx_GRCh38_hla_decoy_ebv.tar.gz \
-s $1 \
-t 6 \
/var/spool/data/$1_DNA_R1.fastq.gz \
/var/spool/data/$1_DNA_R2.fastq.gz \'

cgpwgs command

`tumor=$1
normal=$2

mkdir /users/hslee/cancer/WGS_hg38/cgpwgs_results/$1 &&
chmod 777 /users/hslee/cancer/WGS_hg38/cgpwgs_results/$1

docker run \
    --tmpfs /tmp \
    -v /users/hslee/ref/hg38/CGP:/var/spool/ref:rw \
    -v /users/hslee/cancer/WGS_hg38/cgpmap_bam:/var/spool/data \
    -v /users/hslee/cancer/WGS_hg38/cgpwgs_results/$1:/home/ubuntu \
    quay.io/wtsicgp/dockstore-cgpwgs:2.1.1 \
    ds-cgpwgs.pl \
    -r /var/spool/ref \
    -a /var/spool/ref \
    -si /var/spool/ref \
    -cs /var/spool/ref \
    -qc /var/spool/ref \
    -t /var/spool/data/$1.bam \
    -tidx /var/spool/data/$1.bam.bai \
    -n /var/spool/data/$2.bam \
    -nidx /var/spool/data/$2.bam.bai \
    -c 6 \
    -e 'MT,GL%,HLA%','*_*','chrUn%' \
    -o /home/ubuntu
`

ascat error message that in Sanger_CGP_Ascat_Implement_ascat.0.err file

`+ cut -f 1-3 /home/ubuntu/WGS_ADB_LL_vs_ADB_Blood/ascat/tmpAscat/SnpGcCorrections.tsv
+ cd /home/ubuntu/WGS_ADB_LL_vs_ADB_Blood/ascat/tmpAscat/ascat
+ /usr/bin/Rscript /opt/wtsi-cgp/lib/perl5/auto/share/module/Sanger-CGP-Ascat-Implement/ascat/runASCAT.R /opt/wtsi-cgp/lib/perl5/auto/share/module/Sanger-CGP-Ascat-Implement/ascat /home/ubuntu/WGS_ADB_LL_vs_ADB_Blood/ascat/tmpAscat/SnpPositions.tsv /home/ubuntu/WGS_ADB_LL_vs_ADB_Blood/ascat/tmpAscat/SnpGcCorrections.tsv ADB_LL ADB_LL.count ADB_Blood ADB_Blood.count XX 24 /home/ubuntu/WGS_ADB_LL_vs_ADB_Blood/ascat/tmpAscat/ascat/ADB_LL.Rdata
Error in apply(corr_tot, 1, function(x) sum(abs(x * length_tot))/sum(length_tot)) : 
  dim(X) must have a positive length
Calls: ascat.GCcorrect -> apply
Execution halted
Command exited with non-zero status 1
526.36user 12.98system 8:59.45elapsed 99%CPU (0avgtext+0avgdata 2327152maxresident)k
9240inputs+439280outputs (34major+5104014minor)pagefaults 0swaps`

i am stuck with this error almost 5 hours but I have no idea. please help me .....

[keiranmraine]

Are you inputs tumour+normal sequencing or normal/normal, or unmatched samples?

[leehs96]

thank you for reply my inputs are tumor + matched normal bam files aligned by cgpmap, used command is in my question

[keiranmraine]

Likely causes:

1. Insufficient sequencing depth, >15x minimum
2. Tumour/Normal are not actually matched (check genotype concordance)
3. High normal in tumour (or tumour in normal) contamination

[leehs96]

1. BAM files that used in analysis are 30x depth
2. already done swap test for each samples
3. not LCM sectioned... so the tumor purity of tumor samples are quite bad

SO.. could low tumor purity be problem?

[keiranmraine]

Low tumour purity would be a candidate for this error.

[leehs96]

thanks i'll try with high tumor purity sample sooner or later.