Thank you for letting us use your great algorithm.
I have two problems with error messages that start with the phrase; "Expected ASCAT output file missing: ", and can not solve them because I am not so familiar with perl.
Would you help me?
We are using docker image (https://github.com/cancerit/dockstore-cgpwgs), version 2.1.0 and the main part of the command is as follows.
singularity exec -e -B ${bindpath} ${ascatNgs_singularity_image} ascat.pl -o ${output-directory} -t ${TumorBAM} -n ${NormalBAM} -r ${fasta} -sg ${SnpGCcorrectionfile} -pr ${protocol} -g ${sex} -gc chrY -rs "Homo sapiens" -ra GRCh38 -pl ILLUMINA -cpus ${NSLOTS} -nc -nb
It seems that the ascatNgs algorithm finished completely, but the file name had something wrong.
The following files are made in the output-directory.
sample_SM-502:T:DNA.ASCATprofile.png
sample_SM-502:T:DNA.ASPCF.png
sample_SM-502:T:DNA.BAF.PCFed.txt
sample_SM-502:T:DNA.LogR.PCFed.txt
sample_SM-502:T:DNA.copynumber.caveman.csv
sample_SM-502:T:DNA.copynumber.txt
sample_SM-502:T:DNA.germline.png
sample_SM-502:T:DNA.normal.BAF.txt
sample_SM-502:T:DNA.normal.LogR.txt
sample_SM-502:T:DNA.rawprofile.png
sample_SM-502:T:DNA.samplestatistics.txt
sample_SM-502:T:DNA.sunrise.png
sample_SM-502:T:DNA.tumour.BAF.txt
sample_SM-502:T:DNA.tumour.LogR.txt
sample_SM-502:T:DNA.tumour.png
sample_SM-502_N_DNA.count
sample_SM-502_T_DNA.Rdata
sample_SM-502_T_DNA.count
Most of the prefix of each file is "sample_SM-502:T:DNA", but the error is searching files starting with "sample_SM-502_T_DNA".
Using samtools and check the @RG tag (samtools view -H ${BAMfile} | grep ^@RG | awk 'NR==1 {for(i=2; i<=NF; i++) print$i}' | grep ^SM | sed -e "s/^SM://g") shows "sample_SM-502:T:DNA".
How we come over this problem?
Q2. Expected ASCAT output file missing: /home/ha6434/command/ascatNgs/output/BTTR-1790_1790_P01_NC1790T01-F_WGS/tmpAscat/ascat/7a25b147-d4d9-4d4f-9c4c-d48c3ed9c827.copynumber.caveman.csv
Does this mean a problem in copy number estimation?
If so, do we have no solution other than using the force option you mentioned in issue #38 ?
https://github.com/cancerit/ascatNgs/issues/38#issuecomment-200259667
Hi,
Thank you for letting us use your great algorithm. I have two problems with error messages that start with the phrase; "Expected ASCAT output file missing: ", and can not solve them because I am not so familiar with perl. Would you help me? We are using docker image (https://github.com/cancerit/dockstore-cgpwgs), version 2.1.0 and the main part of the command is as follows.
singularity exec -e -B ${bindpath} ${ascatNgs_singularity_image} ascat.pl -o ${output-directory} -t ${TumorBAM} -n ${NormalBAM} -r ${fasta} -sg ${SnpGCcorrectionfile} -pr ${protocol} -g ${sex} -gc chrY -rs "Homo sapiens" -ra GRCh38 -pl ILLUMINA -cpus ${NSLOTS} -nc -nbQ1. Expected ASCAT output file missing: /home/ha6434/command/ascatNgs/output/PT-FB6711_SM-502-T-DNA_P01_A22558_WGS/tmpAscat/ascat/sample_SM-502_T_DNA.ASPCF.png
It seems that the ascatNgs algorithm finished completely, but the file name had something wrong. The following files are made in the output-directory. sample_SM-502:T:DNA.ASCATprofile.png sample_SM-502:T:DNA.ASPCF.png sample_SM-502:T:DNA.BAF.PCFed.txt sample_SM-502:T:DNA.LogR.PCFed.txt sample_SM-502:T:DNA.copynumber.caveman.csv sample_SM-502:T:DNA.copynumber.txt sample_SM-502:T:DNA.germline.png sample_SM-502:T:DNA.normal.BAF.txt sample_SM-502:T:DNA.normal.LogR.txt sample_SM-502:T:DNA.rawprofile.png sample_SM-502:T:DNA.samplestatistics.txt sample_SM-502:T:DNA.sunrise.png sample_SM-502:T:DNA.tumour.BAF.txt sample_SM-502:T:DNA.tumour.LogR.txt sample_SM-502:T:DNA.tumour.png sample_SM-502_N_DNA.count sample_SM-502_T_DNA.Rdata sample_SM-502_T_DNA.count Most of the prefix of each file is "sample_SM-502:T:DNA", but the error is searching files starting with "sample_SM-502_T_DNA". Using samtools and check the @RG tag (samtools view -H ${BAMfile} | grep ^@RG | awk 'NR==1 {for(i=2; i<=NF; i++) print$i}' | grep ^SM | sed -e "s/^SM://g") shows "sample_SM-502:T:DNA". How we come over this problem?
Q2. Expected ASCAT output file missing: /home/ha6434/command/ascatNgs/output/BTTR-1790_1790_P01_NC1790T01-F_WGS/tmpAscat/ascat/7a25b147-d4d9-4d4f-9c4c-d48c3ed9c827.copynumber.caveman.csv Does this mean a problem in copy number estimation? If so, do we have no solution other than using the force option you mentioned in issue #38 ? https://github.com/cancerit/ascatNgs/issues/38#issuecomment-200259667
Tank you for sparing your time.
Best regards, Taku