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KCCG / ClinSV

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
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Sampleinfo.txt error #25

Open gneedle1 opened 2 years ago

gneedle1 commented 2 years ago

When running ClinSV, the sample info.txt file created is blank. If manually making one what should be included?

J-Bradlee commented 2 years ago

Hi @gneedle1,

ClinSV should automatically create the sampleInfo.txt file from your bam/bai files, or otherwise throw an error if it can't do it properly. Do you mind sharing what command you used and any output from ClinSV?

gneedle1 commented 2 years ago

Okay, I think I got it to work, the 'chr' labels were missing from my BAM files before, but now I get the sample info.txt file to generate with txt. I am not sure if it is in the right format though because now I get the error:

samtools depth: can't load index for "/app/project_folder/alignments/38_ref_DD_2/38_ref_DD_2.bam"

where "38_ref_DD_2" is the .bam and .bai files I want to analyze. The sampleinfo.txt file generated says:

"38_ref_DD_2 38_ref_DD_2 38_ref_DD_2 /app/input/38_ref_DD_2.dedup.sorted.bam"

Does this appear to be the correct format?

drmjc commented 2 years ago

Hi, can you try renaming or symlinking your bai files so that they end in .bam.bai?

Which version are you using?

V0.9 of clinsv only works with reads aligned to hs37d5, which don't have chr in the chrom names. V1.0 supports grch38, but didn't have docker so was hard to run. V1.1 (still in a branch) added a docker file and supports grch38 bam files. V1.2 will support hg19 style chrom names for v37 or v38 reference genomes, but that's still in dev.

On Thu, 14 Apr 2022, 2:01 am gneedle1, @.***> wrote:

Okay, I think I got it to work, the 'chr' labels were missing from my BAM files before, but now I get the sample info.txt file to generate with txt. I am not sure if it is in the right format though because now I get the error:

samtools depth: can't load index for "/app/project_folder/alignments/38_ref_DD_2/38_ref_DD_2.bam"

where "38_ref_DD_2" is the .bam and .bai files I want to analyze. The sampleinfo.txt file generated says:

"38_ref_DD_2 38_ref_DD_2 38_ref_DD_2 /app/input/38_ref_DD_2.dedup.sorted.bam"

Does this appear to be the correct format?

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gneedle1 commented 2 years ago

I'm using v1.0, renaming the files works but it still stops during the second task saying:

/app/project_folder/alignments/38_ref_DD_2/bw/sh/bigwig.q0.38_ref_DD_2.sh: line 7: 37061 Killed wigToBigWig /app/project_folder/alignments/38_ref_DD_2/bw/tmp/38_ref_DD_2.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_folder/alignments/38_ref_DD_2/bw/38_ref_DD_2.q0.bw

in the "bigwig.q0.38_ref_DD_2.e" file. Thoughts? (thank you for your help!)

gneedle1 commented 2 years ago

It looks like the error is because the bigwig executable files are made for linux. Is there an osx build with docker?

J-Bradlee commented 2 years ago

Hey @gneedle1 could cat the error file "bigwig.q0.38_ref_DD_2.e" and share it here, you should be able to find it under the project folder you created. I think ClinSV gives some sort path in the output.

Unfortunately at the current time the docker builds are all linux based.

gneedle1 commented 2 years ago

I tried to switch out the bigwig tools and symbolic links in the docker image, but it exits with:

Should I just try and build locally?

drmjc commented 2 years ago

Hi, The last error suggests a key dependency is not in your path.

docker run... on macos should still invoke a Linux container, so it shouldn't matter that it was compiled for Linux. What's your command for running clinsv?

You could try installing it natively on macos, using the Dockerfile as a guide, but as clinsv takes some time to run, it might not be a great experience. How many genomes are you analysing?

On Wed, 27 Apr 2022, 12:37 am gneedle1, @.***> wrote:

I tried to switch out the bigwig tools and symbolic links in the docker image, but it exits with:

  • export PATH=/app/clinsv/bin:/app/clinsv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

  • PATH=/app/clinsv/bin:/app/clinsv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

  • cd /app/project_folder/alignments/FR05812606/bw/
  • wigToBigWig /app/project_folder/alignments/FR05812606/bw/tmp/FR05812606.q0.wig /app/ref-data/refdata-b38/genome/Homo_sapiens_assembly38.fasta.chrom.sizes /app/project_folder/alignments/FR05812606/bw/FR05812606.q0.bw /app/project_folder/alignments/FR05812606/bw/sh/bigwig.q0.FR05812606.sh: line 7: wigToBigWig: command not found

Should I just try and build locally?

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gneedle1 commented 2 years ago

I am running with:

docker run -v $refdata_path:/app/ref-data \ -v $project_folder:/app/project_folder \ -v $input_path:/app/input \ --entrypoint "perl" 690e21ff2ee0 /app/clinsv/bin/clinsv \ -r bigwig \ -p /app/project_folder/ \ -i "/app/input/*.bam" \ -ref /app/ref-data/refdata-b38

where "690e21ff2ee0" is the image ID. I am only trying to analyze the sample BAM at the moment.