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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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HLA-HD silently fails if bowtie2 is not installed/loaded #62

Closed dmgie closed 6 months ago

dmgie commented 1 year ago

Hi,

I had recently been able to run the nextNEOpi pipeline through (after some minor modification). When looking at the results section I noticed that the ./results/neoantigens/[sample]/Class_II folders were empty.

At first I thought that HLA-HD wasn't found, but in Nextflow's output I see the line Found /data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh at: /data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh, so at least the HLA-HD is being found.

I additionally checked ./results/analyses/[sample]/10_HLA_typing/HLA_HD/, but theres only one file which just has Not typed for all of them.

Lastly, I checked the actual work/* folder for the HLA-HD process, and found out that in .command.err it wasn't able to fully run at all:

/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 101: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 102: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 103: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 104: bowtie2: command not found
rm: cannot remove './sample1_tumor_DNA/mapfile/sample1_tumor_DNA.all_exon.R1.D.sam': No such file or directory
rm: cannot remove './sample1_tumor_DNA/mapfile/sample1_tumor_DNA.all_exon.R2.D.sam': No such file or directory
rm: cannot remove './sample1_tumor_DNA/mapfile/sample1_tumor_DNA.all_intron.R1.D.sam': No such file or directory
rm: cannot remove './sample1_tumor_DNA/mapfile/sample1_tumor_DNA.all_intron.R2.D.sam': No such file or directory
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 132: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 133: bowtie2: command not found
mv: cannot stat './sample1_tumor_DNA/mapfile/sample1_tumor_DNA.fastq': No such file or directory
mv: cannot stat './sample1_tumor_DNA/mapfile/sample1_tumor_DNA.fastq': No such file or directory
rm: cannot remove './sample1_tumor_DNA/mapfile/sample1_tumor_DNA_all.R1.sam': No such file or directory
rm: cannot remove './sample1_tumor_DNA/mapfile/sample1_tumor_DNA_all.R2.sam': No such file or directory
rm: cannot remove './sample1_tumor_DNA/mapfile/sample1_tumor_DNA.exon.over.R1.fastq': No such file or directory
rm: cannot remove './sample1_tumor_DNA/mapfile/sample1_tumor_DNA.exon.over.R2.fastq': No such file or directory
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 150: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 151: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 158: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 159: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 182: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 183: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 184: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 185: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 208: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 209: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 210: bowtie2: command not found
/data/HLA-HD/hlahd.1.7.0/bin/hlahd.sh: line 211: bowtie2: command not found
rm: cannot remove './sample1_tumor_DNA/mapfile/sample1_tumor_DNA.all_intron.R1.sam': No such file or directory
rm: cannot remove './sample1_tumor_DNA/mapfile/sample1_tumor_DNA.all_intron.R2.sam': No such file or directory

As I did not have bowtie2 installed on the HPC cluster, HLA-HD wasn't able to run, but still gave an exit code of 0, meaning it was "successful" and Nextflow continued on.

Would pulling a singularity image for bowtie2 (i.e https://hub.docker.com/r/staphb/bowtie2/ or https://hub.docker.com/r/biocontainers/bowtie2/) in this process be a possible solution? Or possibly an error in case there is a missing bowtie2 installation?

(On another note: I had a collected a list of issues that I had run into i.e VepTab, CNNScoreVariants as well as some of the others mainly related to resources; would it be of any help to post/list them somewhere (in an Issue / Wiki Page / PR) in case people encounter similar issues?)

riederd commented 1 year ago

Hi, if you need to run HLA-HD you will also need to provide bowtie2 which needs to be accessible via $PATH.

Thanks for letting us know that HLA-HD still exits with 0 in the case bowtie2 is not found. I'll add a check logic for that case and throw an error at start time if bowtie2 is not in $PATH. I'm not sure if pulling a container is the best solution, because if someone wants to run HLA-HD independent of nextNEOpi she/he will have to provide bowtie2 anyways.

Feel free to post/list your findings/issues with the resources, we would be very happy to implement fixes or instructions.