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t-neumann / slamdunk

Streamlining SLAM-seq analysis with ultra-high sensitivity
GNU Affero General Public License v3.0
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slamdunk all: No tcount files and no error #160

Open andtsouris opened 2 months ago

andtsouris commented 2 months ago

@t-neumann @jkobject While running slamdunk all of the jkobject/slamdunk fork on a set of 10 samples, slamdunk doesn't produce tcount files for 2 of them without any error or other indication of what went wrong. The same behaviour was reproduced with both the forked and original versions, when running slamdunk count on the filtered bam file. Do you know what went wrong and how to fix it?

jkobject commented 2 months ago

Hi, if this error happens even on the un-forked version, I am not sure it concerns the modifications I made..?

Do you have code and/or input data we could look at to understand or reproduce your error?

andtsouris commented 2 months ago

Thanks for the quick response! I too think that it's not due to the modifications you made. My call of slamdunk is pretty basic slamdunk all -r genome.fa -b utr3.bed -o out/${sample} -t 12 ${sample}_R1_001.fastq.gz ${sample}_R2_001.fastq.gz.

Other than that, I'm only importing VarScan prior to calling slamdunk with alias varscan="java -jar /home/myuser/Tools/VarScan.v2.4.4.jar".

What is weird is that all samples are processed in exactly the same way prior to slamdunk but only some fail.

t-neumann commented 2 months ago

Hm that is indeed weird if it works for some but not for all. I second @jkobject I would probably need one of the filtered bam files to see what's going on there