Snakefile calls to LAcheck in shell sections fail

[BradleyRan]

In Snakefile, some of the shell command sections use "cd workdir" but then include "workdir" in the path arguments to LAcheck.

example output:
cd workdir
datander -l500 -e0.980100 '-T1' scaffolds_FINAL
if (( ${SKIP_LACHECK:-0} == 0 ))
then
LAcheck -v scaffolds_FINAL workdir/TAN.scaffolds_FINAL.las || echo Try setting the environment variable SKIP_LACHECK=1 if the error is Duplicate LAs; otherwise rerun this block
else
echo "Skipping LAcheck due to user request"
fi
} &> logs/tandem-alignment.log

[a-ludi]

Thanks for your feedback. The error should be fixed.

[BradleyRan]

This may be dependent on shell, environment, parameters, etc. but I had to make a couple of minor changes to get it to work. Snakemake file Line 302, I had to insert “par.” In front of “strip” like object oriented syntax. Also, I’ve had to wrap all of the calls to “echo {lacheck_failed_notice}” like this: $(echo {lacheck_failed_notice}) *Edit: removed personal and irrelevant information*

[a-ludi]

I will try to fix it. The first issue is because I did not properly test my code before pushing it. For the second issue, I would like to know which shell you are running? *Edit: removed personal and irrelevant information*

[a-ludi]

Both errors should be fixed now.

[BradleyRan]

I am using /bin/sh which, I believe, is bash. We are running CentOS 7 on an SGE cluster. I submitted a job this morning with your changes and so-far, so-good. Thanks! *Edit: removed personal and irrelevant information*

[BradleyRan]

Hi Arne, Thanks for the updates to the Snakefile for dentist. The LAsort and LAmerge calls seem to have a bit of a problem if I use them from the daligner that I installed from git. Notice the “.N@” that gets appended. However, the LAsort and LAmerge from conda seem to work fine. However, the LAcheck from conda fails the “ref_vs_reads_alignment_block” because it tries to append “.las” to the second argument. The LAcheck from the daligner that I installed from git does work fine though. daligner2.0: Command Failed: LAsort /mnt/shared_tmp/376067.1.work.q/daligner.7314/scaffolds_FINAL.1.scaffolds_FINAL.7.N@ So, the furthest that we’ve progressed is with local damapper and LAcheck. The other prerequisites are from conda. The job seems to be stuck in “dentist collect”. The file “workdir/pile-ups.db” was created but it is empty. The node that it is running on shows that 71G of memory is used and 52G available. Here are the last entries in the “collect.log” file. {"thread":140737354013504,"timestamp":637255135504311334,"numPileUps":260,"numAlignmentChains":3186} {"thread":140737354013504,"timestamp":637255135504323016,"state":"exit","function":"dentist.commands.collectPileUps.PileUpCollector.buildPileUps","timeElapsed":25742682} {"thread":140737354013504,"timestamp":637255135504332559,"state":"enter","function":"dentist.commands.collectPileUps.PileUpCollector.writePileUps"} Do you have any ideas? Could there be a problem with the pipeline before it hit dentist collect? Watching it run is a thing of beauty! Regards, Randy