droeatumn / kpi Goto Github PK

Dear Dave Roe,

I am struggling with this issue, the input fastqs are present. I believe something wrong goes in the kmc_tools part as it doesn't generate a file which is used in the next substep

./main.nf --id FND00001567 --raw /kpi/input/ --output /kpi/output/

N E X T F L O W ~ version 22.04.3
Launching ./main.nf [happy_austin] DSL1 - revision: b4644491c2
executor > local (1)
[78/788d62] process > makeKmerDB (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > db2Locus -
[- ] process > hapInterp -
Error executing process > 'makeKmerDB (1)'

Caused by:
Missing output file(s) *_hits.txt expected by process makeKmerDB (1)

Command executed:

export JAVA_OPTS='-Xmx200g'
./probeFastqsKMC.groovy -d FND00001567 -p input -o . -w . 2> probeFastqsKMC.log
./filterMarkersKMC2.groovy -d . -p markers -o . -w . 2> filterMarkersKMC2.log
find . -type f -size 0 | xargs rm # remove 0 length files, especially hits.txt files

Command exit status:
0

Command output:
(empty)

Work dir:
/kpi/work/78/788d62945d51b8b2fa782cb5b64a42

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

If the app hangs, a work around is to enter the container and run the workflow.
e.g., docker run --rm -it -v $PWD/input:/opt/kpi/raw -v $PWD/output:/opt/kpi/output/ droeatumn/kpi:latest /bin/bash

Then

cd /opt/kpi/raw
./main.nf --id <id>

The file name is included in the id column of the prediction.txt file.

The kmer counting program has a limit of 255. kmers occurring 255 or more are considered off-kir. In general, coverage shouldn't be too high, because then errors can start looking like non-errors. The work around is to down-sample the input data.

This limit should be addressed and removed. Ideally, it would learn the correct min/max counts based on the input.

./main.nf --id id1 --raw ./input --output ./output
N E X T F L O W ~ version 22.10.7
Launching ./main.nf [sad_poitras] DSL1 - revision: bb0bf38dd6
executor > local (1)
[3b/c1ca2c] process > makeKmerDB (1) [100%] 1 of 1, failed: 1 ✘
[- ] process > db2Locus -
[- ] process > hapInterp -
Error executing process > 'makeKmerDB (1)'

Caused by:
Process makeKmerDB (1) terminated with an error exit status (1)

Command executed:

export JAVA_OPTS='-Xmx200g'
./probeFastqsKMC.groovy -d id1 -p input -t fq -o . -w . 2> probeFastqsKMC.log
./filterMarkersKMC2.groovy -d . -p markers -o . -w . 2> filterMarkersKMC2.log
find . -type f -size 0 | xargs rm # remove 0 length files, especially hits.txt files

Command exit status:
1

Command output:
(empty)

Work dir:
/home/archaemenes/software/KPI/kpi/work/3b/c1ca2c39110386c48b83daad7c34e1

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line