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./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)
What is the input? For example, short-read whole genome sequences? If so, do you have at least 13 CPU, 16G RAM total and 100G temp disk space? Or, are you extracting sequences from an alignment?
Also, if you could share the input file(s) with me, I'd be happy to take a look. You can email the details to me.
./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: bb0bf38dd6executor > 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 lineThe text was updated successfully, but these errors were encountered: