Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Not able to go beyond makeKmerDB, please help #5

Closed
archaemenes opened this issue Dec 10, 2023 · 3 comments
Closed

Not able to go beyond makeKmerDB, please help #5

archaemenes opened this issue Dec 10, 2023 · 3 comments

Comments

@archaemenes
Copy link

./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

@droeatpm
Copy link

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.

@archaemenes
Copy link
Author

./main.nf --id id1 --raw input --output output

I am just trying out the examples given
The system configurations are satisfied 16 CPUs 32G RAM 500G disk space

@archaemenes
Copy link
Author

SOLVED!

worked after adding the following to $HOME/.nextflow/config

docker.enabled = true
docker.fixOwnership = true

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants