tedil
commented
3 weeks ago Hm yes, perhaps the post-deploy.sh script for cyrcular.yaml does not correctly install the binaries (in the right place). I will have a look, thank you for the report!
Open swcho-HYBigLab opened 3 weeks ago
tedil
commented
3 weeks ago Hm yes, perhaps the post-deploy.sh script for cyrcular.yaml does not correctly install the binaries (in the right place). I will have a look, thank you for the report!
tedil
commented
3 weeks ago Try again with the newest release of this workflow. If you run into any other issues, please let me know :)
swcho-HYBigLab
commented
3 weeks ago Thank you! I will try the release, and let you know as soon as the results come out
swcho-HYBigLab
commented
3 weeks ago This is my running command
snakemake --cores 40 --use-conda
I checked the cyrcular was correctly installed, but unfortunately I got the same error :(
[Tue Aug 20 15:32:42 2024]
localrule circle_bnds:
input: results/calling/mapping/S23-10097.bam, results/calling/mapping/S23-10097.bam.bai, resources/homo_sapiens.GRCh38.107.fasta, resources/homo_sapiens.GRCh38.107.fasta.fai
output: results/calling/candidates/S23-10097.bcf, results/calling/graphs/S23-10097.graph, results/calling/graphs/S23-10097
log: logs/cyrcular/S23-10097.log
jobid: 7
benchmark: benchmarks/cyrcular/S23-10097.txt
reason: Missing output files: results/calling/graphs/S23-10097.graph, results/calling/graphs/S23-10097, results/calling/candidates/S23-10097.bcf
wildcards: sample=S23-10097
threads: 4
resources: tmpdir=/tmp
Activating conda environment: .snakemake/conda/91799390de7870b6300fcef12d4e036b_
/usr/bin/bash: line 1: 135306 Killed cyrcular graph breakends results/calling/mapping/S23-10097.bam --reference resources/homo_sapiens.GRCh38.107.fasta --min-read-depth 2 --min-split-reads 5 --max-paths-per-component 15 --max-deletion-length 10000 -t 4 --output results/calling/candidates/S23-10097.bcf --graph results/calling/graphs/S23-10097.graph --dot results/calling/graphs/S23-10097 2> logs/cyrcular/S23-10097.log
[Tue Aug 20 17:24:05 2024]
Error in rule circle_bnds:
jobid: 7
input: results/calling/mapping/S23-10097.bam, results/calling/mapping/S23-10097.bam.bai, resources/homo_sapiens.GRCh38.107.fasta, resources/homo_sapiens.GRCh38.107.fasta.fai
output: results/calling/candidates/S23-10097.bcf, results/calling/graphs/S23-10097.graph, results/calling/graphs/S23-10097
log: logs/cyrcular/S23-10097.log (check log file(s) for error details)
conda-env: /lustre/export/home/swcho/1_ecDNA/3_data_for_WGS/nanopore_targeted/cyrcular-calling/.snakemake/conda/91799390de7870b6300fcef12d4e036b_
shell:
cyrcular graph breakends results/calling/mapping/S23-10097.bam --reference resources/homo_sapiens.GRCh38.107.fasta --min-read-depth 2 --min-split-reads 5 --max-paths-per-component 15 --max-deletion-length 10000 -t 4 --output results/calling/candidates/S23-10097.bcf --graph results/calling/graphs/S23-10097.graph --dot results/calling/graphs/S23-10097 2> logs/cyrcular/S23-10097.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-08-20T152938.659126.snakemake.log
WorkflowError:
At least one job did not complete successfully.And the logs/cyrcular is saved as
mean read depth: 8.3784
Calculating coverage took: 144.033059079s
Found 10574441 split reads
Building split read info
Building split-read info took: 207.717488729s
Step 1: Determining breakpoints (by coverage)
1.338594207s
Step 2: Insert breakpoint nodes
(number of breakpoints: 1953283)
474.314899ms
Step 3: Inserting edges between neighbouring breakpoints
6.720517866s
Step 4: Inserting edges between split-read nodes
5844.616390635s
Step 5: Pruning graph, first removing certain edges, then removing nodes with no edges left (or not part of a circle)
Number of components (pre-pruning): 249646
Number of components (after edge removal): 1040163
Number of components (after node removal #1): 945908
Number of components (after node removal #2): 6994
19.591672393s
Generating breakend events from graph
Number of components: 6994It seems like there's an error in the process itself (maybe my running command), I wonder if the allocation of too many cores could be the problem
tedil
commented
3 weeks ago It seems like the process is killed, I suspect memory limits. How much memory do you have available / did you request (if on a cluster system or similar)? (Judging from the cyrcular log, it is almost done, too.)
swcho-HYBigLab
commented
3 weeks ago I'm not sure that I'm answering your question correctly,
but I ran the command with --cores 40 on the cluster below
node6: [CPU] 43.2/96 (45.0%) [MEM] 39G/754G (5.2%)
I don't think the process was killed because the cluster ran out of memory or cores,
Maybe should I do it as workflow --cores all without specifying the number of cores?
Hello, I'm a graduated student studying bioinformatics in South Korea. I'm trying to do detect extrachromosomal DNA (ecDNA) in nanopore long-read targeted sequencing data.
I followed the workflow you described here.
I have tried two times of that workflow, but had same error in my job.
This is my standard log above
and this is the error log which place in
logs/cyrcular/I think it seems like the
cyrcular-callingpackages isn't installing properly from your github. Please check my logs and it will be grateful if you answer my question asap.Thank you.