Comments (11)
I set the memory as the following:
`process {
withLabel:process_high {
memory = 500.GB
}
withName:'KALLISTOBUSTOOLS_REF' {
memory = 250.GB
}
withName:'KALLISTOBUSTOOLS_COUNT' {
memory = 250.GB
}
}`
from scrnaseq.
Solved by giving more memory to the process in the config file.
from scrnaseq.
You could try supplying a separate config that overwrites what kallisto is using for all steps, e.g. https://nf-co.re/usage/configuration#custom-configuration-files and then supplying something for memory
:
withName: 'KALLISTOBUSTOOLS_REF' {
memory : '32.GB'
}
from scrnaseq.
It didn't work, same error.
Here are the logs:
`[2022-06-22 09:29:53,353] INFO [ref_lamanno] Preparing sc_ncbi_genome.fasta, sc_gene_models_ncbi_no_genes_no_contigs_notrnas.gtf
[2022-06-22 09:30:27,852] INFO [ref_lamanno] Splitting genome sc_ncbi_genome.fasta into cDNA at /shared/ifbstor1/projects/bsbii/sc_single_cell_brain/work/ca/8de08f1ecfab6f41d8cc1f94e45c52/tmp/tmp_aaaucz5
[2022-06-22 09:31:08,887] INFO [ref_lamanno] Creating cDNA transcripts-to-capture at /shared/ifbstor1/projects/bsbii/sc_single_cell_brain/work/ca/8de08f1ecfab6f41d8cc1f94e45c52/tmp/tmpxx9d3eue
[2022-06-22 09:31:09,220] INFO [ref_lamanno] Splitting genome into introns at /shared/ifbstor1/projects/bsbii/sc_single_cell_brain/work/ca/8de08f1ecfab6f41d8cc1f94e45c52/tmp/tmp_4zx6l_e
[2022-06-22 09:37:03,403] INFO [ref_lamanno] Creating intron transcripts-to-capture at /shared/ifbstor1/projects/bsbii/sc_single_cell_brain/work/ca/8de08f1ecfab6f41d8cc1f94e45c52/tmp/tmpw8sjit6k
[2022-06-22 09:37:11,916] INFO [ref_lamanno] Concatenating 1 cDNA FASTAs to cdna.fa
[2022-06-22 09:37:12,346] INFO [ref_lamanno] Concatenating 1 cDNA transcripts-to-captures to cdna_t2c.txt
[2022-06-22 09:37:12,369] INFO [ref_lamanno] Concatenating 1 intron FASTAs to intron.fa
[2022-06-22 09:37:28,411] INFO [ref_lamanno] Concatenating 1 intron transcripts-to-captures to intron_t2c.txt
[2022-06-22 09:37:28,593] INFO [ref_lamanno] Concatenating cDNA and intron FASTAs to /shared/ifbstor1/projects/bsbii/sc_single_cell_brain/work/ca/8de08f1ecfab6f41d8cc1f94e45c52/tmp/tmp4jp7quuj
[2022-06-22 09:37:46,283] INFO [ref_lamanno] Creating transcript-to-gene mapping at t2g.txt
[2022-06-22 09:38:01,695] INFO [ref_lamanno] Indexing /shared/ifbstor1/projects/bsbii/sc_single_cell_brain/work/ca/8de08f1ecfab6f41d8cc1f94e45c52/tmp/tmp4jp7quuj to kb_ref_out.idx
[2022-06-22 09:47:41,663] ERROR [ref_lamanno]
[build] loading fasta file /shared/ifbstor1/projects/bsbii/sc_single_cell_brain/work/ca/8de08f1ecfab6f41d8cc1f94e45c52/tmp/tmp4jp7quuj
[build] k-mer length: 31
[build] warning: clipped off poly-A tail (longer than 10)
from 242 target sequences
[build] warning: replaced 24801554 non-ACGUT characters in the input sequence
with pseudorandom nucleotides
[build] counting k-mers ...
[2022-06-22 09:47:41,679] ERROR [main] An exception occurred
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/kb_python/main.py", line 856, in main
COMMAND_TO_FUNCTION[args.command](parser, args, temp_dir=temp_dir)
File "/usr/local/lib/python3.9/site-packages/kb_python/main.py", line 131, in parse_ref
ref_lamanno(
File "/usr/local/lib/python3.9/site-packages/ngs_tools/logging.py", line 62, in inner
return func(*args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/kb_python/ref.py", line 661, in ref_lamanno
index_result = kallisto_index(combined_path, index_path, k=k or 31)
File "/usr/local/lib/python3.9/site-packages/kb_python/ref.py", line 212, in kallisto_index
run_executable(command)
File "/usr/local/lib/python3.9/site-packages/kb_python/dry/init.py", line 24, in inner
return func(*args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/kb_python/utils.py", line 195, in run_executable
raise sp.CalledProcessError(p.returncode, ' '.join(command))
subprocess.CalledProcessError: Command '/usr/local/bin/kallisto index -i kb_ref_out.idx -k 31 /shared/ifbstor1/projects/bsbii/sc_single_cell_brain/work/ca/8de08f1ecfab6f41d8cc1f94e45c52/tmp/tmp4jp7quuj' died wit
h <Signals.SIGKILL: 9>.
slurmstepd: error: Detected 1 oom-kill event(s) in StepId=23442481.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.`
from scrnaseq.
Link to profile configuration if needed: https://github.com/nf-core/configs/blob/master/conf/ifb_core.config
from scrnaseq.
Ok, then lets add another profile for you that automatically does that for your cluster
from scrnaseq.
Good!
from scrnaseq.
Can you share what/how you modified the memory in the process config file? Then we can simply copy that
from scrnaseq.
Any chance this got fixed also for less memory now that we added the -m <MEMORY>
flag in the kallisto module?
from scrnaseq.
This issue seems to be resolved. @apeltzer, is there anything else that can be done here?
from scrnaseq.
No, if it works we can just close here 👍🏻
from scrnaseq.
Related Issues (20)
- exceeded running time limit (8h) HOT 3
- Crash when specifying existing --star_index using star aligner HOT 2
- Bump up kb to 0.28.0 HOT 3
- Use nf-validation plugin HOT 1
- Update or remove universc HOT 8
- Tests for cellranger-arc HOT 1
- MuData conversion
- Utilize central modules for simpleaf workflow HOT 1
- The cellrangerarc cannot start successfully HOT 2
- When aligner is cellrangerarc the step MTX_TO_SEURAT failed HOT 3
- Avoid error on unknown headers in input.csv HOT 4
- Issues with samplesheet.csv as well as additional columns in the samplesheet HOT 3
- Samplesheet Check Bug HOT 1
- Flexible input read format with STARsolo with --soloBarcodeReadLength HOT 1
- Make scrnaseq pipeline v2.5.1 compatible with nextflow v22.04.0 HOT 1
- Clean up mtx conversion code
- Update to the latest simpleaf HOT 3
- allow use of .gz when specifying fast and gtf HOT 4
- Use compressed (gzip) fasta and gtf HOT 3
- cellranger_count.py: remove any existing output directory HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from scrnaseq.