Comments (10)
Yes, that's right. Give it a go and report back.
from rnasplice.
Hi @paolo-kunderfranco - if you no longer have an issue with DRIMSEQ_FILTER or STAR_ALIGN are you happy for me to close this issue? I believe we are working on another issue you opened for SUPPA #71.
from rnasplice.
Please could you try to re-run the pipeline with the following dmFilter parameters set to zero:
- min_samps_gene_expr
- min_samps_feature_expr
- min_samps_feature_prop
- min_feature_expr
- min_feature_prop
- min_gene_expr
This can be done in the nextflow.config file - we are trying to ascertain whether there is a bug or the filters are too stringent for your samples.
from rnasplice.
ok now it seems working, but now I am again as always with different pipelines blocked in STAR segmentation error.
from rnasplice.
I believe this is a known issue with STAR 2.7.10a but the nf-core modules have not been updated. In the meantime, if you are able to use conda, you can download the pipeline and replace bioconda::star=2.7.10a
with bioconda::star=2.7.10b
in each of the main.nf files for the STAR modules.
from rnasplice.
you mean here?
for both genomegenerate and align modules?
`process STAR_ALIGN {
tag "$meta.id"
label 'process_high'
conda "bioconda::star=2.7.10a bioconda::samtools=1.16.1 conda-forge::gawk=5.1.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
`
from rnasplice.
error still persist
Error executing process > NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN_IGENOMES (CP28)
Caused by:
Process NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN_IGENOMES (CP28) terminated with an error exit status (139)
Command executed:
STAR \
--genomeDir STARIndex \
--readFilesIn CP28_1_val_1.fq.gz CP28_2_val_2.fq.gz \
--runThreadN 16 \
--outFileNamePrefix CP28. \
\
--sjdbGTFfile genes.gtf \
--outSAMattrRGline ID:CP28 'SM:CP28' \
--quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend
if [ -f CP28.Unmapped.out.mate1 ]; then
mv CP28.Unmapped.out.mate1 CP28.unmapped_1.fastq
gzip CP28.unmapped_1.fastq
fi
if [ -f CP28.Unmapped.out.mate2 ]; then
mv CP28.Unmapped.out.mate2 CP28.unmapped_2.fastq
gzip CP28.unmapped_2.fastq
fi
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASPLICE:RNASPLICE:ALIGN_STAR:STAR_ALIGN_IGENOMES":
star: $(STAR --version | sed -e "s/STAR_//g")
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
gawk: $(echo $(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/ .*$//')
END_VERSIONS
Command exit status:
139
Command output:
(empty)
Command error:
.command.sh: line 10: 10242 Segmentation fault STAR --genomeDir STARIndex --readFilesIn CP28_1_val_1.fq.gz CP28_2_val_2.fq.gz --runThreadN 16 --outFileNamePrefix CP28. --sjdbGTFfile genes.gtf --outSAMattrRGline ID:CP28 'SM:CP28' --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand gunzip -c --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend
from rnasplice.
any suggestion??
from rnasplice.
Hi @paolo-kunderfranco are you running with singularity? If so could you try running with conda and the changed versions as @jma1991 suggested? Trying with docker would also give us some useful information.
from rnasplice.
Hi @bensouthgate , I succesfully align samples with docker, but failed in SUPPA
from rnasplice.
Related Issues (20)
- Missing rMATS arguments HOT 2
- DEXSeq-DTU Stager pScreenAdjusted HOT 1
- sashimi_plot error HOT 2
- contrast file problem? HOT 7
- EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.9a HOT 2
- MISO error HOT 3
- The processes for splitting files are running very slowly with large numbers of input samples HOT 5
- Error: suppa_split_file.R Input_file must contain samplesheet samples. HOT 2
- ERROR ~ Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER (1)' HOT 11
- Error in DRIMSeq::dmDSdata(counts = counts, samples = samps) HOT 3
- Error single-end execution HOT 1
- Error in SUPPA: Clustergroups are assigned incorrectly HOT 4
- Miso error HOT 8
- `NFCORE_RNASPLICE:RNASPLICE:DRIMSEQ_DEXSEQ_DTU_SALMON:DEXSEQ_DTU (1)` HOT 7
- RNA splice output
- Merged genes output HOT 3
- DRIMSEQ_DEXSEQ_DTU_SALMON:DRIMSEQ_FILTER not working with special characters in sample names
- AWSmegatests are failing
- Spare memory for samtools issue
- Implement IsoformSwitchAnalyzeR HOT 1
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 rnasplice.