Comments (5)
Aha - if it keeps running then it's possible that we noticed the error but figured it wasn't causing any problems so just ignored it. I assume the results look ok?
The error with null
memory is indeed specific to nextflow 0.32.0 and is fixed in the most recent release. See #95
Ok - so if everything is working as expected, then I might close this if that's ok 😁I don't think that a warning message with no consequence on the results is worth fighting with. If you think it's more severe than this then please let us know though.
Phil
from rnaseq.
Hi @hekatonkhieres,
v0.20.1 is really really old. I’m kind of amazed that the pipeline runs at all, as we make use of several features that were released in later versions of nextflow. How come you’re locked to that version?
I don’t really want to get in to trying to fix this on such an old version of nextflow tbh.
Phil
from rnaseq.
Hi @santiagorevale,
Thanks for reporting this. It's the first time I've seen this error, which is strange - typically problems like this no longer happen when using Singularity. The fact that you're using v1.1 and I only released this two days ago makes me suspicious though (also the fact that I updated Picard in this release).
Have you tried running v1.0 of the pipeline? Do you get the same error? You should be able to run it by just adding -r 1.0
to your nextflow command.
Phil
from rnaseq.
Hi @ewels,
I forgot to mention that besides the warning message, the pipeline keeps running. Sorry for that.
However, I've tried running it with version 1.0 and the same warning is happening. On the other hand, I came across an error on version 1.0 when running on Nextflow version 0.32.0 which I'm detailing below. Please, let me know if you want me to create a new issue with it and remove it from here.
Oct-08 09:05:11.573 [Actor Thread 42] ERROR nextflow.processor.TaskProcessor - Error executing process > 'star (Ganglion_WT_S2)'
Caused by:
Not a valid memory value: null
Source block:
prefix = reads[0].toString() - ~/(_R1)?(_trimmed)?(_val_1)?(\.fq)?(\.fastq)?(\.gz)?$/
def avail_mem = task.memory == null ? '' : "--limitBAMsortRAM ${task.memory.toBytes() - 100000000}"
seqCenter = params.seqCenter ? "--outSAMattrRGline ID:$prefix 'CN:$params.seqCenter'" : ''
"""
STAR --genomeDir $index \\
--sjdbGTFfile $gtf \\
--readFilesIn $reads \\
--runThreadN ${task.cpus} \\
--twopassMode Basic \\
--outWigType bedGraph \\
--outSAMtype BAM SortedByCoordinate $avail_mem \\
--readFilesCommand zcat \\
--runDirPerm All_RWX \\
--outFileNamePrefix $prefix $seqCenter \\
"""
Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option `-resume`
Oct-08 09:05:11.575 [Actor Thread 42] DEBUG nextflow.Session - Session aborted -- Cause: Process `null` script contains error(s)
from rnaseq.
Hi @ewels ,
I noticed in your post above that you said it "no longer" happens. That means the "cannot change locale" issue happened before but was resolved somehow?
Can you share what the fix was for this? I am stuck using Nextflow v0.20.1 and I experience this issue now and then. I'd love to be able to solve it.
from rnaseq.
Related Issues (20)
- MultiQC report is missing fastQC results on the dev branch HOT 11
- Dog seems unsupported, first issue is igenomes reference fasta dir vs RNAseq regex HOT 5
- GUNZIP does not work for relative paths specified with --fasta and --gtf HOT 1
- External Argument Documentation HOT 3
- Error running process `NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION`
- pipeline no longer compatible with newest STAR 2.7.11b
- Show Salmon-based strand inference in MultiQC report HOT 1
- Add `tximport` for RSEM outputs
- modules missing stub
- Custom content plots missing in MultiQC ouptut HOT 1
- Unable to go from FASTQ to Salmon Quantification
- Add support to use the pipeline with NGS generated using zymo research kit HOT 3
- Stubs all the way down
- NFCORE_RNASEQ takes values from global scope
- Accept uncompressed files, for instance fastq HOT 1
- Test profiles broken for Platform
- Updating picard to 3.2.0 fails pipeline level tests HOT 1
- To use STAR module, how should the GTF file look like
- NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (SRR15731653)` terminated with an error exit status (1)
- Sanity-check the sample names before committing to any data processing
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 rnaseq.