Error executing process > 'pipeline:differential_expression:build_minimap_index_transcriptome' #82
Comments
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I fixed the problem increasing the memory in a config file as in other issues. CLI command run./nextflow run epi2me-labs/wf-transcriptomes Log outputN E X T F L O W ~ version 23.10.1 WARN: Found unexpected parameters:
|||||||||| _____ ____ ___ ____ __ __ _____ _ _ Core Nextflow options Input Options Output Options Sample Options Differential Expression Options ! Only displaying parameters that differ from the pipeline defaults ! If you use epi2me-labs/wf-transcriptomes for your analysis please cite: The nf-core framework This is epi2me-labs/wf-transcriptomes v1.1.1-g999fb4e. Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files. ERROR ~ Error executing process > 'pipeline:differential_expression:deAnalysis' Caused by: Command executed: mkdir merged Command exit status: executor > local (127) Caused by: Command executed: mkdir merged Command exit status: Caused by: Command executed: mkdir merged Command exit status: Caused by: Command executed: mkdir merged Command exit status: Command output: Command error: Work dir: Tip: when you have fixed the problem you can continue the execution adding the option -- Check '.nextflow.log' file for details |
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Hi there, I have had the exact same issue with the same error: minimap2 -t "4" -k14 -I 1000G -d "genome_index.mmi" "final_non_redundant_transcriptome.fasta" The PC I'm using has 8 cores, and 64GB of RAM. I increased the WSL2 allocated RAM to around 54GB and I changed the nextflow config file from 8GB to 54GB. I am still getting the same error message, what would you recommend I do? kamegh what did you set the config file to? Thanks for the help. |
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Hi @kocinajaltin, The config file contains this: |
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Thanks for the help, @kamegh. However, I am a complete novice with these systems. I have created the file as instructed but then when I run the epi2me program, and use the configuration tab in the nextflow configuration to run -c mem.config, I get an error. I have tried to add the file into every section of the epi2me folder. It just keeps throwing an error. So,
Apologies if these are all basic questions Thanks again in advance. |
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@kocinajaltin is the error you are are getting the same as above? 137? or different? |
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@kamegh It looks like for some reason the samples in the sample sheet are not present in the counts tsv, would you mind sharing the sample sheet you are using? also just checking is this direct RNA or cDNA you are using? |
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Morning @sarahjeeeze, Thanks for your reply. Yes it's the same error exit status 137. Altin |
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Sure, here is the sample sheet and I'm using cDNA. Thanks for the help. |
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Hi, sorry for the late reply. Currently unfortunately i think the aliases can't be a number - Could you possible include some letters for now and see if that works? - We have an update coming that will fix this issue. |
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Dear @sarahjeeeze, ERROR ~ Index 11 out of bounds for length 10 -- Check '.nextflow.log' file for details The code was as follows. This is the output. WARN: Found unexpected parameters:
|||||||||| _____ ____ ___ ____ __ __ _____ _ _ Core Nextflow options Input Options Output Options Sample Options Differential Expression Options Only displaying parameters that differ from the pipeline defaults !! If you use epi2me-labs/wf-transcriptomes for your analysis please cite:
This is epi2me-labs/wf-transcriptomes v1.1.1-g999fb4e. Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files. -- Check '.nextflow.log' file for details Best. |
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Hi @kamegh Could you reply and attach the .nextflow.log please? |
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Hi @nrhorner , Here is the .nextflow.log file. Best |
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Hi, I'm wondering whether you find a solution for the issue. |
Not yet. I'm still waiting for an answer. |
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I´ll be back here soon to check if there is a solution for this issue. Unfortunately, I'm getting the same error when running the wf-transcriptomes pipeline. @sarahjeeeze @nrhorner |
I think I have a solution. in the file of differential_expression.nf, line 125, change to |
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Hi, thanks for this feedback, we have not seen this but will investigate - are you running this on ARM? |
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Yes, we were running it on MacBook Pro, M3 chip |
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I was able to recreate the error 137 - you need to use the full genome as the ref_genome instead of the primary assembly so Homo_sapiens.GRCh38.dna.alt.fa.gz instead of Homo_sapiens.GRCh38.dna.primary_assembly.fa. Let me know if this solves it. This is also true for the out of index error. Sorry for the delay, i only just got round to looking in to it. |
Thank you! I will try it again later today. Will keep you posted. |
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Hi, sorry it has been a while - in this case the references in the full genome match with the references in the annotation file provided. Where as the primary assembly uses a different format so the workflow is unable to reconcile them. I am unsure if this is also the case for ensemble or gencode datasets. |
Operating System
macOS
Other Linux
No response
Workflow Version
v1.1.1-g999fb4e
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
./nextflow run epi2me-labs/wf-transcriptomes
--fastq /Users/kamegalan/analisis/reads_2
--de_analysis --ref_genome /Users/kamegalan/analisis/referencias/GRCh38_latest_genomic.fna.gz
--transcriptome-source reference-guided
--ref_annotation /Users/kamegalan/analisis/referencias/GRCh38_latest_genomic.gff.gz
--sample_sheet /Users/kamegalan/analisis/sample_sheet.csv
--out_dir output_3 -profile standard
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
I am running the analysis comparing infected and non infected cells. Just two groups, in triplicate.
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
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