ERROR ~ Error executing process > 'NFCORE_RNASEQRNASEQALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP2)' Caused by: Process

NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP2)

terminated with an error exit status (112) Command executed: STAR \ --genomeDir star \ --readFilesIn input1/RAP1_UNINDUCED_REP2_primary.fastq.gz \ --runThreadN 4 \ --outFileNamePrefix RAP1_UNINDUCED_REP2. \ \ --sjdbGTFfile genome_gfp.gtf \ --outSAMattrRGline 'ID:RAP1_UNINDUCED_REP2' 'SM:RAP1_UNINDUCED_REP2' \ --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --quantTranscriptomeSAMoutput BanSingleEnd if [ -f RAP1_UNINDUCED_REP2.Unmapped.out.mate1 ]; then mv RAP1_UNINDUCED_REP2.Unmapped.out.mate1 RAP1_UNINDUCED_REP2.unmapped_1.fastq gzip RAP1_UNINDUCED_REP2.unmapped_1.fastq fi if [ -f RAP1_UNINDUCED_REP2.Unmapped.out.mate2 ]; then mv RAP1_UNINDUCED_REP2.Unmapped.out.mate2 RAP1_UNINDUCED_REP2.unmapped_2.fastq gzip RAP1_UNINDUCED_REP2.unmapped_2.fastq fi cat <<-END_VERSIONS > versions.yml "NFCORE_RNASEQRNASEQALIGN_STAR:STAR_ALIGN": 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: 112 Command output: (empty) Command error: Exiting because of FATAL ERROR: could not create FIFO file RAP1_UNINDUCED_REP2._STARtmp/tmp.fifo.read1 SOLUTION: check the if run directory supports FIFO files. If run partition does not support FIFO (e.g. Windows partitions FAT, NTFS), re-run on a Linux partition, or point --outTmpDir to a Linux partition. May 21 204533 ...... FATAL ERROR, exiting Work dir: /mnt/c/Users/moeba/work/3f/dedf759e8b7595dbf55ccf6f4b6fd9 Container: quay.io/nf-core/htslib_samtools_star_gawk:311d422a50e6d829 Tip: when you have fixed the problem you can continue the execution adding the option

-resume

to the run command line -- Check '.nextflow.log' file for details ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting -- Check '.nextflow.log' file for details

If someone could help me, that would be nice!

Hi newbie here, I have some modifications on Sarek and I want to post these modifications on Github. For the ease of use (so future user wont be troubleshooting for syntax error), I want to upload the whole modified file such as

workflow/main.nf

, is that appropriate if I just make citation in the readme?

Hi, I'm currently trying to add optional inputs to #C068T3R7LAE . I was following the Nextflow pattern for that (https://nextflow-io.github.io/patterns/optional-input/). I created a file

assets/NO_FILE

and my main Nextflow config contains

aod = "$projectDir/assets/NO_FILE"

as the default. The schema entry looks like this:

"aod": {
                    "type": "string",
                    "default": "${projectDir}/assets/NO_FILE",
                    "fa_icon": "fas fa-spray-can",
                    "description": "Custom Aerosol Optical Depth data.",
                    "help_text": "Directory containing a lookup table with custom Aerosol Optical Depth data. For the concrete format see the [FORCE docs](<https://force-eo.readthedocs.io/en/latest/components/lower-level/level2/depend.html>). This can be disregarded in most cases.",
                    "format": "path"
       },

When I run

nf-core pipelines schema build

, I get:

✨ Default for 'params.aod' in the pipeline config does not match schema. (schema: '<class 'str'>: ${projectDir}/assets/NO_FILE'  | config: '<class 'str'>: <some_path_on_my_system>/nf-core-rangeland/assets/NO_FILE'). Update pipeline schema? [y/n]:n

This is obviously caused by

$projectDir

being evaluated only in the config and not in the schema. Can I just ignore this, or is there a more nf-core-coherent way to implement optional inputs?

Hey all 🙂 can somebody tell me how to join the rnaseq channel ?

Hi, is anyone else having trouble collecting trace data? It’s not working for me.

.command.trace

files are being created correctly, but they don’t appear in the global trace file or the HTML report. I’m seeing this error in the log:

[TaskFinalizer-2] DEBUG nextflow.trace.TraceRecord - Not a valid trace `realtime` value: '2'

Tried running the tests profiles of: • mag 4.0.0 and sarek 3.5.1, slurm cluster + singularity • mag 4.0.0, local + docker None of these configurations work. However, running

rnaseq-nf

works, so I it could be something more closely related to nf-core pipelines.

Hi ! I have a broad licence issue / question. There is the impute5 tool that I would like to use in nf-core/phaseimpute, however it's licence is currently restrictive. I would like to ask the developer for a more permissive licence but can it be academic-use-only in bioconda and in nf-core ?

If I want to group a channel on 2 or more items in a meta map, what is the best way to do this? Is it some

groupKey

+

groupTuple

wizardry?

Hello, I am trying to run the nfcore-mag pipeline. I keep getting an error (see reply - so I don't fill the chat), and not sure what to do. I am running the pipeline on my universities HPC, and I think its an issue with allocated memory.

Hi everyone. I have been learning pangenome graphs (focusing on bacteria currently) and would like to use these squeezed graphs (from the pangenome pipeline) for structural variant calling. I would like to know if there's a pipeline for variant calls and downstream processing (visualisation or association studies) starting from variant graphs. Please share relevant resources you may know of. TIA.

Hello! I had a quick question about meta tags - let's say I want to implement a function or process that modifies a meta map based on some feature of the data, such as making sure a .vcf file has variants in it. My first thought was to use a process that emits some environment variable, then use that in the workflow to make a decision about the data:

process BOOL_VARIANTS_EXIST {
    tag "$meta.id"
    label 'process_low'

    input:
    tuple val(meta), path(vcf)

    output:
    env 'VAR_EXIST'

    """
    if [ "\$(zgrep -cv '#' ${vcf})" -eq 0 ]; then
        VAR_EXIST=0
    else
        VAR_EXIST=1
    fi
    """
}

This feels a little roundabout though, and I wanted to ask if it's possible to modify the meta in the process and emit it with the additional field

'vars_exist':0 or 'vars_exist':1

? I've also considered that perhaps I should be using a groovy function for this instead, or some kind of workflow syntax rather than a process. I guess I would love to do something like:

// SNIP
    output:
    tuple val(meta + ['vars_exist':$VAR_EXIST]), path(vcf)

but clearly this is not valid syntax (?) Would appreciate any advice!

Hi, When migrating to nf-test

cellranger-arc/mkfastq

I observed a big difference in number of reads depending on the number of cpu used. Simon told me to

If this tool is dependent on the number of CPUs to produce reproducible output, I would explicitly request the appropriate amount inside the tool, alongside the label.

However I don't know how and what he mean by that... Does anybody know ?

Hi all, I am hoping to use the nf-core/rnaseq pipeline to analyse my bulk RNAseq dataset. I am using UCL myriad cluster to setup this pipeline. Following is what I have done so far and where I am stuck! First, I installed the nextflow workflow manager as described in this link: https://nf-co.re/configs/ucl_myriad/ Tested the hello world and I am confident the nextflow is correctly set up as it works. Second, I tried to do test the nf-core/rnaseq pipeline using the following command: nextflow run nf-core/rnaseq -profile ucl_myriad --outdir /home/xxx/Scratch/nextflow/rnaseq I got an error code: 255 saying it timed out while trying to connect to the apptainer from my understanding it is not able to connect to apptainer hence not able to pull the dependencies next tired this nextflow run nf-core/rnaseq -profile test,ucl_myriad --outdir /home/xxxx/Scratch/nextflow/rnaseq -c <(echo "apptainer.pullTimeout = '1d' ") it seemed to work yesterday but today this is failing so not sure how to have a permanent fix to have stable connection Yesterday when the above command worked I got another error of code =126, saying permission denied I was wondering if anyone have faced these issues or can help me how to resolve this issue?

Is it normal that the new ARM64 test on modules is failing silently ? https://github.com/nf-core/modules/actions/runs/15348326731/job/43189938774?pr=8573

Hi everyone, I have a question regarding nf-core/rnaseq pipeline. I ran the pipeline and it said:

Pipeline completed successfully

However, I noticed that many processes such as

RSEM_CALCULATEEXPRESSION

,

SAMTOOLS_SORT

,

SAMTOOLS_STATS

, and others did not run — they were still listed as "waiting for tasks" even after the pipeline finished. I’ve tried different pipeline versions, including

-r 3.16.0

and

-r dev

, and the issue is consistent. How can I troubleshoot or fix this? Any help would be greatly appreciated!

#C02TBSA8NQ3 I have been trying to run the nf-core nanostring pipeline since sometime. Most of the steps work fine, but it fails at multiqc step. I tried increasing the memory to 100GB and time 24 hrs for the multiqc step but it is still running into error. Currently, I am testing the pipeline with 6 samples only. I am getting exit error status: 140. These are the resources used before the job fails. Cores: 1 CPU Utilized: 000937 CPU Efficiency: 0.67% of 235913 core-walltime Job Wall-clock time: 235913 Memory Utilized: 4.70 GB Memory Efficiency: 4.70% of 100.00 GB I can see following message in the .command.err file. write_results | Rendering plots. Export plots to formats png, svg, pdf is requested, so it might take a while. To disable plot export, set

export_plots: false

in config, or remove the

--export-plots

command line flag plot | Failure adding logo to the plot: cannot identify image file _io.BytesIO object at 0x155546b1f880

Anybody using the Nextflow vs-code extension ever get this error ?

Is it common to run into deadlocked channels, and are there some good ways to troubleshoot that? I'm trying to work around a seemingly pretty complicated issue where our samplesheet is sometimes generated dynamically, so I can not set the path to it statically, to send to the

samplesheetToList()

function, and I try to instead pick up the path from a channel, like so: https://github.com/genomic-medicine-sweden/gms_16S/blob/78-consolidate-pipeline-in[…]ORKAROUND/subworkflows/local/utils_nfcore_taco_pipeline/main.nf ... but the pipeline seems to just stall when test-running, where the same test use to finish pretty quickly when not doing this. I have a hunch that the problem is in my `runValidation()`` function, that I somehow don't "drive" the channel there in a proper way, since it is not returning any channel from the function: https://github.com/genomic-medicine-sweden/gms_16S/blob/78-consolidate-pipeline-in[…]ORKAROUND/subworkflows/local/utils_nfcore_taco_pipeline/main.nf I tried adding a

.view()

call in the end there, to force the channels to be consumed, but it doesn't seem to help.

I am trying to understand how to get the count matrix from rnaseq. After I run the pipeline, I see the multiqc to contain the table that says the total reads and aligned and uniquely aligned. This is shown under the "Summary Statistics" . . . Now, I am trying to find out which output file has these counts - of the aligned values. I understand that salmon.merged.gene_counts.tsv is estimated from salmon. But I was more curious where to extract the reads based on which the alignment summary stats or the featureCounts count estimates are created. Overall I am curious to extract the gene level counts using Star.

What is the standard approach for dealing with large temporary files generated by processes and stored in work/ ?

nextflow clean -f if I'm not mistaken, will remove all of the temporary files from the most recent nextflow run

Hi I am running nf-core metatdenovo pipeline. It shows the pipeline completed successfully, but the ORF and function annotation skipped, but I didn't indicate to skip it. Also a big problem is, I cant use resume function on the HPC of my university (CREATE from KCL). Every time it shows same error:

less nextflow-metatdenovo.out

NXF_HOME=/scratch/prj/cd_omics/IADR/nxf_home_link
NXF_WORK=/scratch/prj/cd_omics/IADR/metatdenovo_1/metatdenovo_run1/work
Running in: /scratch/prj/cd_omics/IADR/metatdenovo_1/metatdenovo_run1

 N E X T F L O W   ~  version 24.10.5

Launching `<https://github.com/nf-core/metatdenovo>` [small_mclean] DSL2 - revision: c42a8d4a0c [1.1.1]

ERROR ~ Can't open cache DB: /cephfs/volumes/hpc_data_prj/cd_omics/ce528200-f1f4-42d4-90ac-34e944b900f9/IADR/metatdenovo_1/metatdenovo_run1/.nextflow/cache/45d8139a-89f5-4bc9-a010-1a238fcf5a30/db

Nextflow needs to be executed in a shared file system that supports file locks.
Alternatively, you can run it in a local directory and specify the shared work
directory by using the `-w` command line option.

 -- Check '.nextflow.log' file for details

I am wondering anyone knows how to fix this error and allows to use resume? Many thanks!

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I had to rip apart my nextflow process to find this issue: The following works:

output:
  path "bcl_output/Undetermined_R1_001.fastq.gz",  emit: fastq_r1_undet
  path "bcl_output/Undetermined_R2_001.fastq.gz",  emit: fastq_r2_undet, optional: true

The following causes the pipeline to stall forever on this process:

path "bcl_output/Undetermined_R1_001.fastq.gz",  emit: fastq_r1_undet
  path "bcl_output/Undetermined_R2_001.fastq.gz",  emit: fastq_r2_undet, optional: true
  path "bcl_output/**/*_R1_001.fastq.gz",          emit: fastq_r1_det

If I remove the recursive glob, the pipeline completes:

path "bcl_output/Undetermined_R1_001.fastq.gz",  emit: fastq_r1_undet
  path "bcl_output/Undetermined_R2_001.fastq.gz",  emit: fastq_r2_undet, optional: true
  path "bcl_output/*_R1_001.fastq.gz",          emit: fastq_r1_det

Any ideas why a recursive glob with cause Nextflow to stall forever? I can't even control-c interrupt the pipeline. I have to hard-kill the Nextflow job. This pipeline was working fine up until recently. I'm using

Nextflow 25.04.3

. This pipeline is critical for our operations.

Hi there, I have a question regarding the

meta.yml

schema (is there a specific channel for it?), for a module. I have a module where I would like to specify alternative input types, like:

input:
  - - foo:
        type: file or directory

or

type: ["file", "directory"]

Currently not possible, but how about allowing it?

👋 Hi all, I have a failed test that says mismatched snapshots in my PR that changes the layout of TUI, however I don't really see the difference very clearly all the time and i'm not sure how to deal with this kind of issue. Does anyone may have an idea about this?

I am trying to update the fgbio modules in

nf-core/modules

using

nf-core modules bump-versions fgbio/fastqtobam

but I get the error:

Could not download container tags: Could not find singularity container for fgbio

I am using

nf-core

3.3.1. Any guidance would be appreciated.

Hi, i have a problem with running nf-test in Github. I always get the error:

fl:filesystem:InvalidArgument: Absolute path not permitted

. My processes are compiled matlab applications that have problems finding my input directory when provided symlinks. • I tried converting symlinks to real paths in the script block - which worked locally but not on github CI. • I tried to convert symlinks to real paths within my matlab compiled application - works locally but not on github • i tried

stageInMode 'copy'

and `'rellink`` (only for test profile) -

copy

did not work because my application cannot find the input_dir,

rellink

does not work in github • i changed only the first process for testing all options, not the others not sure if this would be a problem but it fails always on the first process. • i changed the output file paths from

results/file.mat

to

./results/file.mat

- didn’t work. • it could be a Matlab problem … this is the PR https://github.com/nf-core/lsmquant/pull/15 Maybe someone has an idea what is going wrong 🙏

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