Hey! Could someone help me out with this? I am running rnaseq - nextflow run nf-core/rnaseq -r 3.14.0 -resume -params-file nf-params.json --input samplesheet.csv -profile docker. It works until the alignment step with STAR. STAR is not able to create a FIFO file because this is a windows system eventhough I am using wsl. The error is as follows: -[nf-core/rnaseq] Pipeline completed with errors- ERROR ~ Error executing process > 'NFCORE_RNASEQRNASEQALIGN_STAR:STAR_ALIGN (NEG5)' Caused by: Process

NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (NEG5)

terminated with an error exit status (112) Command executed: STAR \ --genomeDir star_index \ --readFilesIn input1/NEG5_1.fastp.fastq.gz input2/NEG5_2.fastp.fastq.gz \ --runThreadN 10 \ --outFileNamePrefix NEG5. \ \ --sjdbGTFfile GRCm39.genome.filtered.gtf \ --outSAMattrRGline 'ID:NEG5' 'SM:NEG5' \ --quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend --outSAMstrandField intronMotif --sjdbOverhang 49 if [ -f NEG5.Unmapped.out.mate1 ]; then mv NEG5.Unmapped.out.mate1 NEG5.unmapped_1.fastq gzip NEG5.unmapped_1.fastq fi if [ -f NEG5.Unmapped.out.mate2 ]; then mv NEG5.Unmapped.out.mate2 NEG5.unmapped_2.fastq gzip NEG5.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 NEG5._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. Aug 29 221220 ...... FATAL ERROR, exiting Work dir: /mnt/d/Shivani/bulkrna_activerun/work/93/edacc63fb17775510387f61522e585 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

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.

Well, installing WSL does (fortunately) not reformat your disks, so indeed FIFOs are not supported, because they work significantly different on Windows. For that reason, I have previously rejected pull requests in the modules directory that contained explicit

mkfifo

commands. However, I could not find a single module in the

rnaseq

pipeline that would use FIFOs explicitly. I know that Nextflow optionally uses them when supported to stage files, but that should just not happen on WSL. I noticed that several people have created similar issues on the repo (usually in conjunction with the HISAT aligner), but the investigations into this direction were not very successful. Do you have the option to use another drive (e.g. an external disk formatted as ext4 or the like) as work and result directory?

Hi Matthias, I don't know a lot about what you said, I am very new to bioinformatic analyses, programming and nfcore pipelines as well. So I am very hesitant to make any modifications to any configuration file etc... because I just dont know enough. But I was trying out different things to try and solve this while waiting for a response here. And I found something that seems to work? From what I understood, the problem was that even though I am using WSL which supports Linux files systems and FIFO files, the temporary files and working directory were being stored in the same normal windows compatible folder where my other input files etc... are located (/mnt/d/...) So I ran a command on the terminal to use a wsl environment where I created directories for the temporary files to be store there instead of my current working directory that is on a windows files system. Eg: export TMPDIR=/home/rnaseqlab/tmpdir mkdir -p $TMPDIR /home/rnaseqlab/nf_work. Now the FIFO files are being created and stored there and its is within the wsl environment so it is supported. As of now this is working. I dont know if I will run into problems later because of the change in location. But next time I guess I will create the directories first and then run the pipeline so it stores everything there and deletes it when the pipeline is successfully completed. Let me know what you think!