bpipe error

[kristianunger]

Ask away!

When executing the workflow I get the error "Command error: mkdir: cannot create directory '/home/kunger': Read-only file system ln: failed to create symbolic link '/home/kunger/.bpipedb/jobs/74': No such file or directory" at the minimap2 step.

I am trying to execute he workflow using the following command:

export NXF_HOME=/data2/core-strahl-kitso/NFX export NXF_SINGULARITY_CACHEDIR=/data2/csk/NFX_SNGLTY

ref=/data2/csk/ref/nanopore/hg38.fa gtf=/data2/csk/ref/nanopore/ENCFF824ZKD.gtf jaffal_refBase=/data2/csk/ref/nanopore fastq_dir=/data2/csk/HBG/DNA_transciptome_fastq/fastq sheet=sample_sheet.csv nextflow run epi2me-labs/wf-transcriptomes \ --fastq ${fastq_dir} \ --de_analysis False \ --sample_sheet ${sheet} \ --ref_genome ${ref} \ --transcriptome-source reference-guided \ --ref_annotation ${gtf} \ --direct_rna False --minimap2_index_opts '-k 15' \ --jaffal_refBase ${jaffal_refBase} --jaffal_genome hg38 --jaffal_annotation genCode22 \ -profile singularity -resume

Could you please have a look at the .nextflow.log that was generated? nextflow.log

Many thanks!

[MikeWLloyd]

How did you solve this error? I am having trouble with this same issue.

[kristianunger]

How did you solve this error? I am having trouble with this same issue.

My issue was caused by providing a too low amount of RAM. Increasing resolved the issue.