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snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
MIT License
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Unable to download requested sequence data from Ensembl #127

Open fangpingmu opened 2 days ago

fangpingmu commented 2 days ago

I am using singularity to run this pipeline.

Unable to download requested sequence data from Ensembl (ftp://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz). Please check whether above URL is currently available (might be a temporal server issue). Apart from that, did you check that this combination of species, build, and release is actually provided?

singularity exec --home '/ix1/genomics/demo/snakemake/rna-seq-kallisto-sleuth/demo' /ix1/genomics/demo/snakemake/rna-seq-kallisto-sleuth/demo/.snakemake/singularity/89e397d32d0575ad5d1e8e61ae29b7da.simg bash -c 'set -euo pipefail; Rscript --vanilla /ix1/genomics/demo/snakemake/rna-seq-kallisto-sleuth/demo/.snakemake/scripts/tmpz4s7fqll.get-transcript-info.R' Activating singularity image /ix1/genomics/demo/snakemake/rna-seq-kallisto-sleuth/demo/.snakemake/singularity/89e397d32d0575ad5d1e8e61ae29b7da.simg /usr/bin/bash: line 1: Rscript: command not found

I did shell into the singularity image, and there is no R or Rscript.

singularity shell 89e397d32d0575ad5d1e8e61ae29b7da.simg Singularity> which R Singularity> which Rscript Singularity>

dlaehnemann commented 1 day ago

How exactly do you do this?

I am not sure how running a workflow with singularity actually works, as I haven't done this before. Also, I'm not sure this is possible with this workflow, as we haven't done anything to enable this (there's no container: image defined globally or for any of the rules). But maybe, if you provide more details of the setup, I can help.