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nanoporetech / pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
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Error with alignment to reference in gene_expression tutorial #30

Open john-hancock opened 3 years ago

john-hancock commented 3 years ago

I'm running the gene_expression tutorial on a MacBook Air with the Apple chip.

I get the following error:

Error in rule build_minimap_index: jobid: 0 output: index/transcriptome_index.mmi shell:

    minimap2 -t 4  -I 1000G -d index/transcriptome_index.mmi /epi2melabs/differential-expression/sample_data/Homo_sapiens.GRCh38.cdna.all.fa.gz

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Is there a solution to this? I have just run the tutorial straightforwardly without any tinkering so it looks like a scripting/parameterization issue

Full log:

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 4 Rules claiming more threads will be scaled down. Conda environments: ignored Job counts: count jobs 1 build_minimap_index 1

[Thu Aug 5 10:42:13 2021] rule build_minimap_index: input: /epi2melabs/differential-expression/sample_data/Homo_sapiens.GRCh38.cdna.all.fa.gz output: index/transcriptome_index.mmi jobid: 0 threads: 4

[Thu Aug 5 10:42:32 2021] Error in rule build_minimap_index: jobid: 0 output: index/transcriptome_index.mmi shell:

    minimap2 -t 4  -I 1000G -d index/transcriptome_index.mmi /epi2melabs/differential-expression/sample_data/Homo_sapiens.GRCh38.cdna.all.fa.gz

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job build_minimap_index since they might be corrupted: index/transcriptome_index.mmi Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /epi2melabs/differential-expression/.snakemake/log/2021-08-05T104211.761394.snakemake.log