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Hoohm / dropSeqPipe

A SingleCell RNASeq pre-processing snakemake workflow
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create_star_index: #112

Closed jkubis96 closed 4 years ago

jkubis96 commented 4 years ago

Hi, I have installed DropSeqPip with instruction on two others computer and it doesn't work. I have ERROR MESSAGE

LOG:

Building DAG of jobs... Using shell: /usr/bin/bash Provided cores: 20 Rules claiming more threads will be scaled down. Singularity containers: ignored Job counts: count jobs 1 DetectBeadSubstitutionErrors 1 MergeBamAlignment 1 STAR_align 2 SingleCellRnaSeqMetricsCollector_species 1 TagReadWithGeneExon 1 all 1 bam_hist 1 bead_errors_metrics 4 convert_long_to_mtx_species 1 create_dict 1 create_intervals 1 create_refFlat 1 create_star_index 2 extract_all_umi_expression 2 extract_reads_expression_species 2 extract_umi_expression_species 1 multiqc_star 1 pigz_unmapped 1 plot_barnyard 1 plot_knee_plot 2 plot_rna_metrics_species 1 plot_yield 1 reduce_gtf 1 repair_barcodes 2 split_bam_species 34

[Wed Sep 9 09:28:50 2020] rule create_star_index: input: /mnt/e/Nadia/DropSeqPip/Workplace/References/mixed_mus_musculus_homo_sapiens_38.38_91.91/genome.fa, /mnt/e/Nadia/DropSeqPip/Workplace/References/mixed_mus_musculus_homo_sapiens_38.38_91.91/curated_annotation.gtf output: /mnt/e/Nadia/DropSeqPip/Workplace/References/mixed_mus_musculus_homo_sapiens_38.38_91.91/STAR_INDEX/SA_75/SA jobid: 1 wildcards: ref_path=/mnt/e/Nadia/DropSeqPip/Workplace/References, species=mixed_mus_musculus_homo_sapiens, build=38.38, release=91.91, read_length=75 threads: 20

Activating conda environment: /mnt/e/Nadia/DropSeqPip/Workplace/.snakemake/conda/a23025f1 [Wed Sep 9 09:28:53 2020] Error in rule create_star_index: jobid: 1 output: /mnt/e/Nadia/DropSeqPip/Workplace/References/mixed_mus_musculus_homo_sapiens_38.38_91.91/STAR_INDEX/SA_75/SA conda-env: /mnt/e/Nadia/DropSeqPip/Workplace/.snakemake/conda/a23025f1 shell: mkdir -p /mnt/e/Nadia/DropSeqPip/Workplace/References/mixed_mus_musculus_homo_sapiens_38.38_91.91/STAR_INDEX/SA_75; STAR --runThreadN 20 --runMode genomeGenerate --genomeDir /mnt/e/Nadia/DropSeqPip/Workplace/References/mixed_mus_musculus_homo_sapiens_38.38_91.91/STAR_INDEX/SA_75 --genomeFastaFiles /mnt/e/Nadia/DropSeqPip/Workplace/References/mixed_mus_musculus_homo_sapiens_38.38_91.91/genome.fa --sjdbGTFfile /mnt/e/Nadia/DropSeqPip/Workplace/References/mixed_mus_musculus_homo_sapiens_38.38_91.91/curated_annotation.gtf --sjdbOverhang 74 --genomeChrBinNbits 18 --genomeSAsparseD 2

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

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /mnt/e/Nadia/DropSeqPip/Workplace/.snakemake/log/2020-09-09T092849.550450.snakemake.log