ERROR IN Job 26: Calculates mean heterozygosity per sex and 5kb window

[zhuangfjnu]

Hi , I encounter a error message in job26, the following is the report. Could you help me to solve it?

Job 26: Calculates mean heterozygosity per sex and 5kb window

Activating conda environment: /share/workplace/HIC/Software/findZX/.snakemake/conda/b083848ef9e9c8e2bab236b9bb0f6d16 /usr/bin/bash: line 1: workflow/scripts/sum_heterozygosity_per_5kb.sh: Permission denied [Tue Jan 11 08:12:48 2022] Error in rule proportion_heterozygosity_window_2: jobid: 26 output: results/wa_female/variant_calling/wa.build.chr.heterozygosity.5kb.windows.NR.bed, results/wa_female/variant_calling/wa.build.chr.heterozygosity.sexAverage.NR.bed conda-env: /share/workplace/HIC/Software/findZX/.snakemake/conda/b083848ef9e9c8e2bab236b9bb0f6d16 shell:

    workflow/scripts/sum_heterozygosity_per_5kb.sh results/wa_female/variant_calling/wa.build.chr.heterozygosity.5kb.windows.bed > results/wa_female/variant_calling/wa.build.chr.heterozygosity.5kb.windows.NR.bed

    python3 workflow/scripts/mean_heterozygosity_per_sex.py results/wa_female/variant_calling/wa.build.chr.heterozygosity.5kb.windows.NR.bed no-synteny het:369__heterogametic homo:jxw23__homogametic > results/wa_female/variant_calling/wa.build.chr.heterozygosity.sexAverage.NR.bed

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

Removing output files of failed job proportion_heterozygosity_window_2 since they might be corrupted: results/wa_female/variant_calling/wa.build.chr.heterozygosity.5kb.windows.NR.bed Job failed, going on with independent jobs.

[zhuangfjnu]

chmod +x sum_heterozygosity_per_5kb.sh Solve this error.

[hsigeman]

Hi,

Thanks a lot for bringing this issue (and the solution!) to my attention. I have now updated the file permissions for all bash scripts in Git (git update-index --chmod=+x), so that they should be set automatically when downloading findZX.

Hanna