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Error - overlapping regions in bedGraph line #167

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Chenjunjie1996 opened this issue Nov 1, 2023 · 0 comments
Open

Error - overlapping regions in bedGraph line #167

Chenjunjie1996 opened this issue Nov 1, 2023 · 0 comments

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@Chenjunjie1996
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Error - overlapping regions in bedGraph line 8812159 of Result/Analysis/A0920_3_ME_YSPB_WX_D_T7_EDTA5030/A0920_3_ME_YSPB_WX_D_T7_EDTA5030_sort .bdg
[Tue Oct 31 20:18:50 2023]
Error in rule scatac_bdg2bw:
jobid: 1
output: Result/Analysis/A0920_3_ME_YSPB_WX_D_T7_EDTA5030/A0920_3_ME_YSPB_WX_D_T7_EDTA5030.bw
shell:
bedtools slop -i Result/Analysis/A0920_3_ME_YSPB_WX_D_T7_EDTA5030/A0920_3_ME_YSPB_WX_D_T7_EDTA5030_all_treat_pileup.bdg -g /SGRNJ/Publ ic/Software/conda_env/MAESTRO1/lib/python3.8/site-packages/MAESTRO/annotations/GRCm38_chrom_len.txt -b 0 | /SGRNJ/Public/Software/conda_env/MA ESTRO1/lib/python3.8/site-packages/MAESTRO/utils/bedClip stdin /SGRNJ/Public/Software/conda_env/MAESTRO1/lib/python3.8/site-packages/MAESTRO/a nnotations/GRCm38_chrom_len.txt Result/Analysis/A0920_3_ME_YSPB_WX_D_T7_EDTA5030/A0920_3_ME_YSPB_WX_D_T7_EDTA5030_sort.clip;sort -k1,1 -k2,2n Result/Analysis/A0920_3_ME_YSPB_WX_D_T7_EDTA5030/A0920_3_ME_YSPB_WX_D_T7_EDTA5030_sort.clip > Result/Analysis/A0920_3_ME_YSPB_WX_D_T7_EDTA5030 /A0920_3_ME_YSPB_WX_D_T7_EDTA5030_sort.bdg;/SGRNJ/Public/Software/conda_env/MAESTRO1/lib/python3.8/site-packages/MAESTRO/utils/bedGraphToBigWi g Result/Analysis/A0920_3_ME_YSPB_WX_D_T7_EDTA5030/A0920_3_ME_YSPB_WX_D_T7_EDTA5030_sort.bdg /SGRNJ/Public/Software/conda_env/MAESTRO1/lib/pyt hon3.8/site-packages/MAESTRO/annotations/GRCm38_chrom_len.txt Result/Analysis/A0920_3_ME_YSPB_WX_D_T7_EDTA5030/A0920_3_ME_YSPB_WX_D_T7_EDTA503 0.bw;rm Result/Analysis/A0920_3_ME_YSPB_WX_D_T7_EDTA5030/A0920_3_ME_YSPB_WX_D_T7_EDTA5030_sort.bdg;rm Result/Analysis/A0920_3_ME_YSPB_WX_D_T7_ EDTA5030/A0920_3_ME_YSPB_WX_D_T7_EDTA5030_sort.clip
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job scatac_bdg2bw since they might be corrupted:
Result/Analysis/A0920_3_ME_YSPB_WX_D_T7_EDTA5030/A0920_3_ME_YSPB_WX_D_T7_EDTA5030.bw

How to deal with this error?

best

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