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kundajelab / atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
BSD 3-Clause "New" or "Revised" License
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Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. #93

Closed sky-peng closed 6 years ago

sky-peng commented 6 years ago

Hello I met a problem when i run the pipelines as follows: bds /home/ye/atac_dnase_pipelines/atac.bds -species hg19 -nth 10 -fastq1_1 ENCLB112FTD_R1.fastq.gz -fastq1_2 ENCLB112FTD_R2.fastq.gz -auto_detect_adapter The error was like this:

/ngs/data/ATACseq/human/out/peak/macs2/rep1/ENCLB112FTD_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph is not case-sensitive sorted at line 2. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again. Task failed: Program & line : '/home/ye/atac_dnase_pipelines/modules/callpeak_macs2_atac.bds', line 74 Task Name : 'macs2 n/s rep1' Task ID : 'atac.bds.20180302_125823_487/task.callpeak_macs2_atac.macs2_n_s_rep1.line_74.id_32' Task PID : '14181' Task hint : 'if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi; export PATH=/home/ye/atac' Task resources : 'cpus: -1 mem: -1.0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1' Input files : '[/ngs/data/ATACseq/human/out/align/rep1/ENCLB112FTD_R1.trim.PE2SE.nodup.tn5.tagAlign.gz]' Output files : '[/ngs/data/ATACseq/human/out/peak/macs2/rep1/ENCLB112FTD_R1.trim.PE2SE.nodup.tn5.pf.pval0.01.300K.narrowPeak.gz, /ngs/data/ATACseq/human/out/signal/macs2/rep1/ENCLB112FTD_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.bigwig, /ngs/data/ATACseq/human/out/signal/macs2/rep1/ENCLB112FTD_R1.trim.PE2SE.nodup.tn5.pf.pval.signal.bigwig]' Script file : '/ngs/data/ATACseq/human/atac.bds.20180302_125823_487/task.callpeak_macs2_atac.macs2_n_s_rep1.line_74.id_32.sh' Exit status : '1' StdErr (10 lines) : INFO @ Fri, 02 Mar 2018 15:04:18: #4 Write peak in narrowPeak format file... /ngs/data/ATACseq/human/out/peak/macs2/rep1/ENCLB112FTD_R1.trim.PE2SE.nodup.tn5.pf_peaks.narrowPeak INFO @ Fri, 02 Mar 2018 15:04:21: #4 Write summits bed file... /ngs/data/ATACseq/human/out/peak/macs2/rep1/ENCLB112FTD_R1.trim.PE2SE.nodup.tn5.pf_summits.bed INFO @ Fri, 02 Mar 2018 15:04:23: Done! INFO @ Fri, 02 Mar 2018 15:04:31: Read and build treatment bedGraph... INFO @ Fri, 02 Mar 2018 15:05:06: Read and build control bedGraph... INFO @ Fri, 02 Mar 2018 15:05:23: Build scoreTrackII... INFO @ Fri, 02 Mar 2018 15:05:38: Calculate scores comparing treatment and control by 'FE'... INFO @ Fri, 02 Mar 2018 15:08:24: Write bedGraph of scores... INFO @ Fri, 02 Mar 2018 15:10:03: Finished 'FE'! Please check '/ngs/data/ATACseq/human/out/peak/macs2/rep1/ENCLB112FTD_R1.trim.PE2SE.nodup.tn5.pf_FE.bdg'! /ngs/data/ATACseq/human/out/peak/macs2/rep1/ENCLB112FTD_R1.trim.PE2SE.nodup.tn5.pf.fc.signal.srt.bedgraph is not case-sensitive sorted at line 2. Please use "sort -k1,1 -k2,2n" with LC_COLLATE=C, or bedSort and try again.

Fatal error: /home/ye/atac_dnase_pipelines/atac.bds, line 1200, pos 2. Task/s failed. atac.bds, line 82 : main() atac.bds, line 85 : void main() { // atac pipeline starts here atac.bds, line 97 : call_peaks() atac.bds, line 1018 : void call_peaks() { // for pooling two replicates and calling peaks on them atac.bds, line 1200 : wait

What should i do to solve this error? Can you give me some suggestions? Thanks a lot!

boxiangliu commented 6 years ago

Hello @leepc12, have you had a chance to look at this yet?

leepc12 commented 6 years ago

It's weird. Pipeline already uses sort -k1,1 -k2,2n with export LC_COLLATE=C. I changed the sorting command line a bit to directly specify LC_COLLATE. Please update the pipeline and try again.

boxiangliu commented 6 years ago

Sorry for the delay. We will reinstall and let you know!

leepc12 commented 6 years ago

closing this due to long inactivity