aquas_chipseq pipline idr error

[adroubsa]

Hello

could you kindly help me to fix an error i keep getting when running aquas_chipseq pipeline , the error jam getting is as below:

00:16:53.803 Wait: Waiting for task to finish: chipseq.bds.20180325_124007_960/task.callpeak_idr.idr2_rep1_pr.line_80.id_36, state: ERROR Task failed: Program & line : '/home/adroubsa/TF_chipseq_pipeline/modules/callpeak_idr.bds', line 80 Task Name : 'idr2 rep1-pr' Task ID : 'chipseq.bds.20180325_124007_960/task.callpeak_idr.idr2_rep1_pr.line_80.id_36' Task PID : '41355' Task hint : 'idr --samples /scratch/dragon/intel/adroubsa/HDAC2_Chip_Seq_DMD/HDAC_T6_DMD/DMD_T6_HDAC2_sam_files/HDAC2_DMD_T6_Chip_Seq_analysis/peak/macs2/pseudo_reps/rep1/pr1/D9813_T6_HDAC2_merged_Rep1.nodup.pr1.tagAlign_x_D9813_T6_HDAC2_Input1.nodup.tagAlign.pval0.01.500K.narrowPeak.gz /scratch/dragon/intel/adr' Task resources : 'cpus: -1 mem: -1.0 B wall-timeout: 8640000' State : 'ERROR' Dependency state : 'ERROR' Retries available : '1'

your kind help is much appreciated

[leepc12]

@adroubsa I need more info for debugging. Please post a full log.

[adroubsa]

Dear Jin

Kindly find attached the full log file , i have changed the html report file to txt file to be able to upload it .

i checked the number of peaks in rep1-rep2- idr thresholded and its 0 ( no peaks ) could that be the reason . also some of the finished tasks in the html report has [i] , what does it mean

chipseq.bds.20180403_212245_923.report.txt.gz

Thanks again in advance

[leepc12]

You have a lot of warnings in that log saying:

WARNING: Query NB501598:443:HWF3JAFXX:1:11111:12701:10770 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping

These warning occurred in the BAM-filtering step. so I think this has something to do with the reason that you don't have any IDR peaks.

Please check your BAM files and also check if they are paired end.

[leepc12]

closing this due to long inactivity