aquas_chipseq pipline idr error
adroubsa opened this issue · 4 comments
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
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
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.
closing this due to long inactivity