Job ID = 1291495 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,947,648 reads read : 15,947,648 reads written : 15,947,648 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:30 15947648 reads; of these: 15947648 (100.00%) were unpaired; of these: 442588 (2.78%) aligned 0 times 9759533 (61.20%) aligned exactly 1 time 5745527 (36.03%) aligned >1 times 97.22% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 7452641 / 15505060 = 0.4807 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 02 Jun 2019 16:03:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 16:03:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:03:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:03:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 16:03:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:03:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:03:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 16:03:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:03:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:03:17: 1000000 INFO @ Sun, 02 Jun 2019 16:03:18: 1000000 INFO @ Sun, 02 Jun 2019 16:03:18: 1000000 INFO @ Sun, 02 Jun 2019 16:03:24: 2000000 INFO @ Sun, 02 Jun 2019 16:03:26: 2000000 INFO @ Sun, 02 Jun 2019 16:03:26: 2000000 INFO @ Sun, 02 Jun 2019 16:03:31: 3000000 INFO @ Sun, 02 Jun 2019 16:03:33: 3000000 INFO @ Sun, 02 Jun 2019 16:03:33: 3000000 INFO @ Sun, 02 Jun 2019 16:03:38: 4000000 INFO @ Sun, 02 Jun 2019 16:03:41: 4000000 INFO @ Sun, 02 Jun 2019 16:03:41: 4000000 INFO @ Sun, 02 Jun 2019 16:03:45: 5000000 INFO @ Sun, 02 Jun 2019 16:03:49: 5000000 INFO @ Sun, 02 Jun 2019 16:03:49: 5000000 INFO @ Sun, 02 Jun 2019 16:03:52: 6000000 INFO @ Sun, 02 Jun 2019 16:03:57: 6000000 INFO @ Sun, 02 Jun 2019 16:03:57: 6000000 INFO @ Sun, 02 Jun 2019 16:03:59: 7000000 INFO @ Sun, 02 Jun 2019 16:04:04: 7000000 INFO @ Sun, 02 Jun 2019 16:04:04: 7000000 INFO @ Sun, 02 Jun 2019 16:04:06: 8000000 INFO @ Sun, 02 Jun 2019 16:04:06: #1 tag size is determined as 49 bps INFO @ Sun, 02 Jun 2019 16:04:06: #1 tag size = 49 INFO @ Sun, 02 Jun 2019 16:04:06: #1 total tags in treatment: 8052419 INFO @ Sun, 02 Jun 2019 16:04:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:04:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:04:06: #1 tags after filtering in treatment: 8052419 INFO @ Sun, 02 Jun 2019 16:04:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:04:06: #1 finished! INFO @ Sun, 02 Jun 2019 16:04:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:04:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:04:07: #2 number of paired peaks: 3093 INFO @ Sun, 02 Jun 2019 16:04:07: start model_add_line... INFO @ Sun, 02 Jun 2019 16:04:07: start X-correlation... INFO @ Sun, 02 Jun 2019 16:04:07: end of X-cor INFO @ Sun, 02 Jun 2019 16:04:07: #2 finished! INFO @ Sun, 02 Jun 2019 16:04:07: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 16:04:07: #2 alternative fragment length(s) may be 2,12,66,123 bps INFO @ Sun, 02 Jun 2019 16:04:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.05_model.r WARNING @ Sun, 02 Jun 2019 16:04:07: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:04:07: #2 You may need to consider one of the other alternative d(s): 2,12,66,123 WARNING @ Sun, 02 Jun 2019 16:04:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:04:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:04:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:04:12: 8000000 INFO @ Sun, 02 Jun 2019 16:04:12: 8000000 INFO @ Sun, 02 Jun 2019 16:04:12: #1 tag size is determined as 49 bps INFO @ Sun, 02 Jun 2019 16:04:12: #1 tag size = 49 INFO @ Sun, 02 Jun 2019 16:04:12: #1 total tags in treatment: 8052419 INFO @ Sun, 02 Jun 2019 16:04:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:04:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:04:12: #1 tags after filtering in treatment: 8052419 INFO @ Sun, 02 Jun 2019 16:04:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:04:12: #1 finished! INFO @ Sun, 02 Jun 2019 16:04:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:04:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:04:13: #1 tag size is determined as 49 bps INFO @ Sun, 02 Jun 2019 16:04:13: #1 tag size = 49 INFO @ Sun, 02 Jun 2019 16:04:13: #1 total tags in treatment: 8052419 INFO @ Sun, 02 Jun 2019 16:04:13: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:04:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:04:13: #1 tags after filtering in treatment: 8052419 INFO @ Sun, 02 Jun 2019 16:04:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:04:13: #1 finished! INFO @ Sun, 02 Jun 2019 16:04:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:04:13: #2 number of paired peaks: 3093 INFO @ Sun, 02 Jun 2019 16:04:13: start model_add_line... INFO @ Sun, 02 Jun 2019 16:04:14: start X-correlation... INFO @ Sun, 02 Jun 2019 16:04:14: end of X-cor INFO @ Sun, 02 Jun 2019 16:04:14: #2 finished! INFO @ Sun, 02 Jun 2019 16:04:14: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 16:04:14: #2 alternative fragment length(s) may be 2,12,66,123 bps INFO @ Sun, 02 Jun 2019 16:04:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.20_model.r WARNING @ Sun, 02 Jun 2019 16:04:14: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:04:14: #2 You may need to consider one of the other alternative d(s): 2,12,66,123 WARNING @ Sun, 02 Jun 2019 16:04:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:04:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:04:14: #2 number of paired peaks: 3093 INFO @ Sun, 02 Jun 2019 16:04:14: start model_add_line... INFO @ Sun, 02 Jun 2019 16:04:14: start X-correlation... INFO @ Sun, 02 Jun 2019 16:04:14: end of X-cor INFO @ Sun, 02 Jun 2019 16:04:14: #2 finished! INFO @ Sun, 02 Jun 2019 16:04:14: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 16:04:14: #2 alternative fragment length(s) may be 2,12,66,123 bps INFO @ Sun, 02 Jun 2019 16:04:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.10_model.r WARNING @ Sun, 02 Jun 2019 16:04:14: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:04:14: #2 You may need to consider one of the other alternative d(s): 2,12,66,123 WARNING @ Sun, 02 Jun 2019 16:04:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:04:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:04:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:04:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:04:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:04:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:04:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:04:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.05_summits.bed INFO @ Sun, 02 Jun 2019 16:04:36: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.20_summits.bed INFO @ Sun, 02 Jun 2019 16:04:42: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:04:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:04:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:04:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999198/ERX1999198.10_summits.bed INFO @ Sun, 02 Jun 2019 16:04:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。