Job ID = 1292340 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,479,825 reads read : 20,479,825 reads written : 20,479,825 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: 00:05:45 20479825 reads; of these: 20479825 (100.00%) were unpaired; of these: 3402689 (16.61%) aligned 0 times 14182181 (69.25%) aligned exactly 1 time 2894955 (14.14%) aligned >1 times 83.39% overall alignment rate Time searching: 00:05:45 Overall time: 00:05:45 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] 5220255 / 17077136 = 0.3057 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 18:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.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 18:21:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:21:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.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 18:21:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:21:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.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 18:21:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:21:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:21:42: 1000000 INFO @ Sun, 02 Jun 2019 18:21:42: 1000000 INFO @ Sun, 02 Jun 2019 18:21:43: 1000000 INFO @ Sun, 02 Jun 2019 18:21:54: 2000000 INFO @ Sun, 02 Jun 2019 18:21:55: 2000000 INFO @ Sun, 02 Jun 2019 18:21:55: 2000000 INFO @ Sun, 02 Jun 2019 18:22:08: 3000000 INFO @ Sun, 02 Jun 2019 18:22:08: 3000000 INFO @ Sun, 02 Jun 2019 18:22:08: 3000000 INFO @ Sun, 02 Jun 2019 18:22:21: 4000000 INFO @ Sun, 02 Jun 2019 18:22:21: 4000000 INFO @ Sun, 02 Jun 2019 18:22:22: 4000000 INFO @ Sun, 02 Jun 2019 18:22:34: 5000000 INFO @ Sun, 02 Jun 2019 18:22:35: 5000000 INFO @ Sun, 02 Jun 2019 18:22:35: 5000000 INFO @ Sun, 02 Jun 2019 18:22:47: 6000000 INFO @ Sun, 02 Jun 2019 18:22:48: 6000000 INFO @ Sun, 02 Jun 2019 18:22:48: 6000000 INFO @ Sun, 02 Jun 2019 18:22:59: 7000000 INFO @ Sun, 02 Jun 2019 18:23:01: 7000000 INFO @ Sun, 02 Jun 2019 18:23:01: 7000000 INFO @ Sun, 02 Jun 2019 18:23:13: 8000000 INFO @ Sun, 02 Jun 2019 18:23:13: 8000000 INFO @ Sun, 02 Jun 2019 18:23:14: 8000000 INFO @ Sun, 02 Jun 2019 18:23:26: 9000000 INFO @ Sun, 02 Jun 2019 18:23:26: 9000000 INFO @ Sun, 02 Jun 2019 18:23:27: 9000000 INFO @ Sun, 02 Jun 2019 18:23:39: 10000000 INFO @ Sun, 02 Jun 2019 18:23:40: 10000000 INFO @ Sun, 02 Jun 2019 18:23:40: 10000000 INFO @ Sun, 02 Jun 2019 18:23:52: 11000000 INFO @ Sun, 02 Jun 2019 18:23:53: 11000000 INFO @ Sun, 02 Jun 2019 18:23:53: 11000000 INFO @ Sun, 02 Jun 2019 18:24:03: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:24:03: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:24:03: #1 total tags in treatment: 11856881 INFO @ Sun, 02 Jun 2019 18:24:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:24:03: #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 18:24:03: #1 tags after filtering in treatment: 11856881 INFO @ Sun, 02 Jun 2019 18:24:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:24:03: #1 finished! INFO @ Sun, 02 Jun 2019 18:24:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:24:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:24:04: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:24:04: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:24:04: #1 total tags in treatment: 11856881 INFO @ Sun, 02 Jun 2019 18:24:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:24:04: #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 18:24:04: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:24:04: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:24:04: #1 total tags in treatment: 11856881 INFO @ Sun, 02 Jun 2019 18:24:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:24:04: #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 18:24:04: #1 tags after filtering in treatment: 11856881 INFO @ Sun, 02 Jun 2019 18:24:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:24:04: #1 finished! INFO @ Sun, 02 Jun 2019 18:24:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:24:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:24:04: #2 number of paired peaks: 395 WARNING @ Sun, 02 Jun 2019 18:24:04: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 02 Jun 2019 18:24:04: start model_add_line... INFO @ Sun, 02 Jun 2019 18:24:04: #1 tags after filtering in treatment: 11856881 INFO @ Sun, 02 Jun 2019 18:24:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:24:04: #1 finished! INFO @ Sun, 02 Jun 2019 18:24:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:24:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:24:04: start X-correlation... INFO @ Sun, 02 Jun 2019 18:24:05: end of X-cor INFO @ Sun, 02 Jun 2019 18:24:05: #2 finished! INFO @ Sun, 02 Jun 2019 18:24:05: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 18:24:05: #2 alternative fragment length(s) may be 2,41 bps INFO @ Sun, 02 Jun 2019 18:24:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.05_model.r WARNING @ Sun, 02 Jun 2019 18:24:05: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:24:05: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Sun, 02 Jun 2019 18:24:05: #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 18:24:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:24:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:24:06: #2 number of paired peaks: 395 WARNING @ Sun, 02 Jun 2019 18:24:06: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 02 Jun 2019 18:24:06: start model_add_line... INFO @ Sun, 02 Jun 2019 18:24:06: #2 number of paired peaks: 395 WARNING @ Sun, 02 Jun 2019 18:24:06: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 02 Jun 2019 18:24:06: start model_add_line... INFO @ Sun, 02 Jun 2019 18:24:06: start X-correlation... INFO @ Sun, 02 Jun 2019 18:24:06: end of X-cor INFO @ Sun, 02 Jun 2019 18:24:06: #2 finished! INFO @ Sun, 02 Jun 2019 18:24:06: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 18:24:06: #2 alternative fragment length(s) may be 2,41 bps INFO @ Sun, 02 Jun 2019 18:24:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.10_model.r WARNING @ Sun, 02 Jun 2019 18:24:06: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:24:06: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Sun, 02 Jun 2019 18:24:06: #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 18:24:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:24:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:24:07: start X-correlation... INFO @ Sun, 02 Jun 2019 18:24:07: end of X-cor INFO @ Sun, 02 Jun 2019 18:24:07: #2 finished! INFO @ Sun, 02 Jun 2019 18:24:07: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 18:24:07: #2 alternative fragment length(s) may be 2,41 bps INFO @ Sun, 02 Jun 2019 18:24:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.20_model.r WARNING @ Sun, 02 Jun 2019 18:24:07: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:24:07: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Sun, 02 Jun 2019 18:24:07: #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 18:24:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:24:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:24:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:24:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:24:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:25:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:25:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:25:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:25:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.05_summits.bed INFO @ Sun, 02 Jun 2019 18:25:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:25:11: Done! INFO @ Sun, 02 Jun 2019 18:25:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.10_summits.bed INFO @ Sun, 02 Jun 2019 18:25:11: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (378 records, 4 fields): 2 millis pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (857 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331364/SRX331364.20_summits.bed INFO @ Sun, 02 Jun 2019 18:25:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (141 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。