Job ID = 2003734 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,524,233 reads read : 65,048,466 reads written : 32,524,233 reads 0-length : 32,524,233 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:35:16 32524233 reads; of these: 32524233 (100.00%) were unpaired; of these: 2342285 (7.20%) aligned 0 times 18103207 (55.66%) aligned exactly 1 time 12078741 (37.14%) aligned >1 times 92.80% overall alignment rate Time searching: 00:35:17 Overall time: 00:35:17 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 2423073 / 30181948 = 0.0803 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 @ Fri, 05 Jul 2019 14:59:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 14:59:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:59:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:59:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 14:59:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:59:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 14:59:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:59:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:59:43: 1000000 INFO @ Fri, 05 Jul 2019 14:59:44: 1000000 INFO @ Fri, 05 Jul 2019 14:59:45: 1000000 INFO @ Fri, 05 Jul 2019 14:59:52: 2000000 INFO @ Fri, 05 Jul 2019 14:59:52: 2000000 INFO @ Fri, 05 Jul 2019 14:59:55: 2000000 INFO @ Fri, 05 Jul 2019 15:00:00: 3000000 INFO @ Fri, 05 Jul 2019 15:00:00: 3000000 INFO @ Fri, 05 Jul 2019 15:00:04: 3000000 INFO @ Fri, 05 Jul 2019 15:00:08: 4000000 INFO @ Fri, 05 Jul 2019 15:00:08: 4000000 INFO @ Fri, 05 Jul 2019 15:00:13: 4000000 INFO @ Fri, 05 Jul 2019 15:00:16: 5000000 INFO @ Fri, 05 Jul 2019 15:00:16: 5000000 INFO @ Fri, 05 Jul 2019 15:00:22: 5000000 INFO @ Fri, 05 Jul 2019 15:00:24: 6000000 INFO @ Fri, 05 Jul 2019 15:00:25: 6000000 INFO @ Fri, 05 Jul 2019 15:00:32: 6000000 INFO @ Fri, 05 Jul 2019 15:00:32: 7000000 INFO @ Fri, 05 Jul 2019 15:00:33: 7000000 INFO @ Fri, 05 Jul 2019 15:00:40: 8000000 INFO @ Fri, 05 Jul 2019 15:00:41: 7000000 INFO @ Fri, 05 Jul 2019 15:00:41: 8000000 INFO @ Fri, 05 Jul 2019 15:00:48: 9000000 INFO @ Fri, 05 Jul 2019 15:00:49: 9000000 INFO @ Fri, 05 Jul 2019 15:00:50: 8000000 INFO @ Fri, 05 Jul 2019 15:00:56: 10000000 INFO @ Fri, 05 Jul 2019 15:00:57: 10000000 INFO @ Fri, 05 Jul 2019 15:00:59: 9000000 INFO @ Fri, 05 Jul 2019 15:01:04: 11000000 INFO @ Fri, 05 Jul 2019 15:01:05: 11000000 INFO @ Fri, 05 Jul 2019 15:01:08: 10000000 INFO @ Fri, 05 Jul 2019 15:01:12: 12000000 INFO @ Fri, 05 Jul 2019 15:01:13: 12000000 INFO @ Fri, 05 Jul 2019 15:01:17: 11000000 INFO @ Fri, 05 Jul 2019 15:01:20: 13000000 INFO @ Fri, 05 Jul 2019 15:01:21: 13000000 INFO @ Fri, 05 Jul 2019 15:01:26: 12000000 INFO @ Fri, 05 Jul 2019 15:01:28: 14000000 INFO @ Fri, 05 Jul 2019 15:01:29: 14000000 INFO @ Fri, 05 Jul 2019 15:01:35: 13000000 INFO @ Fri, 05 Jul 2019 15:01:36: 15000000 INFO @ Fri, 05 Jul 2019 15:01:37: 15000000 INFO @ Fri, 05 Jul 2019 15:01:44: 16000000 INFO @ Fri, 05 Jul 2019 15:01:45: 14000000 INFO @ Fri, 05 Jul 2019 15:01:45: 16000000 INFO @ Fri, 05 Jul 2019 15:01:52: 17000000 INFO @ Fri, 05 Jul 2019 15:01:53: 17000000 INFO @ Fri, 05 Jul 2019 15:01:54: 15000000 INFO @ Fri, 05 Jul 2019 15:02:00: 18000000 INFO @ Fri, 05 Jul 2019 15:02:02: 18000000 INFO @ Fri, 05 Jul 2019 15:02:03: 16000000 INFO @ Fri, 05 Jul 2019 15:02:08: 19000000 INFO @ Fri, 05 Jul 2019 15:02:10: 19000000 INFO @ Fri, 05 Jul 2019 15:02:12: 17000000 INFO @ Fri, 05 Jul 2019 15:02:16: 20000000 INFO @ Fri, 05 Jul 2019 15:02:18: 20000000 INFO @ Fri, 05 Jul 2019 15:02:21: 18000000 INFO @ Fri, 05 Jul 2019 15:02:23: 21000000 INFO @ Fri, 05 Jul 2019 15:02:26: 21000000 INFO @ Fri, 05 Jul 2019 15:02:31: 19000000 INFO @ Fri, 05 Jul 2019 15:02:32: 22000000 INFO @ Fri, 05 Jul 2019 15:02:34: 22000000 INFO @ Fri, 05 Jul 2019 15:02:40: 23000000 INFO @ Fri, 05 Jul 2019 15:02:40: 20000000 INFO @ Fri, 05 Jul 2019 15:02:43: 23000000 INFO @ Fri, 05 Jul 2019 15:02:48: 24000000 INFO @ Fri, 05 Jul 2019 15:02:49: 21000000 INFO @ Fri, 05 Jul 2019 15:02:51: 24000000 INFO @ Fri, 05 Jul 2019 15:02:56: 25000000 INFO @ Fri, 05 Jul 2019 15:02:58: 22000000 INFO @ Fri, 05 Jul 2019 15:02:59: 25000000 INFO @ Fri, 05 Jul 2019 15:03:04: 26000000 INFO @ Fri, 05 Jul 2019 15:03:07: 26000000 INFO @ Fri, 05 Jul 2019 15:03:08: 23000000 INFO @ Fri, 05 Jul 2019 15:03:12: 27000000 INFO @ Fri, 05 Jul 2019 15:03:16: 27000000 INFO @ Fri, 05 Jul 2019 15:03:17: 24000000 INFO @ Fri, 05 Jul 2019 15:03:18: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 15:03:18: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 15:03:18: #1 total tags in treatment: 27758875 INFO @ Fri, 05 Jul 2019 15:03:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:03:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:03:19: #1 tags after filtering in treatment: 27758782 INFO @ Fri, 05 Jul 2019 15:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:03:19: #1 finished! INFO @ Fri, 05 Jul 2019 15:03:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:03:22: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 15:03:22: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 15:03:22: #1 total tags in treatment: 27758875 INFO @ Fri, 05 Jul 2019 15:03:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:03:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:03:22: #2 number of paired peaks: 6456 INFO @ Fri, 05 Jul 2019 15:03:22: start model_add_line... INFO @ Fri, 05 Jul 2019 15:03:23: #1 tags after filtering in treatment: 27758782 INFO @ Fri, 05 Jul 2019 15:03:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:03:23: #1 finished! INFO @ Fri, 05 Jul 2019 15:03:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:03:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:03:23: start X-correlation... INFO @ Fri, 05 Jul 2019 15:03:23: end of X-cor INFO @ Fri, 05 Jul 2019 15:03:23: #2 finished! INFO @ Fri, 05 Jul 2019 15:03:23: #2 predicted fragment length is 49 bps INFO @ Fri, 05 Jul 2019 15:03:23: #2 alternative fragment length(s) may be 49,132,204,211,406 bps INFO @ Fri, 05 Jul 2019 15:03:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.20_model.r WARNING @ Fri, 05 Jul 2019 15:03:23: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:03:23: #2 You may need to consider one of the other alternative d(s): 49,132,204,211,406 WARNING @ Fri, 05 Jul 2019 15:03:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:03:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:03:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:03:26: #2 number of paired peaks: 6456 INFO @ Fri, 05 Jul 2019 15:03:26: start model_add_line... INFO @ Fri, 05 Jul 2019 15:03:26: 25000000 INFO @ Fri, 05 Jul 2019 15:03:26: start X-correlation... INFO @ Fri, 05 Jul 2019 15:03:26: end of X-cor INFO @ Fri, 05 Jul 2019 15:03:26: #2 finished! INFO @ Fri, 05 Jul 2019 15:03:26: #2 predicted fragment length is 49 bps INFO @ Fri, 05 Jul 2019 15:03:26: #2 alternative fragment length(s) may be 49,132,204,211,406 bps INFO @ Fri, 05 Jul 2019 15:03:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.10_model.r WARNING @ Fri, 05 Jul 2019 15:03:26: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:03:26: #2 You may need to consider one of the other alternative d(s): 49,132,204,211,406 WARNING @ Fri, 05 Jul 2019 15:03:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:03:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:03:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:03:36: 26000000 INFO @ Fri, 05 Jul 2019 15:03:45: 27000000 INFO @ Fri, 05 Jul 2019 15:03:52: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 15:03:52: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 15:03:52: #1 total tags in treatment: 27758875 INFO @ Fri, 05 Jul 2019 15:03:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:03:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:03:52: #1 tags after filtering in treatment: 27758782 INFO @ Fri, 05 Jul 2019 15:03:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:03:52: #1 finished! INFO @ Fri, 05 Jul 2019 15:03:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:03:56: #2 number of paired peaks: 6456 INFO @ Fri, 05 Jul 2019 15:03:56: start model_add_line... INFO @ Fri, 05 Jul 2019 15:03:56: start X-correlation... INFO @ Fri, 05 Jul 2019 15:03:56: end of X-cor INFO @ Fri, 05 Jul 2019 15:03:56: #2 finished! INFO @ Fri, 05 Jul 2019 15:03:56: #2 predicted fragment length is 49 bps INFO @ Fri, 05 Jul 2019 15:03:56: #2 alternative fragment length(s) may be 49,132,204,211,406 bps INFO @ Fri, 05 Jul 2019 15:03:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.05_model.r WARNING @ Fri, 05 Jul 2019 15:03:56: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:03:56: #2 You may need to consider one of the other alternative d(s): 49,132,204,211,406 WARNING @ Fri, 05 Jul 2019 15:03:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:03:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:03:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:04:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:04:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:05:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:05:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:05:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:05:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.20_summits.bed INFO @ Fri, 05 Jul 2019 15:05:31: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:05:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:05:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:05:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.10_summits.bed INFO @ Fri, 05 Jul 2019 15:05:35: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (1222 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 15:06:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:06:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:06:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333727/SRX5333727.05_summits.bed INFO @ Fri, 05 Jul 2019 15:06:04: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (2113 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。