Job ID = 2590461 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,219,213 reads read : 14,438,426 reads written : 7,219,213 reads 0-length : 7,219,213 spots read : 7,208,554 reads read : 14,417,108 reads written : 7,208,554 reads 0-length : 7,208,554 spots read : 7,233,925 reads read : 14,467,850 reads written : 7,233,925 reads 0-length : 7,233,925 spots read : 7,274,964 reads read : 14,549,928 reads written : 7,274,964 reads 0-length : 7,274,964 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: 00:10:13 28936656 reads; of these: 28936656 (100.00%) were unpaired; of these: 862362 (2.98%) aligned 0 times 22410336 (77.45%) aligned exactly 1 time 5663958 (19.57%) aligned >1 times 97.02% overall alignment rate Time searching: 00:10:13 Overall time: 00:10:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3745628 / 28074294 = 0.1334 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 @ Mon, 12 Aug 2019 22:11:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 22:11:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:11:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:11:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 22:11:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:11:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:11:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 22:11:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:11:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:11:39: 1000000 INFO @ Mon, 12 Aug 2019 22:11:40: 1000000 INFO @ Mon, 12 Aug 2019 22:11:42: 1000000 INFO @ Mon, 12 Aug 2019 22:11:47: 2000000 INFO @ Mon, 12 Aug 2019 22:11:48: 2000000 INFO @ Mon, 12 Aug 2019 22:11:50: 2000000 INFO @ Mon, 12 Aug 2019 22:11:54: 3000000 INFO @ Mon, 12 Aug 2019 22:11:55: 3000000 INFO @ Mon, 12 Aug 2019 22:11:59: 3000000 INFO @ Mon, 12 Aug 2019 22:12:01: 4000000 INFO @ Mon, 12 Aug 2019 22:12:03: 4000000 INFO @ Mon, 12 Aug 2019 22:12:07: 4000000 INFO @ Mon, 12 Aug 2019 22:12:09: 5000000 INFO @ Mon, 12 Aug 2019 22:12:10: 5000000 INFO @ Mon, 12 Aug 2019 22:12:15: 5000000 INFO @ Mon, 12 Aug 2019 22:12:16: 6000000 INFO @ Mon, 12 Aug 2019 22:12:18: 6000000 INFO @ Mon, 12 Aug 2019 22:12:23: 6000000 INFO @ Mon, 12 Aug 2019 22:12:23: 7000000 INFO @ Mon, 12 Aug 2019 22:12:26: 7000000 INFO @ Mon, 12 Aug 2019 22:12:31: 8000000 INFO @ Mon, 12 Aug 2019 22:12:32: 7000000 INFO @ Mon, 12 Aug 2019 22:12:33: 8000000 INFO @ Mon, 12 Aug 2019 22:12:38: 9000000 INFO @ Mon, 12 Aug 2019 22:12:40: 8000000 INFO @ Mon, 12 Aug 2019 22:12:41: 9000000 INFO @ Mon, 12 Aug 2019 22:12:45: 10000000 INFO @ Mon, 12 Aug 2019 22:12:48: 9000000 INFO @ Mon, 12 Aug 2019 22:12:48: 10000000 INFO @ Mon, 12 Aug 2019 22:12:52: 11000000 INFO @ Mon, 12 Aug 2019 22:12:56: 11000000 INFO @ Mon, 12 Aug 2019 22:12:56: 10000000 INFO @ Mon, 12 Aug 2019 22:13:00: 12000000 INFO @ Mon, 12 Aug 2019 22:13:03: 12000000 INFO @ Mon, 12 Aug 2019 22:13:04: 11000000 INFO @ Mon, 12 Aug 2019 22:13:07: 13000000 INFO @ Mon, 12 Aug 2019 22:13:11: 13000000 INFO @ Mon, 12 Aug 2019 22:13:12: 12000000 INFO @ Mon, 12 Aug 2019 22:13:14: 14000000 INFO @ Mon, 12 Aug 2019 22:13:18: 14000000 INFO @ Mon, 12 Aug 2019 22:13:20: 13000000 INFO @ Mon, 12 Aug 2019 22:13:21: 15000000 INFO @ Mon, 12 Aug 2019 22:13:26: 15000000 INFO @ Mon, 12 Aug 2019 22:13:28: 14000000 INFO @ Mon, 12 Aug 2019 22:13:28: 16000000 INFO @ Mon, 12 Aug 2019 22:13:33: 16000000 INFO @ Mon, 12 Aug 2019 22:13:36: 17000000 INFO @ Mon, 12 Aug 2019 22:13:36: 15000000 INFO @ Mon, 12 Aug 2019 22:13:41: 17000000 INFO @ Mon, 12 Aug 2019 22:13:43: 18000000 INFO @ Mon, 12 Aug 2019 22:13:44: 16000000 INFO @ Mon, 12 Aug 2019 22:13:48: 18000000 INFO @ Mon, 12 Aug 2019 22:13:50: 19000000 INFO @ Mon, 12 Aug 2019 22:13:52: 17000000 INFO @ Mon, 12 Aug 2019 22:13:56: 19000000 INFO @ Mon, 12 Aug 2019 22:13:57: 20000000 INFO @ Mon, 12 Aug 2019 22:14:00: 18000000 INFO @ Mon, 12 Aug 2019 22:14:03: 20000000 INFO @ Mon, 12 Aug 2019 22:14:04: 21000000 INFO @ Mon, 12 Aug 2019 22:14:08: 19000000 INFO @ Mon, 12 Aug 2019 22:14:11: 21000000 INFO @ Mon, 12 Aug 2019 22:14:11: 22000000 INFO @ Mon, 12 Aug 2019 22:14:16: 20000000 INFO @ Mon, 12 Aug 2019 22:14:18: 22000000 INFO @ Mon, 12 Aug 2019 22:14:19: 23000000 INFO @ Mon, 12 Aug 2019 22:14:24: 21000000 INFO @ Mon, 12 Aug 2019 22:14:26: 23000000 INFO @ Mon, 12 Aug 2019 22:14:27: 24000000 INFO @ Mon, 12 Aug 2019 22:14:29: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:14:29: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:14:29: #1 total tags in treatment: 24328666 INFO @ Mon, 12 Aug 2019 22:14:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:14:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:14:30: #1 tags after filtering in treatment: 24328666 INFO @ Mon, 12 Aug 2019 22:14:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:14:30: #1 finished! INFO @ Mon, 12 Aug 2019 22:14:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:14:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:14:32: #2 number of paired peaks: 179 WARNING @ Mon, 12 Aug 2019 22:14:32: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Mon, 12 Aug 2019 22:14:32: start model_add_line... INFO @ Mon, 12 Aug 2019 22:14:32: start X-correlation... INFO @ Mon, 12 Aug 2019 22:14:32: end of X-cor INFO @ Mon, 12 Aug 2019 22:14:32: #2 finished! INFO @ Mon, 12 Aug 2019 22:14:32: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 22:14:32: #2 alternative fragment length(s) may be 4,48 bps INFO @ Mon, 12 Aug 2019 22:14:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.05_model.r WARNING @ Mon, 12 Aug 2019 22:14:32: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:14:32: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Mon, 12 Aug 2019 22:14:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:14:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:14:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:14:33: 22000000 INFO @ Mon, 12 Aug 2019 22:14:33: 24000000 INFO @ Mon, 12 Aug 2019 22:14:36: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:14:36: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:14:36: #1 total tags in treatment: 24328666 INFO @ Mon, 12 Aug 2019 22:14:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:14:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:14:36: #1 tags after filtering in treatment: 24328666 INFO @ Mon, 12 Aug 2019 22:14:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:14:36: #1 finished! INFO @ Mon, 12 Aug 2019 22:14:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:14:38: #2 number of paired peaks: 179 WARNING @ Mon, 12 Aug 2019 22:14:38: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Mon, 12 Aug 2019 22:14:38: start model_add_line... INFO @ Mon, 12 Aug 2019 22:14:39: start X-correlation... INFO @ Mon, 12 Aug 2019 22:14:39: end of X-cor INFO @ Mon, 12 Aug 2019 22:14:39: #2 finished! INFO @ Mon, 12 Aug 2019 22:14:39: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 22:14:39: #2 alternative fragment length(s) may be 4,48 bps INFO @ Mon, 12 Aug 2019 22:14:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.10_model.r WARNING @ Mon, 12 Aug 2019 22:14:39: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:14:39: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Mon, 12 Aug 2019 22:14:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:14:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:14:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:14:41: 23000000 INFO @ Mon, 12 Aug 2019 22:14:49: 24000000 INFO @ Mon, 12 Aug 2019 22:14:52: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:14:52: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:14:52: #1 total tags in treatment: 24328666 INFO @ Mon, 12 Aug 2019 22:14:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:14:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:14:52: #1 tags after filtering in treatment: 24328666 INFO @ Mon, 12 Aug 2019 22:14:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:14:52: #1 finished! INFO @ Mon, 12 Aug 2019 22:14:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:14:54: #2 number of paired peaks: 179 WARNING @ Mon, 12 Aug 2019 22:14:54: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Mon, 12 Aug 2019 22:14:54: start model_add_line... INFO @ Mon, 12 Aug 2019 22:14:54: start X-correlation... INFO @ Mon, 12 Aug 2019 22:14:54: end of X-cor INFO @ Mon, 12 Aug 2019 22:14:54: #2 finished! INFO @ Mon, 12 Aug 2019 22:14:54: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 22:14:54: #2 alternative fragment length(s) may be 4,48 bps INFO @ Mon, 12 Aug 2019 22:14:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.20_model.r WARNING @ Mon, 12 Aug 2019 22:14:55: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:14:55: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Mon, 12 Aug 2019 22:14:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:14:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:14:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:15:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:15:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:15:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.05_summits.bed INFO @ Mon, 12 Aug 2019 22:16:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2895 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.10_summits.bed INFO @ Mon, 12 Aug 2019 22:16:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1200 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:16:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:16:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:16:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981692/SRX3981692.20_summits.bed INFO @ Mon, 12 Aug 2019 22:16:23: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (551 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。