Job ID = 2590349 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,243,305 reads read : 26,486,610 reads written : 13,243,305 reads 0-length : 13,243,305 spots read : 13,031,080 reads read : 26,062,160 reads written : 13,031,080 reads 0-length : 13,031,080 spots read : 13,220,701 reads read : 26,441,402 reads written : 13,220,701 reads 0-length : 13,220,701 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: 00:11:30 39495086 reads; of these: 39495086 (100.00%) were unpaired; of these: 1172763 (2.97%) aligned 0 times 30008614 (75.98%) aligned exactly 1 time 8313709 (21.05%) aligned >1 times 97.03% overall alignment rate Time searching: 00:11:30 Overall time: 00:11:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 5584893 / 38322323 = 0.1457 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 21:28:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.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 21:28:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:28:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.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 21:28:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:28:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:28:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.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 21:28:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:28:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:28:09: 1000000 INFO @ Mon, 12 Aug 2019 21:28:10: 1000000 INFO @ Mon, 12 Aug 2019 21:28:14: 1000000 INFO @ Mon, 12 Aug 2019 21:28:17: 2000000 INFO @ Mon, 12 Aug 2019 21:28:18: 2000000 INFO @ Mon, 12 Aug 2019 21:28:25: 2000000 INFO @ Mon, 12 Aug 2019 21:28:25: 3000000 INFO @ Mon, 12 Aug 2019 21:28:26: 3000000 INFO @ Mon, 12 Aug 2019 21:28:33: 4000000 INFO @ Mon, 12 Aug 2019 21:28:34: 4000000 INFO @ Mon, 12 Aug 2019 21:28:36: 3000000 INFO @ Mon, 12 Aug 2019 21:28:41: 5000000 INFO @ Mon, 12 Aug 2019 21:28:41: 5000000 INFO @ Mon, 12 Aug 2019 21:28:46: 4000000 INFO @ Mon, 12 Aug 2019 21:28:49: 6000000 INFO @ Mon, 12 Aug 2019 21:28:49: 6000000 INFO @ Mon, 12 Aug 2019 21:28:57: 7000000 INFO @ Mon, 12 Aug 2019 21:28:57: 5000000 INFO @ Mon, 12 Aug 2019 21:28:57: 7000000 INFO @ Mon, 12 Aug 2019 21:29:05: 8000000 INFO @ Mon, 12 Aug 2019 21:29:05: 8000000 INFO @ Mon, 12 Aug 2019 21:29:08: 6000000 INFO @ Mon, 12 Aug 2019 21:29:13: 9000000 INFO @ Mon, 12 Aug 2019 21:29:13: 9000000 INFO @ Mon, 12 Aug 2019 21:29:19: 7000000 INFO @ Mon, 12 Aug 2019 21:29:21: 10000000 INFO @ Mon, 12 Aug 2019 21:29:21: 10000000 INFO @ Mon, 12 Aug 2019 21:29:29: 11000000 INFO @ Mon, 12 Aug 2019 21:29:29: 11000000 INFO @ Mon, 12 Aug 2019 21:29:29: 8000000 INFO @ Mon, 12 Aug 2019 21:29:37: 12000000 INFO @ Mon, 12 Aug 2019 21:29:37: 12000000 INFO @ Mon, 12 Aug 2019 21:29:40: 9000000 INFO @ Mon, 12 Aug 2019 21:29:44: 13000000 INFO @ Mon, 12 Aug 2019 21:29:45: 13000000 INFO @ Mon, 12 Aug 2019 21:29:50: 10000000 INFO @ Mon, 12 Aug 2019 21:29:52: 14000000 INFO @ Mon, 12 Aug 2019 21:29:53: 14000000 INFO @ Mon, 12 Aug 2019 21:30:00: 15000000 INFO @ Mon, 12 Aug 2019 21:30:01: 15000000 INFO @ Mon, 12 Aug 2019 21:30:01: 11000000 INFO @ Mon, 12 Aug 2019 21:30:08: 16000000 INFO @ Mon, 12 Aug 2019 21:30:08: 16000000 INFO @ Mon, 12 Aug 2019 21:30:11: 12000000 INFO @ Mon, 12 Aug 2019 21:30:16: 17000000 INFO @ Mon, 12 Aug 2019 21:30:16: 17000000 INFO @ Mon, 12 Aug 2019 21:30:22: 13000000 INFO @ Mon, 12 Aug 2019 21:30:23: 18000000 INFO @ Mon, 12 Aug 2019 21:30:24: 18000000 INFO @ Mon, 12 Aug 2019 21:30:31: 19000000 INFO @ Mon, 12 Aug 2019 21:30:31: 19000000 INFO @ Mon, 12 Aug 2019 21:30:32: 14000000 INFO @ Mon, 12 Aug 2019 21:30:39: 20000000 INFO @ Mon, 12 Aug 2019 21:30:39: 20000000 INFO @ Mon, 12 Aug 2019 21:30:43: 15000000 INFO @ Mon, 12 Aug 2019 21:30:46: 21000000 INFO @ Mon, 12 Aug 2019 21:30:47: 21000000 INFO @ Mon, 12 Aug 2019 21:30:53: 16000000 INFO @ Mon, 12 Aug 2019 21:30:54: 22000000 INFO @ Mon, 12 Aug 2019 21:30:55: 22000000 INFO @ Mon, 12 Aug 2019 21:31:02: 23000000 INFO @ Mon, 12 Aug 2019 21:31:02: 23000000 INFO @ Mon, 12 Aug 2019 21:31:03: 17000000 INFO @ Mon, 12 Aug 2019 21:31:09: 24000000 INFO @ Mon, 12 Aug 2019 21:31:10: 24000000 INFO @ Mon, 12 Aug 2019 21:31:13: 18000000 INFO @ Mon, 12 Aug 2019 21:31:17: 25000000 INFO @ Mon, 12 Aug 2019 21:31:18: 25000000 INFO @ Mon, 12 Aug 2019 21:31:23: 19000000 INFO @ Mon, 12 Aug 2019 21:31:25: 26000000 INFO @ Mon, 12 Aug 2019 21:31:26: 26000000 INFO @ Mon, 12 Aug 2019 21:31:33: 27000000 INFO @ Mon, 12 Aug 2019 21:31:34: 20000000 INFO @ Mon, 12 Aug 2019 21:31:34: 27000000 INFO @ Mon, 12 Aug 2019 21:31:41: 28000000 INFO @ Mon, 12 Aug 2019 21:31:42: 28000000 INFO @ Mon, 12 Aug 2019 21:31:44: 21000000 INFO @ Mon, 12 Aug 2019 21:31:49: 29000000 INFO @ Mon, 12 Aug 2019 21:31:50: 29000000 INFO @ Mon, 12 Aug 2019 21:31:54: 22000000 INFO @ Mon, 12 Aug 2019 21:31:57: 30000000 INFO @ Mon, 12 Aug 2019 21:31:57: 30000000 INFO @ Mon, 12 Aug 2019 21:32:03: 23000000 INFO @ Mon, 12 Aug 2019 21:32:05: 31000000 INFO @ Mon, 12 Aug 2019 21:32:05: 31000000 INFO @ Mon, 12 Aug 2019 21:32:12: 24000000 INFO @ Mon, 12 Aug 2019 21:32:13: 32000000 INFO @ Mon, 12 Aug 2019 21:32:14: 32000000 INFO @ Mon, 12 Aug 2019 21:32:19: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:32:19: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:32:19: #1 total tags in treatment: 32737430 INFO @ Mon, 12 Aug 2019 21:32:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:32:19: #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 21:32:20: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:32:20: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:32:20: #1 total tags in treatment: 32737430 INFO @ Mon, 12 Aug 2019 21:32:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:32:20: #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 21:32:20: #1 tags after filtering in treatment: 32737430 INFO @ Mon, 12 Aug 2019 21:32:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:32:20: #1 finished! INFO @ Mon, 12 Aug 2019 21:32:20: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:32:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:32:20: #1 tags after filtering in treatment: 32737430 INFO @ Mon, 12 Aug 2019 21:32:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:32:20: #1 finished! INFO @ Mon, 12 Aug 2019 21:32:20: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:32:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:32:22: 25000000 INFO @ Mon, 12 Aug 2019 21:32:22: #2 number of paired peaks: 135 WARNING @ Mon, 12 Aug 2019 21:32:22: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Mon, 12 Aug 2019 21:32:22: start model_add_line... INFO @ Mon, 12 Aug 2019 21:32:23: start X-correlation... INFO @ Mon, 12 Aug 2019 21:32:23: end of X-cor INFO @ Mon, 12 Aug 2019 21:32:23: #2 finished! INFO @ Mon, 12 Aug 2019 21:32:23: #2 predicted fragment length is 76 bps INFO @ Mon, 12 Aug 2019 21:32:23: #2 alternative fragment length(s) may be 2,42,65,69,76 bps INFO @ Mon, 12 Aug 2019 21:32:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.10_model.r WARNING @ Mon, 12 Aug 2019 21:32:23: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:32:23: #2 You may need to consider one of the other alternative d(s): 2,42,65,69,76 WARNING @ Mon, 12 Aug 2019 21:32:23: #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 21:32:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:32:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:32:23: #2 number of paired peaks: 135 WARNING @ Mon, 12 Aug 2019 21:32:23: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Mon, 12 Aug 2019 21:32:23: start model_add_line... INFO @ Mon, 12 Aug 2019 21:32:23: start X-correlation... INFO @ Mon, 12 Aug 2019 21:32:23: end of X-cor INFO @ Mon, 12 Aug 2019 21:32:23: #2 finished! INFO @ Mon, 12 Aug 2019 21:32:23: #2 predicted fragment length is 76 bps INFO @ Mon, 12 Aug 2019 21:32:23: #2 alternative fragment length(s) may be 2,42,65,69,76 bps INFO @ Mon, 12 Aug 2019 21:32:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.05_model.r WARNING @ Mon, 12 Aug 2019 21:32:23: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:32:23: #2 You may need to consider one of the other alternative d(s): 2,42,65,69,76 WARNING @ Mon, 12 Aug 2019 21:32:23: #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 21:32:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:32:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:32:31: 26000000 INFO @ Mon, 12 Aug 2019 21:32:40: 27000000 INFO @ Mon, 12 Aug 2019 21:32:50: 28000000 INFO @ Mon, 12 Aug 2019 21:32:58: 29000000 INFO @ Mon, 12 Aug 2019 21:33:07: 30000000 INFO @ Mon, 12 Aug 2019 21:33:16: 31000000 INFO @ Mon, 12 Aug 2019 21:33:26: 32000000 INFO @ Mon, 12 Aug 2019 21:33:32: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:33:32: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:33:32: #1 total tags in treatment: 32737430 INFO @ Mon, 12 Aug 2019 21:33:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:33:32: #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 21:33:33: #1 tags after filtering in treatment: 32737430 INFO @ Mon, 12 Aug 2019 21:33:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:33:33: #1 finished! INFO @ Mon, 12 Aug 2019 21:33:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:33:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:33:36: #2 number of paired peaks: 135 WARNING @ Mon, 12 Aug 2019 21:33:36: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Mon, 12 Aug 2019 21:33:36: start model_add_line... INFO @ Mon, 12 Aug 2019 21:33:36: start X-correlation... INFO @ Mon, 12 Aug 2019 21:33:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:33:36: end of X-cor INFO @ Mon, 12 Aug 2019 21:33:36: #2 finished! INFO @ Mon, 12 Aug 2019 21:33:36: #2 predicted fragment length is 76 bps INFO @ Mon, 12 Aug 2019 21:33:36: #2 alternative fragment length(s) may be 2,42,65,69,76 bps INFO @ Mon, 12 Aug 2019 21:33:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.20_model.r WARNING @ Mon, 12 Aug 2019 21:33:36: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:33:36: #2 You may need to consider one of the other alternative d(s): 2,42,65,69,76 WARNING @ Mon, 12 Aug 2019 21:33:36: #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 21:33:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:33:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:33:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:34:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:34:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:34:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.10_summits.bed INFO @ Mon, 12 Aug 2019 21:34:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3005 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:34:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:34:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:34:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.05_summits.bed INFO @ Mon, 12 Aug 2019 21:34:12: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8222 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:34:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:35:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:35:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981623/SRX3981623.20_summits.bed INFO @ Mon, 12 Aug 2019 21:35:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (541 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。