Job ID = 2590378 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,927,289 reads read : 27,854,578 reads written : 13,927,289 reads 0-length : 13,927,289 spots read : 13,812,650 reads read : 27,625,300 reads written : 13,812,650 reads 0-length : 13,812,650 spots read : 13,796,604 reads read : 27,593,208 reads written : 13,796,604 reads 0-length : 13,796,604 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: 00:11:00 41536543 reads; of these: 41536543 (100.00%) were unpaired; of these: 1296002 (3.12%) aligned 0 times 34374035 (82.76%) aligned exactly 1 time 5866506 (14.12%) aligned >1 times 96.88% overall alignment rate Time searching: 00:11:00 Overall time: 00:11:00 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 20 files... [bam_rmdupse_core] 9106218 / 40240541 = 0.2263 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 21:40:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.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 21:40:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:40:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:40:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.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 21:40:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:40:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.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 21:40:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:40:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:40:16: 1000000 INFO @ Mon, 12 Aug 2019 21:40:17: 1000000 INFO @ Mon, 12 Aug 2019 21:40:18: 1000000 INFO @ Mon, 12 Aug 2019 21:40:23: 2000000 INFO @ Mon, 12 Aug 2019 21:40:24: 2000000 INFO @ Mon, 12 Aug 2019 21:40:25: 2000000 INFO @ Mon, 12 Aug 2019 21:40:30: 3000000 INFO @ Mon, 12 Aug 2019 21:40:31: 3000000 INFO @ Mon, 12 Aug 2019 21:40:32: 3000000 INFO @ Mon, 12 Aug 2019 21:40:37: 4000000 INFO @ Mon, 12 Aug 2019 21:40:38: 4000000 INFO @ Mon, 12 Aug 2019 21:40:39: 4000000 INFO @ Mon, 12 Aug 2019 21:40:44: 5000000 INFO @ Mon, 12 Aug 2019 21:40:46: 5000000 INFO @ Mon, 12 Aug 2019 21:40:46: 5000000 INFO @ Mon, 12 Aug 2019 21:40:51: 6000000 INFO @ Mon, 12 Aug 2019 21:40:53: 6000000 INFO @ Mon, 12 Aug 2019 21:40:53: 6000000 INFO @ Mon, 12 Aug 2019 21:40:58: 7000000 INFO @ Mon, 12 Aug 2019 21:41:00: 7000000 INFO @ Mon, 12 Aug 2019 21:41:01: 7000000 INFO @ Mon, 12 Aug 2019 21:41:05: 8000000 INFO @ Mon, 12 Aug 2019 21:41:07: 8000000 INFO @ Mon, 12 Aug 2019 21:41:08: 8000000 INFO @ Mon, 12 Aug 2019 21:41:12: 9000000 INFO @ Mon, 12 Aug 2019 21:41:14: 9000000 INFO @ Mon, 12 Aug 2019 21:41:15: 9000000 INFO @ Mon, 12 Aug 2019 21:41:19: 10000000 INFO @ Mon, 12 Aug 2019 21:41:21: 10000000 INFO @ Mon, 12 Aug 2019 21:41:22: 10000000 INFO @ Mon, 12 Aug 2019 21:41:26: 11000000 INFO @ Mon, 12 Aug 2019 21:41:28: 11000000 INFO @ Mon, 12 Aug 2019 21:41:29: 11000000 INFO @ Mon, 12 Aug 2019 21:41:33: 12000000 INFO @ Mon, 12 Aug 2019 21:41:36: 12000000 INFO @ Mon, 12 Aug 2019 21:41:36: 12000000 INFO @ Mon, 12 Aug 2019 21:41:40: 13000000 INFO @ Mon, 12 Aug 2019 21:41:43: 13000000 INFO @ Mon, 12 Aug 2019 21:41:43: 13000000 INFO @ Mon, 12 Aug 2019 21:41:47: 14000000 INFO @ Mon, 12 Aug 2019 21:41:50: 14000000 INFO @ Mon, 12 Aug 2019 21:41:50: 14000000 INFO @ Mon, 12 Aug 2019 21:41:54: 15000000 INFO @ Mon, 12 Aug 2019 21:41:57: 15000000 INFO @ Mon, 12 Aug 2019 21:41:57: 15000000 INFO @ Mon, 12 Aug 2019 21:42:01: 16000000 INFO @ Mon, 12 Aug 2019 21:42:04: 16000000 INFO @ Mon, 12 Aug 2019 21:42:04: 16000000 INFO @ Mon, 12 Aug 2019 21:42:08: 17000000 INFO @ Mon, 12 Aug 2019 21:42:11: 17000000 INFO @ Mon, 12 Aug 2019 21:42:11: 17000000 INFO @ Mon, 12 Aug 2019 21:42:15: 18000000 INFO @ Mon, 12 Aug 2019 21:42:18: 18000000 INFO @ Mon, 12 Aug 2019 21:42:18: 18000000 INFO @ Mon, 12 Aug 2019 21:42:22: 19000000 INFO @ Mon, 12 Aug 2019 21:42:25: 19000000 INFO @ Mon, 12 Aug 2019 21:42:25: 19000000 INFO @ Mon, 12 Aug 2019 21:42:29: 20000000 INFO @ Mon, 12 Aug 2019 21:42:33: 20000000 INFO @ Mon, 12 Aug 2019 21:42:33: 20000000 INFO @ Mon, 12 Aug 2019 21:42:36: 21000000 INFO @ Mon, 12 Aug 2019 21:42:40: 21000000 INFO @ Mon, 12 Aug 2019 21:42:41: 21000000 INFO @ Mon, 12 Aug 2019 21:42:42: 22000000 INFO @ Mon, 12 Aug 2019 21:42:48: 22000000 INFO @ Mon, 12 Aug 2019 21:42:48: 22000000 INFO @ Mon, 12 Aug 2019 21:42:48: 23000000 INFO @ Mon, 12 Aug 2019 21:42:55: 24000000 INFO @ Mon, 12 Aug 2019 21:42:55: 23000000 INFO @ Mon, 12 Aug 2019 21:42:55: 23000000 INFO @ Mon, 12 Aug 2019 21:43:01: 25000000 INFO @ Mon, 12 Aug 2019 21:43:02: 24000000 INFO @ Mon, 12 Aug 2019 21:43:02: 24000000 INFO @ Mon, 12 Aug 2019 21:43:08: 26000000 INFO @ Mon, 12 Aug 2019 21:43:09: 25000000 INFO @ Mon, 12 Aug 2019 21:43:09: 25000000 INFO @ Mon, 12 Aug 2019 21:43:14: 27000000 INFO @ Mon, 12 Aug 2019 21:43:16: 26000000 INFO @ Mon, 12 Aug 2019 21:43:16: 26000000 INFO @ Mon, 12 Aug 2019 21:43:21: 28000000 INFO @ Mon, 12 Aug 2019 21:43:23: 27000000 INFO @ Mon, 12 Aug 2019 21:43:23: 27000000 INFO @ Mon, 12 Aug 2019 21:43:27: 29000000 INFO @ Mon, 12 Aug 2019 21:43:30: 28000000 INFO @ Mon, 12 Aug 2019 21:43:30: 28000000 INFO @ Mon, 12 Aug 2019 21:43:34: 30000000 INFO @ Mon, 12 Aug 2019 21:43:37: 29000000 INFO @ Mon, 12 Aug 2019 21:43:37: 29000000 INFO @ Mon, 12 Aug 2019 21:43:40: 31000000 INFO @ Mon, 12 Aug 2019 21:43:42: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:43:42: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:43:42: #1 total tags in treatment: 31134323 INFO @ Mon, 12 Aug 2019 21:43:42: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:43:42: #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 21:43:42: #1 tags after filtering in treatment: 31134323 INFO @ Mon, 12 Aug 2019 21:43:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:43:42: #1 finished! INFO @ Mon, 12 Aug 2019 21:43:42: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:43:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:43:44: 30000000 INFO @ Mon, 12 Aug 2019 21:43:44: 30000000 INFO @ Mon, 12 Aug 2019 21:43:45: #2 number of paired peaks: 1216 INFO @ Mon, 12 Aug 2019 21:43:45: start model_add_line... INFO @ Mon, 12 Aug 2019 21:43:45: start X-correlation... INFO @ Mon, 12 Aug 2019 21:43:45: end of X-cor INFO @ Mon, 12 Aug 2019 21:43:45: #2 finished! INFO @ Mon, 12 Aug 2019 21:43:45: #2 predicted fragment length is 96 bps INFO @ Mon, 12 Aug 2019 21:43:45: #2 alternative fragment length(s) may be 2,52,72,96 bps INFO @ Mon, 12 Aug 2019 21:43:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.05_model.r WARNING @ Mon, 12 Aug 2019 21:43:45: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:43:45: #2 You may need to consider one of the other alternative d(s): 2,52,72,96 WARNING @ Mon, 12 Aug 2019 21:43:45: #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 21:43:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:43:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:43:51: 31000000 INFO @ Mon, 12 Aug 2019 21:43:51: 31000000 INFO @ Mon, 12 Aug 2019 21:43:52: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:43:52: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:43:52: #1 total tags in treatment: 31134323 INFO @ Mon, 12 Aug 2019 21:43:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:43:52: #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 21:43:52: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:43:52: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:43:52: #1 total tags in treatment: 31134323 INFO @ Mon, 12 Aug 2019 21:43:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:43:52: #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 21:43:52: #1 tags after filtering in treatment: 31134323 INFO @ Mon, 12 Aug 2019 21:43:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:43:52: #1 finished! INFO @ Mon, 12 Aug 2019 21:43:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:43:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:43:53: #1 tags after filtering in treatment: 31134323 INFO @ Mon, 12 Aug 2019 21:43:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:43:53: #1 finished! INFO @ Mon, 12 Aug 2019 21:43:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:43:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:43:55: #2 number of paired peaks: 1216 INFO @ Mon, 12 Aug 2019 21:43:55: start model_add_line... INFO @ Mon, 12 Aug 2019 21:43:56: start X-correlation... INFO @ Mon, 12 Aug 2019 21:43:56: end of X-cor INFO @ Mon, 12 Aug 2019 21:43:56: #2 finished! INFO @ Mon, 12 Aug 2019 21:43:56: #2 predicted fragment length is 96 bps INFO @ Mon, 12 Aug 2019 21:43:56: #2 alternative fragment length(s) may be 2,52,72,96 bps INFO @ Mon, 12 Aug 2019 21:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.20_model.r WARNING @ Mon, 12 Aug 2019 21:43:56: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:43:56: #2 You may need to consider one of the other alternative d(s): 2,52,72,96 WARNING @ Mon, 12 Aug 2019 21:43:56: #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 21:43:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:43:56: #2 number of paired peaks: 1216 INFO @ Mon, 12 Aug 2019 21:43:56: start model_add_line... INFO @ Mon, 12 Aug 2019 21:43:56: start X-correlation... INFO @ Mon, 12 Aug 2019 21:43:56: end of X-cor INFO @ Mon, 12 Aug 2019 21:43:56: #2 finished! INFO @ Mon, 12 Aug 2019 21:43:56: #2 predicted fragment length is 96 bps INFO @ Mon, 12 Aug 2019 21:43:56: #2 alternative fragment length(s) may be 2,52,72,96 bps INFO @ Mon, 12 Aug 2019 21:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.10_model.r WARNING @ Mon, 12 Aug 2019 21:43:56: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:43:56: #2 You may need to consider one of the other alternative d(s): 2,52,72,96 WARNING @ Mon, 12 Aug 2019 21:43:56: #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 21:43:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:44:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:45:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:45:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:45:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:45:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:45:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.05_summits.bed INFO @ Mon, 12 Aug 2019 21:45:28: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (11204 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:45:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:45:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:45:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.20_summits.bed INFO @ Mon, 12 Aug 2019 21:45:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (959 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:45:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:45:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:45:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981648/SRX3981648.10_summits.bed INFO @ Mon, 12 Aug 2019 21:45:39: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4261 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。