Job ID = 2590369 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,675,950 reads read : 27,351,900 reads written : 13,675,950 reads 0-length : 13,675,950 spots read : 13,570,346 reads read : 27,140,692 reads written : 13,570,346 reads 0-length : 13,570,346 spots read : 13,547,731 reads read : 27,095,462 reads written : 13,547,731 reads 0-length : 13,547,731 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: 00:11:04 40794027 reads; of these: 40794027 (100.00%) were unpaired; of these: 1047468 (2.57%) aligned 0 times 33548255 (82.24%) aligned exactly 1 time 6198304 (15.19%) aligned >1 times 97.43% overall alignment rate Time searching: 00:11:04 Overall time: 00:11:04 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] 8711947 / 39746559 = 0.2192 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 21:36:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.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 21:36:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:36:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.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 21:36:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:36:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:36:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.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 21:36:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:36:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:36:30: 1000000 INFO @ Mon, 12 Aug 2019 21:36:30: 1000000 INFO @ Mon, 12 Aug 2019 21:36:31: 1000000 INFO @ Mon, 12 Aug 2019 21:36:38: 2000000 INFO @ Mon, 12 Aug 2019 21:36:39: 2000000 INFO @ Mon, 12 Aug 2019 21:36:40: 2000000 INFO @ Mon, 12 Aug 2019 21:36:47: 3000000 INFO @ Mon, 12 Aug 2019 21:36:49: 3000000 INFO @ Mon, 12 Aug 2019 21:36:49: 3000000 INFO @ Mon, 12 Aug 2019 21:36:56: 4000000 INFO @ Mon, 12 Aug 2019 21:36:58: 4000000 INFO @ Mon, 12 Aug 2019 21:36:58: 4000000 INFO @ Mon, 12 Aug 2019 21:37:05: 5000000 INFO @ Mon, 12 Aug 2019 21:37:06: 5000000 INFO @ Mon, 12 Aug 2019 21:37:07: 5000000 INFO @ Mon, 12 Aug 2019 21:37:14: 6000000 INFO @ Mon, 12 Aug 2019 21:37:15: 6000000 INFO @ Mon, 12 Aug 2019 21:37:16: 6000000 INFO @ Mon, 12 Aug 2019 21:37:22: 7000000 INFO @ Mon, 12 Aug 2019 21:37:24: 7000000 INFO @ Mon, 12 Aug 2019 21:37:25: 7000000 INFO @ Mon, 12 Aug 2019 21:37:31: 8000000 INFO @ Mon, 12 Aug 2019 21:37:33: 8000000 INFO @ Mon, 12 Aug 2019 21:37:34: 8000000 INFO @ Mon, 12 Aug 2019 21:37:40: 9000000 INFO @ Mon, 12 Aug 2019 21:37:42: 9000000 INFO @ Mon, 12 Aug 2019 21:37:43: 9000000 INFO @ Mon, 12 Aug 2019 21:37:49: 10000000 INFO @ Mon, 12 Aug 2019 21:37:50: 10000000 INFO @ Mon, 12 Aug 2019 21:37:52: 10000000 INFO @ Mon, 12 Aug 2019 21:37:58: 11000000 INFO @ Mon, 12 Aug 2019 21:37:59: 11000000 INFO @ Mon, 12 Aug 2019 21:38:01: 11000000 INFO @ Mon, 12 Aug 2019 21:38:06: 12000000 INFO @ Mon, 12 Aug 2019 21:38:08: 12000000 INFO @ Mon, 12 Aug 2019 21:38:10: 12000000 INFO @ Mon, 12 Aug 2019 21:38:15: 13000000 INFO @ Mon, 12 Aug 2019 21:38:17: 13000000 INFO @ Mon, 12 Aug 2019 21:38:20: 13000000 INFO @ Mon, 12 Aug 2019 21:38:24: 14000000 INFO @ Mon, 12 Aug 2019 21:38:25: 14000000 INFO @ Mon, 12 Aug 2019 21:38:29: 14000000 INFO @ Mon, 12 Aug 2019 21:38:33: 15000000 INFO @ Mon, 12 Aug 2019 21:38:34: 15000000 INFO @ Mon, 12 Aug 2019 21:38:38: 15000000 INFO @ Mon, 12 Aug 2019 21:38:41: 16000000 INFO @ Mon, 12 Aug 2019 21:38:43: 16000000 INFO @ Mon, 12 Aug 2019 21:38:47: 16000000 INFO @ Mon, 12 Aug 2019 21:38:50: 17000000 INFO @ Mon, 12 Aug 2019 21:38:52: 17000000 INFO @ Mon, 12 Aug 2019 21:38:56: 17000000 INFO @ Mon, 12 Aug 2019 21:38:59: 18000000 INFO @ Mon, 12 Aug 2019 21:39:00: 18000000 INFO @ Mon, 12 Aug 2019 21:39:05: 18000000 INFO @ Mon, 12 Aug 2019 21:39:08: 19000000 INFO @ Mon, 12 Aug 2019 21:39:09: 19000000 INFO @ Mon, 12 Aug 2019 21:39:14: 19000000 INFO @ Mon, 12 Aug 2019 21:39:16: 20000000 INFO @ Mon, 12 Aug 2019 21:39:18: 20000000 INFO @ Mon, 12 Aug 2019 21:39:23: 20000000 INFO @ Mon, 12 Aug 2019 21:39:25: 21000000 INFO @ Mon, 12 Aug 2019 21:39:26: 21000000 INFO @ Mon, 12 Aug 2019 21:39:32: 21000000 INFO @ Mon, 12 Aug 2019 21:39:34: 22000000 INFO @ Mon, 12 Aug 2019 21:39:35: 22000000 INFO @ Mon, 12 Aug 2019 21:39:41: 22000000 INFO @ Mon, 12 Aug 2019 21:39:43: 23000000 INFO @ Mon, 12 Aug 2019 21:39:44: 23000000 INFO @ Mon, 12 Aug 2019 21:39:51: 23000000 INFO @ Mon, 12 Aug 2019 21:39:52: 24000000 INFO @ Mon, 12 Aug 2019 21:39:53: 24000000 INFO @ Mon, 12 Aug 2019 21:40:00: 24000000 INFO @ Mon, 12 Aug 2019 21:40:00: 25000000 INFO @ Mon, 12 Aug 2019 21:40:02: 25000000 INFO @ Mon, 12 Aug 2019 21:40:09: 25000000 INFO @ Mon, 12 Aug 2019 21:40:09: 26000000 INFO @ Mon, 12 Aug 2019 21:40:11: 26000000 INFO @ Mon, 12 Aug 2019 21:40:18: 26000000 INFO @ Mon, 12 Aug 2019 21:40:20: 27000000 INFO @ Mon, 12 Aug 2019 21:40:21: 27000000 INFO @ Mon, 12 Aug 2019 21:40:27: 27000000 INFO @ Mon, 12 Aug 2019 21:40:28: 28000000 INFO @ Mon, 12 Aug 2019 21:40:29: 28000000 INFO @ Mon, 12 Aug 2019 21:40:35: 29000000 INFO @ Mon, 12 Aug 2019 21:40:36: 29000000 INFO @ Mon, 12 Aug 2019 21:40:36: 28000000 INFO @ Mon, 12 Aug 2019 21:40:43: 30000000 INFO @ Mon, 12 Aug 2019 21:40:43: 30000000 INFO @ Mon, 12 Aug 2019 21:40:46: 29000000 INFO @ Mon, 12 Aug 2019 21:40:50: 31000000 INFO @ Mon, 12 Aug 2019 21:40:50: 31000000 INFO @ Mon, 12 Aug 2019 21:40:50: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:40:50: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:40:50: #1 total tags in treatment: 31034612 INFO @ Mon, 12 Aug 2019 21:40:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:40:50: #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 21:40:51: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:40:51: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:40:51: #1 total tags in treatment: 31034612 INFO @ Mon, 12 Aug 2019 21:40:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:40:51: #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 21:40:51: #1 tags after filtering in treatment: 31034612 INFO @ Mon, 12 Aug 2019 21:40:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:40:51: #1 finished! INFO @ Mon, 12 Aug 2019 21:40:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:40:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:40:51: #1 tags after filtering in treatment: 31034612 INFO @ Mon, 12 Aug 2019 21:40:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:40:51: #1 finished! INFO @ Mon, 12 Aug 2019 21:40:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:40:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:40:54: #2 number of paired peaks: 1030 INFO @ Mon, 12 Aug 2019 21:40:54: start model_add_line... INFO @ Mon, 12 Aug 2019 21:40:54: start X-correlation... INFO @ Mon, 12 Aug 2019 21:40:54: #2 number of paired peaks: 1030 INFO @ Mon, 12 Aug 2019 21:40:54: start model_add_line... INFO @ Mon, 12 Aug 2019 21:40:54: end of X-cor INFO @ Mon, 12 Aug 2019 21:40:54: #2 finished! INFO @ Mon, 12 Aug 2019 21:40:54: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 21:40:54: #2 alternative fragment length(s) may be 2,50,72,96 bps INFO @ Mon, 12 Aug 2019 21:40:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.10_model.r WARNING @ Mon, 12 Aug 2019 21:40:54: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:40:54: #2 You may need to consider one of the other alternative d(s): 2,50,72,96 WARNING @ Mon, 12 Aug 2019 21:40:54: #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 21:40:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:40:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:40:54: start X-correlation... INFO @ Mon, 12 Aug 2019 21:40:54: end of X-cor INFO @ Mon, 12 Aug 2019 21:40:54: #2 finished! INFO @ Mon, 12 Aug 2019 21:40:54: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 21:40:54: #2 alternative fragment length(s) may be 2,50,72,96 bps INFO @ Mon, 12 Aug 2019 21:40:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.20_model.r WARNING @ Mon, 12 Aug 2019 21:40:54: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:40:54: #2 You may need to consider one of the other alternative d(s): 2,50,72,96 WARNING @ Mon, 12 Aug 2019 21:40:54: #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 21:40:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:40:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:40:55: 30000000 INFO @ Mon, 12 Aug 2019 21:41:04: 31000000 INFO @ Mon, 12 Aug 2019 21:41:04: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:41:04: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:41:04: #1 total tags in treatment: 31034612 INFO @ Mon, 12 Aug 2019 21:41:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:41:04: #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 21:41:05: #1 tags after filtering in treatment: 31034612 INFO @ Mon, 12 Aug 2019 21:41:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:41:05: #1 finished! INFO @ Mon, 12 Aug 2019 21:41:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:41:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:41:08: #2 number of paired peaks: 1030 INFO @ Mon, 12 Aug 2019 21:41:08: start model_add_line... INFO @ Mon, 12 Aug 2019 21:41:08: start X-correlation... INFO @ Mon, 12 Aug 2019 21:41:08: end of X-cor INFO @ Mon, 12 Aug 2019 21:41:08: #2 finished! INFO @ Mon, 12 Aug 2019 21:41:08: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 21:41:08: #2 alternative fragment length(s) may be 2,50,72,96 bps INFO @ Mon, 12 Aug 2019 21:41:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.05_model.r WARNING @ Mon, 12 Aug 2019 21:41:08: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 21:41:08: #2 You may need to consider one of the other alternative d(s): 2,50,72,96 WARNING @ Mon, 12 Aug 2019 21:41:08: #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 21:41:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:41:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:41:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:41:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:42:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:42:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:42:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:42:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.10_summits.bed INFO @ Mon, 12 Aug 2019 21:42:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:42:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:42:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:42:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.20_summits.bed INFO @ Mon, 12 Aug 2019 21:42:16: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:42:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:42:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:42:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981641/SRX3981641.05_summits.bed INFO @ Mon, 12 Aug 2019 21:42:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。