Job ID = 10195031 sra ファイルのダウンロード中... Completed: 1580385K bytes transferred in 31 seconds (411137K bits/sec), in 1 file. Completed: 317051K bytes transferred in 7 seconds (354743K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 13512102 spots for /home/okishinya/chipatlas/results/rn6/SRX913500/SRR1870937.sra Written 13512102 spots total Written 51453887 spots for /home/okishinya/chipatlas/results/rn6/SRX913500/SRR1870938.sra Written 51453887 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:54:36 64965989 reads; of these: 64965989 (100.00%) were unpaired; of these: 10925527 (16.82%) aligned 0 times 40332885 (62.08%) aligned exactly 1 time 13707577 (21.10%) aligned >1 times 83.18% overall alignment rate Time searching: 00:54:42 Overall time: 00:54:42 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 24 files... [bam_rmdupse_core] 6812857 / 54040462 = 0.1261 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 @ Sat, 11 Nov 2017 07:52:59: # Command line: callpeak -t SRX913500.bam -f BAM -g 2.15e9 -n SRX913500.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913500.05 # format = BAM # ChIP-seq file = ['SRX913500.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 @ Sat, 11 Nov 2017 07:52:59: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:52:59: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:52:59: # Command line: callpeak -t SRX913500.bam -f BAM -g 2.15e9 -n SRX913500.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913500.20 # format = BAM # ChIP-seq file = ['SRX913500.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 @ Sat, 11 Nov 2017 07:52:59: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:52:59: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:52:59: # Command line: callpeak -t SRX913500.bam -f BAM -g 2.15e9 -n SRX913500.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913500.10 # format = BAM # ChIP-seq file = ['SRX913500.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 @ Sat, 11 Nov 2017 07:52:59: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:52:59: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:53:09: 1000000 INFO @ Sat, 11 Nov 2017 07:53:09: 1000000 INFO @ Sat, 11 Nov 2017 07:53:10: 1000000 INFO @ Sat, 11 Nov 2017 07:53:19: 2000000 INFO @ Sat, 11 Nov 2017 07:53:19: 2000000 INFO @ Sat, 11 Nov 2017 07:53:22: 2000000 INFO @ Sat, 11 Nov 2017 07:53:28: 3000000 INFO @ Sat, 11 Nov 2017 07:53:31: 3000000 INFO @ Sat, 11 Nov 2017 07:53:33: 3000000 INFO @ Sat, 11 Nov 2017 07:53:37: 4000000 INFO @ Sat, 11 Nov 2017 07:53:41: 4000000 INFO @ Sat, 11 Nov 2017 07:53:44: 4000000 INFO @ Sat, 11 Nov 2017 07:53:46: 5000000 INFO @ Sat, 11 Nov 2017 07:53:50: 5000000 INFO @ Sat, 11 Nov 2017 07:53:55: 5000000 INFO @ Sat, 11 Nov 2017 07:53:56: 6000000 INFO @ Sat, 11 Nov 2017 07:54:00: 6000000 INFO @ Sat, 11 Nov 2017 07:54:05: 7000000 INFO @ Sat, 11 Nov 2017 07:54:06: 6000000 INFO @ Sat, 11 Nov 2017 07:54:09: 7000000 INFO @ Sat, 11 Nov 2017 07:54:14: 8000000 INFO @ Sat, 11 Nov 2017 07:54:17: 7000000 INFO @ Sat, 11 Nov 2017 07:54:19: 8000000 INFO @ Sat, 11 Nov 2017 07:54:24: 9000000 INFO @ Sat, 11 Nov 2017 07:54:28: 9000000 INFO @ Sat, 11 Nov 2017 07:54:29: 8000000 INFO @ Sat, 11 Nov 2017 07:54:33: 10000000 INFO @ Sat, 11 Nov 2017 07:54:38: 10000000 INFO @ Sat, 11 Nov 2017 07:54:40: 9000000 INFO @ Sat, 11 Nov 2017 07:54:43: 11000000 INFO @ Sat, 11 Nov 2017 07:54:48: 11000000 INFO @ Sat, 11 Nov 2017 07:54:51: 10000000 INFO @ Sat, 11 Nov 2017 07:54:52: 12000000 INFO @ Sat, 11 Nov 2017 07:54:58: 12000000 INFO @ Sat, 11 Nov 2017 07:55:02: 13000000 INFO @ Sat, 11 Nov 2017 07:55:02: 11000000 INFO @ Sat, 11 Nov 2017 07:55:08: 13000000 INFO @ Sat, 11 Nov 2017 07:55:11: 14000000 INFO @ Sat, 11 Nov 2017 07:55:13: 12000000 INFO @ Sat, 11 Nov 2017 07:55:18: 14000000 INFO @ Sat, 11 Nov 2017 07:55:20: 15000000 INFO @ Sat, 11 Nov 2017 07:55:24: 13000000 INFO @ Sat, 11 Nov 2017 07:55:29: 15000000 INFO @ Sat, 11 Nov 2017 07:55:30: 16000000 INFO @ Sat, 11 Nov 2017 07:55:36: 14000000 INFO @ Sat, 11 Nov 2017 07:55:39: 17000000 INFO @ Sat, 11 Nov 2017 07:55:41: 16000000 INFO @ Sat, 11 Nov 2017 07:55:47: 15000000 INFO @ Sat, 11 Nov 2017 07:55:48: 18000000 INFO @ Sat, 11 Nov 2017 07:55:52: 17000000 INFO @ Sat, 11 Nov 2017 07:55:57: 19000000 INFO @ Sat, 11 Nov 2017 07:55:58: 16000000 INFO @ Sat, 11 Nov 2017 07:56:04: 18000000 INFO @ Sat, 11 Nov 2017 07:56:06: 20000000 INFO @ Sat, 11 Nov 2017 07:56:09: 17000000 INFO @ Sat, 11 Nov 2017 07:56:16: 21000000 INFO @ Sat, 11 Nov 2017 07:56:16: 19000000 INFO @ Sat, 11 Nov 2017 07:56:20: 18000000 INFO @ Sat, 11 Nov 2017 07:56:25: 22000000 INFO @ Sat, 11 Nov 2017 07:56:28: 20000000 INFO @ Sat, 11 Nov 2017 07:56:31: 19000000 INFO @ Sat, 11 Nov 2017 07:56:34: 23000000 INFO @ Sat, 11 Nov 2017 07:56:40: 21000000 INFO @ Sat, 11 Nov 2017 07:56:42: 20000000 INFO @ Sat, 11 Nov 2017 07:56:43: 24000000 INFO @ Sat, 11 Nov 2017 07:56:52: 22000000 INFO @ Sat, 11 Nov 2017 07:56:52: 25000000 INFO @ Sat, 11 Nov 2017 07:56:54: 21000000 INFO @ Sat, 11 Nov 2017 07:57:01: 26000000 INFO @ Sat, 11 Nov 2017 07:57:04: 23000000 INFO @ Sat, 11 Nov 2017 07:57:05: 22000000 INFO @ Sat, 11 Nov 2017 07:57:10: 27000000 INFO @ Sat, 11 Nov 2017 07:57:15: 24000000 INFO @ Sat, 11 Nov 2017 07:57:16: 23000000 INFO @ Sat, 11 Nov 2017 07:57:20: 28000000 INFO @ Sat, 11 Nov 2017 07:57:27: 25000000 INFO @ Sat, 11 Nov 2017 07:57:28: 24000000 INFO @ Sat, 11 Nov 2017 07:57:29: 29000000 INFO @ Sat, 11 Nov 2017 07:57:38: 30000000 INFO @ Sat, 11 Nov 2017 07:57:39: 25000000 INFO @ Sat, 11 Nov 2017 07:57:39: 26000000 INFO @ Sat, 11 Nov 2017 07:57:47: 31000000 INFO @ Sat, 11 Nov 2017 07:57:50: 26000000 INFO @ Sat, 11 Nov 2017 07:57:51: 27000000 INFO @ Sat, 11 Nov 2017 07:57:56: 32000000 INFO @ Sat, 11 Nov 2017 07:58:01: 27000000 INFO @ Sat, 11 Nov 2017 07:58:03: 28000000 INFO @ Sat, 11 Nov 2017 07:58:06: 33000000 INFO @ Sat, 11 Nov 2017 07:58:13: 28000000 INFO @ Sat, 11 Nov 2017 07:58:15: 29000000 INFO @ Sat, 11 Nov 2017 07:58:15: 34000000 INFO @ Sat, 11 Nov 2017 07:58:24: 29000000 INFO @ Sat, 11 Nov 2017 07:58:24: 35000000 INFO @ Sat, 11 Nov 2017 07:58:26: 30000000 INFO @ Sat, 11 Nov 2017 07:58:34: 36000000 INFO @ Sat, 11 Nov 2017 07:58:35: 30000000 INFO @ Sat, 11 Nov 2017 07:58:38: 31000000 INFO @ Sat, 11 Nov 2017 07:58:43: 37000000 INFO @ Sat, 11 Nov 2017 07:58:46: 31000000 INFO @ Sat, 11 Nov 2017 07:58:50: 32000000 INFO @ Sat, 11 Nov 2017 07:58:52: 38000000 INFO @ Sat, 11 Nov 2017 07:58:57: 32000000 INFO @ Sat, 11 Nov 2017 07:59:02: 33000000 INFO @ Sat, 11 Nov 2017 07:59:02: 39000000 INFO @ Sat, 11 Nov 2017 07:59:08: 33000000 INFO @ Sat, 11 Nov 2017 07:59:11: 40000000 INFO @ Sat, 11 Nov 2017 07:59:13: 34000000 INFO @ Sat, 11 Nov 2017 07:59:20: 34000000 INFO @ Sat, 11 Nov 2017 07:59:20: 41000000 INFO @ Sat, 11 Nov 2017 07:59:25: 35000000 INFO @ Sat, 11 Nov 2017 07:59:30: 42000000 INFO @ Sat, 11 Nov 2017 07:59:31: 35000000 INFO @ Sat, 11 Nov 2017 07:59:37: 36000000 INFO @ Sat, 11 Nov 2017 07:59:39: 43000000 INFO @ Sat, 11 Nov 2017 07:59:42: 36000000 INFO @ Sat, 11 Nov 2017 07:59:48: 44000000 INFO @ Sat, 11 Nov 2017 07:59:49: 37000000 INFO @ Sat, 11 Nov 2017 07:59:53: 37000000 INFO @ Sat, 11 Nov 2017 07:59:58: 45000000 INFO @ Sat, 11 Nov 2017 08:00:00: 38000000 INFO @ Sat, 11 Nov 2017 08:00:04: 38000000 INFO @ Sat, 11 Nov 2017 08:00:07: 46000000 INFO @ Sat, 11 Nov 2017 08:00:12: 39000000 INFO @ Sat, 11 Nov 2017 08:00:15: 39000000 INFO @ Sat, 11 Nov 2017 08:00:17: 47000000 INFO @ Sat, 11 Nov 2017 08:00:19: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 08:00:19: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 08:00:19: #1 total tags in treatment: 47227605 INFO @ Sat, 11 Nov 2017 08:00:19: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 08:00:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 08:00:20: #1 tags after filtering in treatment: 47227525 INFO @ Sat, 11 Nov 2017 08:00:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 08:00:20: #1 finished! INFO @ Sat, 11 Nov 2017 08:00:20: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 08:00:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 08:00:24: 40000000 INFO @ Sat, 11 Nov 2017 08:00:25: #2 number of paired peaks: 9649 INFO @ Sat, 11 Nov 2017 08:00:25: start model_add_line... INFO @ Sat, 11 Nov 2017 08:00:25: start X-correlation... INFO @ Sat, 11 Nov 2017 08:00:25: end of X-cor INFO @ Sat, 11 Nov 2017 08:00:25: #2 finished! INFO @ Sat, 11 Nov 2017 08:00:25: #2 predicted fragment length is 91 bps INFO @ Sat, 11 Nov 2017 08:00:25: #2 alternative fragment length(s) may be 4,91 bps INFO @ Sat, 11 Nov 2017 08:00:25: #2.2 Generate R script for model : SRX913500.05_model.r WARNING @ Sat, 11 Nov 2017 08:00:25: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 08:00:25: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Sat, 11 Nov 2017 08:00:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 08:00:25: #3 Call peaks... INFO @ Sat, 11 Nov 2017 08:00:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 08:00:26: 40000000 INFO @ Sat, 11 Nov 2017 08:00:35: 41000000 INFO @ Sat, 11 Nov 2017 08:00:37: 41000000 INFO @ Sat, 11 Nov 2017 08:00:47: 42000000 INFO @ Sat, 11 Nov 2017 08:00:48: 42000000 INFO @ Sat, 11 Nov 2017 08:00:58: 43000000 INFO @ Sat, 11 Nov 2017 08:00:59: 43000000 INFO @ Sat, 11 Nov 2017 08:01:09: 44000000 INFO @ Sat, 11 Nov 2017 08:01:10: 44000000 INFO @ Sat, 11 Nov 2017 08:01:21: 45000000 INFO @ Sat, 11 Nov 2017 08:01:21: 45000000 INFO @ Sat, 11 Nov 2017 08:01:32: 46000000 INFO @ Sat, 11 Nov 2017 08:01:32: 46000000 INFO @ Sat, 11 Nov 2017 08:01:43: 47000000 INFO @ Sat, 11 Nov 2017 08:01:43: 47000000 INFO @ Sat, 11 Nov 2017 08:01:46: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 08:01:46: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 08:01:46: #1 total tags in treatment: 47227605 INFO @ Sat, 11 Nov 2017 08:01:46: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 08:01:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 08:01:46: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 08:01:46: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 08:01:46: #1 total tags in treatment: 47227605 INFO @ Sat, 11 Nov 2017 08:01:46: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 08:01:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 08:01:48: #1 tags after filtering in treatment: 47227525 INFO @ Sat, 11 Nov 2017 08:01:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 08:01:48: #1 finished! INFO @ Sat, 11 Nov 2017 08:01:48: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 08:01:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 08:01:48: #1 tags after filtering in treatment: 47227525 INFO @ Sat, 11 Nov 2017 08:01:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 08:01:48: #1 finished! INFO @ Sat, 11 Nov 2017 08:01:48: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 08:01:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 08:01:52: #2 number of paired peaks: 9649 INFO @ Sat, 11 Nov 2017 08:01:52: start model_add_line... INFO @ Sat, 11 Nov 2017 08:01:52: #2 number of paired peaks: 9649 INFO @ Sat, 11 Nov 2017 08:01:52: start model_add_line... INFO @ Sat, 11 Nov 2017 08:01:53: start X-correlation... INFO @ Sat, 11 Nov 2017 08:01:53: start X-correlation... INFO @ Sat, 11 Nov 2017 08:01:53: end of X-cor INFO @ Sat, 11 Nov 2017 08:01:53: end of X-cor INFO @ Sat, 11 Nov 2017 08:01:53: #2 finished! INFO @ Sat, 11 Nov 2017 08:01:53: #2 finished! INFO @ Sat, 11 Nov 2017 08:01:53: #2 predicted fragment length is 91 bps INFO @ Sat, 11 Nov 2017 08:01:53: #2 predicted fragment length is 91 bps INFO @ Sat, 11 Nov 2017 08:01:53: #2 alternative fragment length(s) may be 4,91 bps INFO @ Sat, 11 Nov 2017 08:01:53: #2 alternative fragment length(s) may be 4,91 bps INFO @ Sat, 11 Nov 2017 08:01:53: #2.2 Generate R script for model : SRX913500.10_model.r INFO @ Sat, 11 Nov 2017 08:01:53: #2.2 Generate R script for model : SRX913500.20_model.r WARNING @ Sat, 11 Nov 2017 08:01:53: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 08:01:53: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Sat, 11 Nov 2017 08:01:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 08:01:53: #3 Call peaks... INFO @ Sat, 11 Nov 2017 08:01:53: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 11 Nov 2017 08:01:53: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 08:01:53: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Sat, 11 Nov 2017 08:01:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 08:01:53: #3 Call peaks... INFO @ Sat, 11 Nov 2017 08:01:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 08:02:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 08:03:44: #4 Write output xls file... SRX913500.05_peaks.xls INFO @ Sat, 11 Nov 2017 08:03:44: #4 Write peak in narrowPeak format file... SRX913500.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 08:03:44: #4 Write summits bed file... SRX913500.05_summits.bed INFO @ Sat, 11 Nov 2017 08:03:44: Done! pass1 - making usageList (76 chroms): 3 millis pass2 - checking and writing primary data (1723 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 08:04:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 08:04:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 08:05:45: #4 Write output xls file... SRX913500.10_peaks.xls INFO @ Sat, 11 Nov 2017 08:05:45: #4 Write peak in narrowPeak format file... SRX913500.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 08:05:45: #4 Write summits bed file... SRX913500.10_summits.bed INFO @ Sat, 11 Nov 2017 08:05:45: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (563 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 08:05:46: #4 Write output xls file... SRX913500.20_peaks.xls INFO @ Sat, 11 Nov 2017 08:05:46: #4 Write peak in narrowPeak format file... SRX913500.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 08:05:46: #4 Write summits bed file... SRX913500.20_summits.bed INFO @ Sat, 11 Nov 2017 08:05:46: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (181 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。