Job ID = 10194827 sra ファイルのダウンロード中... Completed: 1259005K bytes transferred in 26 seconds (382904K 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 64832721 spots for /home/okishinya/chipatlas/results/rn6/SRX1977117/SRR3952249.sra Written 64832721 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 rm: cannot remove `[DSE]RR*.fastq': 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: 00:00:00 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 02:16:43 64832721 reads; of these: 64832721 (100.00%) were unpaired; of these: 13304808 (20.52%) aligned 0 times 25361552 (39.12%) aligned exactly 1 time 26166361 (40.36%) aligned >1 times 79.48% overall alignment rate Time searching: 02:16:47 Overall time: 02:16:47 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] 5837905 / 51527913 = 0.1133 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 03:33:40: # Command line: callpeak -t SRX1977117.bam -f BAM -g 2.15e9 -n SRX1977117.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977117.20 # format = BAM # ChIP-seq file = ['SRX1977117.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 03:33:40: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:33:40: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:33:40: # Command line: callpeak -t SRX1977117.bam -f BAM -g 2.15e9 -n SRX1977117.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977117.05 # format = BAM # ChIP-seq file = ['SRX1977117.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 03:33:40: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:33:40: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:33:40: # Command line: callpeak -t SRX1977117.bam -f BAM -g 2.15e9 -n SRX1977117.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977117.10 # format = BAM # ChIP-seq file = ['SRX1977117.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 03:33:40: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:33:40: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:33:46: 1000000 INFO @ Sat, 11 Nov 2017 03:33:46: 1000000 INFO @ Sat, 11 Nov 2017 03:33:46: 1000000 INFO @ Sat, 11 Nov 2017 03:33:53: 2000000 INFO @ Sat, 11 Nov 2017 03:33:53: 2000000 INFO @ Sat, 11 Nov 2017 03:33:54: 2000000 INFO @ Sat, 11 Nov 2017 03:34:00: 3000000 INFO @ Sat, 11 Nov 2017 03:34:00: 3000000 INFO @ Sat, 11 Nov 2017 03:34:01: 3000000 INFO @ Sat, 11 Nov 2017 03:34:07: 4000000 INFO @ Sat, 11 Nov 2017 03:34:07: 4000000 INFO @ Sat, 11 Nov 2017 03:34:07: 4000000 INFO @ Sat, 11 Nov 2017 03:34:13: 5000000 INFO @ Sat, 11 Nov 2017 03:34:13: 5000000 INFO @ Sat, 11 Nov 2017 03:34:14: 5000000 INFO @ Sat, 11 Nov 2017 03:34:19: 6000000 INFO @ Sat, 11 Nov 2017 03:34:19: 6000000 INFO @ Sat, 11 Nov 2017 03:34:20: 6000000 INFO @ Sat, 11 Nov 2017 03:34:26: 7000000 INFO @ Sat, 11 Nov 2017 03:34:26: 7000000 INFO @ Sat, 11 Nov 2017 03:34:27: 7000000 INFO @ Sat, 11 Nov 2017 03:34:32: 8000000 INFO @ Sat, 11 Nov 2017 03:34:33: 8000000 INFO @ Sat, 11 Nov 2017 03:34:34: 8000000 INFO @ Sat, 11 Nov 2017 03:34:38: 9000000 INFO @ Sat, 11 Nov 2017 03:34:39: 9000000 INFO @ Sat, 11 Nov 2017 03:34:40: 9000000 INFO @ Sat, 11 Nov 2017 03:34:45: 10000000 INFO @ Sat, 11 Nov 2017 03:34:46: 10000000 INFO @ Sat, 11 Nov 2017 03:34:46: 10000000 INFO @ Sat, 11 Nov 2017 03:34:52: 11000000 INFO @ Sat, 11 Nov 2017 03:34:52: 11000000 INFO @ Sat, 11 Nov 2017 03:34:53: 11000000 INFO @ Sat, 11 Nov 2017 03:34:58: 12000000 INFO @ Sat, 11 Nov 2017 03:34:59: 12000000 INFO @ Sat, 11 Nov 2017 03:34:59: 12000000 INFO @ Sat, 11 Nov 2017 03:35:04: 13000000 INFO @ Sat, 11 Nov 2017 03:35:05: 13000000 INFO @ Sat, 11 Nov 2017 03:35:05: 13000000 INFO @ Sat, 11 Nov 2017 03:35:11: 14000000 INFO @ Sat, 11 Nov 2017 03:35:11: 14000000 INFO @ Sat, 11 Nov 2017 03:35:11: 14000000 INFO @ Sat, 11 Nov 2017 03:35:17: 15000000 INFO @ Sat, 11 Nov 2017 03:35:18: 15000000 INFO @ Sat, 11 Nov 2017 03:35:18: 15000000 INFO @ Sat, 11 Nov 2017 03:35:24: 16000000 INFO @ Sat, 11 Nov 2017 03:35:24: 16000000 INFO @ Sat, 11 Nov 2017 03:35:24: 16000000 INFO @ Sat, 11 Nov 2017 03:35:30: 17000000 INFO @ Sat, 11 Nov 2017 03:35:31: 17000000 INFO @ Sat, 11 Nov 2017 03:35:31: 17000000 INFO @ Sat, 11 Nov 2017 03:35:36: 18000000 INFO @ Sat, 11 Nov 2017 03:35:37: 18000000 INFO @ Sat, 11 Nov 2017 03:35:37: 18000000 INFO @ Sat, 11 Nov 2017 03:35:43: 19000000 INFO @ Sat, 11 Nov 2017 03:35:43: 19000000 INFO @ Sat, 11 Nov 2017 03:35:44: 19000000 INFO @ Sat, 11 Nov 2017 03:35:49: 20000000 INFO @ Sat, 11 Nov 2017 03:35:50: 20000000 INFO @ Sat, 11 Nov 2017 03:35:50: 20000000 INFO @ Sat, 11 Nov 2017 03:35:55: 21000000 INFO @ Sat, 11 Nov 2017 03:35:56: 21000000 INFO @ Sat, 11 Nov 2017 03:35:57: 21000000 INFO @ Sat, 11 Nov 2017 03:36:02: 22000000 INFO @ Sat, 11 Nov 2017 03:36:03: 22000000 INFO @ Sat, 11 Nov 2017 03:36:04: 22000000 INFO @ Sat, 11 Nov 2017 03:36:08: 23000000 INFO @ Sat, 11 Nov 2017 03:36:10: 23000000 INFO @ Sat, 11 Nov 2017 03:36:11: 23000000 INFO @ Sat, 11 Nov 2017 03:36:15: 24000000 INFO @ Sat, 11 Nov 2017 03:36:16: 24000000 INFO @ Sat, 11 Nov 2017 03:36:18: 24000000 INFO @ Sat, 11 Nov 2017 03:36:22: 25000000 INFO @ Sat, 11 Nov 2017 03:36:23: 25000000 INFO @ Sat, 11 Nov 2017 03:36:25: 25000000 INFO @ Sat, 11 Nov 2017 03:36:28: 26000000 INFO @ Sat, 11 Nov 2017 03:36:29: 26000000 INFO @ Sat, 11 Nov 2017 03:36:32: 26000000 INFO @ Sat, 11 Nov 2017 03:36:35: 27000000 INFO @ Sat, 11 Nov 2017 03:36:36: 27000000 INFO @ Sat, 11 Nov 2017 03:36:40: 27000000 INFO @ Sat, 11 Nov 2017 03:36:41: 28000000 INFO @ Sat, 11 Nov 2017 03:36:42: 28000000 INFO @ Sat, 11 Nov 2017 03:36:47: 28000000 INFO @ Sat, 11 Nov 2017 03:36:48: 29000000 INFO @ Sat, 11 Nov 2017 03:36:49: 29000000 INFO @ Sat, 11 Nov 2017 03:36:54: 29000000 INFO @ Sat, 11 Nov 2017 03:36:54: 30000000 INFO @ Sat, 11 Nov 2017 03:36:55: 30000000 INFO @ Sat, 11 Nov 2017 03:37:01: 31000000 INFO @ Sat, 11 Nov 2017 03:37:02: 30000000 INFO @ Sat, 11 Nov 2017 03:37:03: 31000000 INFO @ Sat, 11 Nov 2017 03:37:09: 32000000 INFO @ Sat, 11 Nov 2017 03:37:09: 31000000 INFO @ Sat, 11 Nov 2017 03:37:09: 32000000 INFO @ Sat, 11 Nov 2017 03:37:16: 33000000 INFO @ Sat, 11 Nov 2017 03:37:16: 33000000 INFO @ Sat, 11 Nov 2017 03:37:17: 32000000 INFO @ Sat, 11 Nov 2017 03:37:22: 34000000 INFO @ Sat, 11 Nov 2017 03:37:24: 34000000 INFO @ Sat, 11 Nov 2017 03:37:25: 33000000 INFO @ Sat, 11 Nov 2017 03:37:30: 35000000 INFO @ Sat, 11 Nov 2017 03:37:32: 35000000 INFO @ Sat, 11 Nov 2017 03:37:33: 34000000 INFO @ Sat, 11 Nov 2017 03:37:39: 36000000 INFO @ Sat, 11 Nov 2017 03:37:40: 36000000 INFO @ Sat, 11 Nov 2017 03:37:40: 35000000 INFO @ Sat, 11 Nov 2017 03:37:46: 37000000 INFO @ Sat, 11 Nov 2017 03:37:47: 36000000 INFO @ Sat, 11 Nov 2017 03:37:48: 37000000 INFO @ Sat, 11 Nov 2017 03:37:54: 38000000 INFO @ Sat, 11 Nov 2017 03:37:55: 37000000 INFO @ Sat, 11 Nov 2017 03:37:57: 38000000 INFO @ Sat, 11 Nov 2017 03:38:03: 39000000 INFO @ Sat, 11 Nov 2017 03:38:05: 38000000 INFO @ Sat, 11 Nov 2017 03:38:06: 39000000 INFO @ Sat, 11 Nov 2017 03:38:14: 40000000 INFO @ Sat, 11 Nov 2017 03:38:15: 39000000 INFO @ Sat, 11 Nov 2017 03:38:16: 40000000 INFO @ Sat, 11 Nov 2017 03:38:21: 41000000 INFO @ Sat, 11 Nov 2017 03:38:24: 40000000 INFO @ Sat, 11 Nov 2017 03:38:24: 41000000 INFO @ Sat, 11 Nov 2017 03:38:30: 42000000 INFO @ Sat, 11 Nov 2017 03:38:31: 41000000 INFO @ Sat, 11 Nov 2017 03:38:32: 42000000 INFO @ Sat, 11 Nov 2017 03:38:37: 43000000 INFO @ Sat, 11 Nov 2017 03:38:39: 43000000 INFO @ Sat, 11 Nov 2017 03:38:40: 42000000 INFO @ Sat, 11 Nov 2017 03:38:46: 44000000 INFO @ Sat, 11 Nov 2017 03:38:46: 44000000 INFO @ Sat, 11 Nov 2017 03:38:50: 43000000 INFO @ Sat, 11 Nov 2017 03:38:53: 45000000 INFO @ Sat, 11 Nov 2017 03:38:54: 45000000 INFO @ Sat, 11 Nov 2017 03:38:58: 44000000 INFO @ Sat, 11 Nov 2017 03:38:59: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:38:59: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:38:59: #1 total tags in treatment: 45690008 INFO @ Sat, 11 Nov 2017 03:38:59: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:38:59: #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 03:39:00: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:39:00: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:39:00: #1 total tags in treatment: 45690008 INFO @ Sat, 11 Nov 2017 03:39:00: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:39:00: #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 03:39:01: #1 tags after filtering in treatment: 45689952 INFO @ Sat, 11 Nov 2017 03:39:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:39:01: #1 finished! INFO @ Sat, 11 Nov 2017 03:39:01: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:39:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:39:02: #1 tags after filtering in treatment: 45689952 INFO @ Sat, 11 Nov 2017 03:39:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:39:02: #1 finished! INFO @ Sat, 11 Nov 2017 03:39:02: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:39:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:39:07: 45000000 INFO @ Sat, 11 Nov 2017 03:39:08: #2 number of paired peaks: 34826 INFO @ Sat, 11 Nov 2017 03:39:08: start model_add_line... INFO @ Sat, 11 Nov 2017 03:39:09: start X-correlation... INFO @ Sat, 11 Nov 2017 03:39:09: end of X-cor INFO @ Sat, 11 Nov 2017 03:39:09: #2 finished! INFO @ Sat, 11 Nov 2017 03:39:09: #2 predicted fragment length is 61 bps INFO @ Sat, 11 Nov 2017 03:39:09: #2 alternative fragment length(s) may be 61 bps INFO @ Sat, 11 Nov 2017 03:39:09: #2.2 Generate R script for model : SRX1977117.05_model.r WARNING @ Sat, 11 Nov 2017 03:39:09: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 03:39:09: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sat, 11 Nov 2017 03:39:09: #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 03:39:09: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:39:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:39:12: #2 number of paired peaks: 34826 INFO @ Sat, 11 Nov 2017 03:39:12: start model_add_line... INFO @ Sat, 11 Nov 2017 03:39:12: start X-correlation... INFO @ Sat, 11 Nov 2017 03:39:12: end of X-cor INFO @ Sat, 11 Nov 2017 03:39:12: #2 finished! INFO @ Sat, 11 Nov 2017 03:39:12: #2 predicted fragment length is 61 bps INFO @ Sat, 11 Nov 2017 03:39:12: #2 alternative fragment length(s) may be 61 bps INFO @ Sat, 11 Nov 2017 03:39:12: #2.2 Generate R script for model : SRX1977117.20_model.r WARNING @ Sat, 11 Nov 2017 03:39:12: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 03:39:12: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sat, 11 Nov 2017 03:39:12: #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 03:39:12: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:39:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:39:14: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:39:14: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:39:14: #1 total tags in treatment: 45690008 INFO @ Sat, 11 Nov 2017 03:39:14: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:39:14: #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 03:39:15: #1 tags after filtering in treatment: 45689952 INFO @ Sat, 11 Nov 2017 03:39:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:39:15: #1 finished! INFO @ Sat, 11 Nov 2017 03:39:15: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:39:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:39:22: #2 number of paired peaks: 34826 INFO @ Sat, 11 Nov 2017 03:39:22: start model_add_line... INFO @ Sat, 11 Nov 2017 03:39:23: start X-correlation... INFO @ Sat, 11 Nov 2017 03:39:23: end of X-cor INFO @ Sat, 11 Nov 2017 03:39:23: #2 finished! INFO @ Sat, 11 Nov 2017 03:39:23: #2 predicted fragment length is 61 bps INFO @ Sat, 11 Nov 2017 03:39:23: #2 alternative fragment length(s) may be 61 bps INFO @ Sat, 11 Nov 2017 03:39:23: #2.2 Generate R script for model : SRX1977117.10_model.r WARNING @ Sat, 11 Nov 2017 03:39:23: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 03:39:23: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sat, 11 Nov 2017 03:39:23: #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 03:39:23: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:39:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:41:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:41:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:41:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:42:34: #4 Write output xls file... SRX1977117.05_peaks.xls INFO @ Sat, 11 Nov 2017 03:42:35: #4 Write peak in narrowPeak format file... SRX1977117.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:42:35: #4 Write summits bed file... SRX1977117.05_summits.bed INFO @ Sat, 11 Nov 2017 03:42:35: Done! pass1 - making usageList (187 chroms): 6 millis pass2 - checking and writing primary data (34332 records, 4 fields): 88 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:42:43: #4 Write output xls file... SRX1977117.20_peaks.xls INFO @ Sat, 11 Nov 2017 03:42:43: #4 Write peak in narrowPeak format file... SRX1977117.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:42:43: #4 Write summits bed file... SRX1977117.20_summits.bed INFO @ Sat, 11 Nov 2017 03:42:43: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (1744 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:42:48: #4 Write output xls file... SRX1977117.10_peaks.xls INFO @ Sat, 11 Nov 2017 03:42:48: #4 Write peak in narrowPeak format file... SRX1977117.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:42:48: #4 Write summits bed file... SRX1977117.10_summits.bed INFO @ Sat, 11 Nov 2017 03:42:48: Done! pass1 - making usageList (94 chroms): 2 millis pass2 - checking and writing primary data (6616 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。