Job ID = 10487612 sra ファイルのダウンロード中... Completed: 1491848K bytes transferred in 102 seconds (118694K 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 56732885 spots for /home/okishinya/chipatlas/results/rn6/SRX3087691/SRR5927327.sra Written 56732885 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:10:55 56732885 reads; of these: 56732885 (100.00%) were unpaired; of these: 1430041 (2.52%) aligned 0 times 40123735 (70.72%) aligned exactly 1 time 15179109 (26.76%) aligned >1 times 97.48% overall alignment rate Time searching: 01:10:57 Overall time: 01:10:57 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] 3187589 / 55302844 = 0.0576 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 @ Sun, 18 Mar 2018 11:38:00: # Command line: callpeak -t SRX3087691.bam -f BAM -g 2.15e9 -n SRX3087691.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087691.10 # format = BAM # ChIP-seq file = ['SRX3087691.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 @ Sun, 18 Mar 2018 11:38:00: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:38:00: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:38:00: # Command line: callpeak -t SRX3087691.bam -f BAM -g 2.15e9 -n SRX3087691.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087691.20 # format = BAM # ChIP-seq file = ['SRX3087691.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 @ Sun, 18 Mar 2018 11:38:00: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:38:00: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:38:00: # Command line: callpeak -t SRX3087691.bam -f BAM -g 2.15e9 -n SRX3087691.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087691.05 # format = BAM # ChIP-seq file = ['SRX3087691.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 @ Sun, 18 Mar 2018 11:38:00: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:38:00: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:38:07: 1000000 INFO @ Sun, 18 Mar 2018 11:38:07: 1000000 INFO @ Sun, 18 Mar 2018 11:38:07: 1000000 INFO @ Sun, 18 Mar 2018 11:38:14: 2000000 INFO @ Sun, 18 Mar 2018 11:38:15: 2000000 INFO @ Sun, 18 Mar 2018 11:38:15: 2000000 INFO @ Sun, 18 Mar 2018 11:38:22: 3000000 INFO @ Sun, 18 Mar 2018 11:38:22: 3000000 INFO @ Sun, 18 Mar 2018 11:38:22: 3000000 INFO @ Sun, 18 Mar 2018 11:38:29: 4000000 INFO @ Sun, 18 Mar 2018 11:38:29: 4000000 INFO @ Sun, 18 Mar 2018 11:38:29: 4000000 INFO @ Sun, 18 Mar 2018 11:38:36: 5000000 INFO @ Sun, 18 Mar 2018 11:38:36: 5000000 INFO @ Sun, 18 Mar 2018 11:38:38: 5000000 INFO @ Sun, 18 Mar 2018 11:38:43: 6000000 INFO @ Sun, 18 Mar 2018 11:38:44: 6000000 INFO @ Sun, 18 Mar 2018 11:38:45: 6000000 INFO @ Sun, 18 Mar 2018 11:38:50: 7000000 INFO @ Sun, 18 Mar 2018 11:38:51: 7000000 INFO @ Sun, 18 Mar 2018 11:38:52: 7000000 INFO @ Sun, 18 Mar 2018 11:38:58: 8000000 INFO @ Sun, 18 Mar 2018 11:38:58: 8000000 INFO @ Sun, 18 Mar 2018 11:38:59: 8000000 INFO @ Sun, 18 Mar 2018 11:39:05: 9000000 INFO @ Sun, 18 Mar 2018 11:39:05: 9000000 INFO @ Sun, 18 Mar 2018 11:39:06: 9000000 INFO @ Sun, 18 Mar 2018 11:39:12: 10000000 INFO @ Sun, 18 Mar 2018 11:39:12: 10000000 INFO @ Sun, 18 Mar 2018 11:39:13: 10000000 INFO @ Sun, 18 Mar 2018 11:39:19: 11000000 INFO @ Sun, 18 Mar 2018 11:39:20: 11000000 INFO @ Sun, 18 Mar 2018 11:39:20: 11000000 INFO @ Sun, 18 Mar 2018 11:39:26: 12000000 INFO @ Sun, 18 Mar 2018 11:39:27: 12000000 INFO @ Sun, 18 Mar 2018 11:39:27: 12000000 INFO @ Sun, 18 Mar 2018 11:39:34: 13000000 INFO @ Sun, 18 Mar 2018 11:39:34: 13000000 INFO @ Sun, 18 Mar 2018 11:39:34: 13000000 INFO @ Sun, 18 Mar 2018 11:39:41: 14000000 INFO @ Sun, 18 Mar 2018 11:39:41: 14000000 INFO @ Sun, 18 Mar 2018 11:39:42: 14000000 INFO @ Sun, 18 Mar 2018 11:39:48: 15000000 INFO @ Sun, 18 Mar 2018 11:39:48: 15000000 INFO @ Sun, 18 Mar 2018 11:39:49: 15000000 INFO @ Sun, 18 Mar 2018 11:39:55: 16000000 INFO @ Sun, 18 Mar 2018 11:39:56: 16000000 INFO @ Sun, 18 Mar 2018 11:39:56: 16000000 INFO @ Sun, 18 Mar 2018 11:40:03: 17000000 INFO @ Sun, 18 Mar 2018 11:40:03: 17000000 INFO @ Sun, 18 Mar 2018 11:40:04: 17000000 INFO @ Sun, 18 Mar 2018 11:40:10: 18000000 INFO @ Sun, 18 Mar 2018 11:40:10: 18000000 INFO @ Sun, 18 Mar 2018 11:40:11: 18000000 INFO @ Sun, 18 Mar 2018 11:40:17: 19000000 INFO @ Sun, 18 Mar 2018 11:40:18: 19000000 INFO @ Sun, 18 Mar 2018 11:40:18: 19000000 INFO @ Sun, 18 Mar 2018 11:40:24: 20000000 INFO @ Sun, 18 Mar 2018 11:40:25: 20000000 INFO @ Sun, 18 Mar 2018 11:40:26: 20000000 INFO @ Sun, 18 Mar 2018 11:40:31: 21000000 INFO @ Sun, 18 Mar 2018 11:40:32: 21000000 INFO @ Sun, 18 Mar 2018 11:40:33: 21000000 INFO @ Sun, 18 Mar 2018 11:40:38: 22000000 INFO @ Sun, 18 Mar 2018 11:40:39: 22000000 INFO @ Sun, 18 Mar 2018 11:40:40: 22000000 INFO @ Sun, 18 Mar 2018 11:40:45: 23000000 INFO @ Sun, 18 Mar 2018 11:40:47: 23000000 INFO @ Sun, 18 Mar 2018 11:40:48: 23000000 INFO @ Sun, 18 Mar 2018 11:40:52: 24000000 INFO @ Sun, 18 Mar 2018 11:40:54: 24000000 INFO @ Sun, 18 Mar 2018 11:40:55: 24000000 INFO @ Sun, 18 Mar 2018 11:40:59: 25000000 INFO @ Sun, 18 Mar 2018 11:41:01: 25000000 INFO @ Sun, 18 Mar 2018 11:41:03: 25000000 INFO @ Sun, 18 Mar 2018 11:41:06: 26000000 INFO @ Sun, 18 Mar 2018 11:41:09: 26000000 INFO @ Sun, 18 Mar 2018 11:41:10: 26000000 INFO @ Sun, 18 Mar 2018 11:41:13: 27000000 INFO @ Sun, 18 Mar 2018 11:41:16: 27000000 INFO @ Sun, 18 Mar 2018 11:41:18: 27000000 INFO @ Sun, 18 Mar 2018 11:41:20: 28000000 INFO @ Sun, 18 Mar 2018 11:41:24: 28000000 INFO @ Sun, 18 Mar 2018 11:41:25: 28000000 INFO @ Sun, 18 Mar 2018 11:41:28: 29000000 INFO @ Sun, 18 Mar 2018 11:41:31: 29000000 INFO @ Sun, 18 Mar 2018 11:41:33: 29000000 INFO @ Sun, 18 Mar 2018 11:41:35: 30000000 INFO @ Sun, 18 Mar 2018 11:41:39: 30000000 INFO @ Sun, 18 Mar 2018 11:41:40: 30000000 INFO @ Sun, 18 Mar 2018 11:41:42: 31000000 INFO @ Sun, 18 Mar 2018 11:41:46: 31000000 INFO @ Sun, 18 Mar 2018 11:41:48: 31000000 INFO @ Sun, 18 Mar 2018 11:41:49: 32000000 INFO @ Sun, 18 Mar 2018 11:41:54: 32000000 INFO @ Sun, 18 Mar 2018 11:41:55: 32000000 INFO @ Sun, 18 Mar 2018 11:41:56: 33000000 INFO @ Sun, 18 Mar 2018 11:42:01: 33000000 INFO @ Sun, 18 Mar 2018 11:42:03: 33000000 INFO @ Sun, 18 Mar 2018 11:42:03: 34000000 INFO @ Sun, 18 Mar 2018 11:42:09: 34000000 INFO @ Sun, 18 Mar 2018 11:42:10: 34000000 INFO @ Sun, 18 Mar 2018 11:42:11: 35000000 INFO @ Sun, 18 Mar 2018 11:42:16: 35000000 INFO @ Sun, 18 Mar 2018 11:42:18: 36000000 INFO @ Sun, 18 Mar 2018 11:42:18: 35000000 INFO @ Sun, 18 Mar 2018 11:42:24: 36000000 INFO @ Sun, 18 Mar 2018 11:42:25: 37000000 INFO @ Sun, 18 Mar 2018 11:42:26: 36000000 INFO @ Sun, 18 Mar 2018 11:42:32: 37000000 INFO @ Sun, 18 Mar 2018 11:42:32: 38000000 INFO @ Sun, 18 Mar 2018 11:42:34: 37000000 INFO @ Sun, 18 Mar 2018 11:42:39: 38000000 INFO @ Sun, 18 Mar 2018 11:42:39: 39000000 INFO @ Sun, 18 Mar 2018 11:42:41: 38000000 INFO @ Sun, 18 Mar 2018 11:42:47: 40000000 INFO @ Sun, 18 Mar 2018 11:42:47: 39000000 INFO @ Sun, 18 Mar 2018 11:42:49: 39000000 INFO @ Sun, 18 Mar 2018 11:42:54: 41000000 INFO @ Sun, 18 Mar 2018 11:42:54: 40000000 INFO @ Sun, 18 Mar 2018 11:42:56: 40000000 INFO @ Sun, 18 Mar 2018 11:43:01: 42000000 INFO @ Sun, 18 Mar 2018 11:43:02: 41000000 INFO @ Sun, 18 Mar 2018 11:43:04: 41000000 INFO @ Sun, 18 Mar 2018 11:43:08: 43000000 INFO @ Sun, 18 Mar 2018 11:43:09: 42000000 INFO @ Sun, 18 Mar 2018 11:43:11: 42000000 INFO @ Sun, 18 Mar 2018 11:43:15: 44000000 INFO @ Sun, 18 Mar 2018 11:43:17: 43000000 INFO @ Sun, 18 Mar 2018 11:43:19: 43000000 INFO @ Sun, 18 Mar 2018 11:43:23: 45000000 INFO @ Sun, 18 Mar 2018 11:43:24: 44000000 INFO @ Sun, 18 Mar 2018 11:43:26: 44000000 INFO @ Sun, 18 Mar 2018 11:43:30: 46000000 INFO @ Sun, 18 Mar 2018 11:43:32: 45000000 INFO @ Sun, 18 Mar 2018 11:43:34: 45000000 INFO @ Sun, 18 Mar 2018 11:43:37: 47000000 INFO @ Sun, 18 Mar 2018 11:43:39: 46000000 INFO @ Sun, 18 Mar 2018 11:43:41: 46000000 INFO @ Sun, 18 Mar 2018 11:43:44: 48000000 INFO @ Sun, 18 Mar 2018 11:43:47: 47000000 INFO @ Sun, 18 Mar 2018 11:43:49: 47000000 INFO @ Sun, 18 Mar 2018 11:43:51: 49000000 INFO @ Sun, 18 Mar 2018 11:43:55: 48000000 INFO @ Sun, 18 Mar 2018 11:43:57: 48000000 INFO @ Sun, 18 Mar 2018 11:43:59: 50000000 INFO @ Sun, 18 Mar 2018 11:44:02: 49000000 INFO @ Sun, 18 Mar 2018 11:44:04: 49000000 INFO @ Sun, 18 Mar 2018 11:44:06: 51000000 INFO @ Sun, 18 Mar 2018 11:44:10: 50000000 INFO @ Sun, 18 Mar 2018 11:44:12: 50000000 INFO @ Sun, 18 Mar 2018 11:44:13: 52000000 INFO @ Sun, 18 Mar 2018 11:44:15: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:44:15: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:44:15: #1 total tags in treatment: 52115255 INFO @ Sun, 18 Mar 2018 11:44:15: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:44:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:44:16: #1 tags after filtering in treatment: 52115205 INFO @ Sun, 18 Mar 2018 11:44:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:44:16: #1 finished! INFO @ Sun, 18 Mar 2018 11:44:16: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:44:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:44:17: 51000000 INFO @ Sun, 18 Mar 2018 11:44:19: 51000000 INFO @ Sun, 18 Mar 2018 11:44:20: #2 number of paired peaks: 5708 INFO @ Sun, 18 Mar 2018 11:44:20: start model_add_line... INFO @ Sun, 18 Mar 2018 11:44:21: start X-correlation... INFO @ Sun, 18 Mar 2018 11:44:21: end of X-cor INFO @ Sun, 18 Mar 2018 11:44:21: #2 finished! INFO @ Sun, 18 Mar 2018 11:44:21: #2 predicted fragment length is 60 bps INFO @ Sun, 18 Mar 2018 11:44:21: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 18 Mar 2018 11:44:21: #2.2 Generate R script for model : SRX3087691.05_model.r WARNING @ Sun, 18 Mar 2018 11:44:21: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 11:44:21: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 18 Mar 2018 11:44:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 11:44:21: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:44:25: 52000000 INFO @ Sun, 18 Mar 2018 11:44:26: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:44:26: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:44:26: #1 total tags in treatment: 52115255 INFO @ Sun, 18 Mar 2018 11:44:26: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:44:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:44:27: 52000000 INFO @ Sun, 18 Mar 2018 11:44:27: #1 tags after filtering in treatment: 52115205 INFO @ Sun, 18 Mar 2018 11:44:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:44:27: #1 finished! INFO @ Sun, 18 Mar 2018 11:44:27: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:44:28: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:44:28: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:44:28: #1 total tags in treatment: 52115255 INFO @ Sun, 18 Mar 2018 11:44:28: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:44:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:44:29: #1 tags after filtering in treatment: 52115205 INFO @ Sun, 18 Mar 2018 11:44:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:44:29: #1 finished! INFO @ Sun, 18 Mar 2018 11:44:29: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:44:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:44:32: #2 number of paired peaks: 5708 INFO @ Sun, 18 Mar 2018 11:44:32: start model_add_line... INFO @ Sun, 18 Mar 2018 11:44:33: start X-correlation... INFO @ Sun, 18 Mar 2018 11:44:33: end of X-cor INFO @ Sun, 18 Mar 2018 11:44:33: #2 finished! INFO @ Sun, 18 Mar 2018 11:44:33: #2 predicted fragment length is 60 bps INFO @ Sun, 18 Mar 2018 11:44:33: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 18 Mar 2018 11:44:33: #2.2 Generate R script for model : SRX3087691.10_model.r WARNING @ Sun, 18 Mar 2018 11:44:33: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 11:44:33: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 18 Mar 2018 11:44:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 11:44:33: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:44:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:44:34: #2 number of paired peaks: 5708 INFO @ Sun, 18 Mar 2018 11:44:34: start model_add_line... INFO @ Sun, 18 Mar 2018 11:44:35: start X-correlation... INFO @ Sun, 18 Mar 2018 11:44:35: end of X-cor INFO @ Sun, 18 Mar 2018 11:44:35: #2 finished! INFO @ Sun, 18 Mar 2018 11:44:35: #2 predicted fragment length is 60 bps INFO @ Sun, 18 Mar 2018 11:44:35: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 18 Mar 2018 11:44:35: #2.2 Generate R script for model : SRX3087691.20_model.r WARNING @ Sun, 18 Mar 2018 11:44:35: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 11:44:35: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 18 Mar 2018 11:44:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 11:44:35: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:44:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:46:23: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:46:41: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:46:41: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:47:31: #4 Write output xls file... SRX3087691.05_peaks.xls INFO @ Sun, 18 Mar 2018 11:47:31: #4 Write peak in narrowPeak format file... SRX3087691.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:47:31: #4 Write summits bed file... SRX3087691.05_summits.bed INFO @ Sun, 18 Mar 2018 11:47:31: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (2589 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:47:53: #4 Write output xls file... SRX3087691.20_peaks.xls INFO @ Sun, 18 Mar 2018 11:47:53: #4 Write peak in narrowPeak format file... SRX3087691.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:47:53: #4 Write summits bed file... SRX3087691.20_summits.bed INFO @ Sun, 18 Mar 2018 11:47:53: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (671 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:47:56: #4 Write output xls file... SRX3087691.10_peaks.xls INFO @ Sun, 18 Mar 2018 11:47:56: #4 Write peak in narrowPeak format file... SRX3087691.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:47:56: #4 Write summits bed file... SRX3087691.10_summits.bed INFO @ Sun, 18 Mar 2018 11:47:56: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (1382 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。