Job ID = 10194734 sra ファイルのダウンロード中... Completed: 1165490K bytes transferred in 16 seconds (570785K bits/sec), in 1 file. Completed: 1246394K bytes transferred in 19 seconds (530889K 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 19476262 spots for /home/okishinya/chipatlas/results/rn6/SRX1056330/SRR2060201.sra Written 19476262 spots total Written 21078291 spots for /home/okishinya/chipatlas/results/rn6/SRX1056330/SRR2060202.sra Written 21078291 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 03:03:45 40554553 reads; of these: 40554553 (100.00%) were unpaired; of these: 2715558 (6.70%) aligned 0 times 28093381 (69.27%) aligned exactly 1 time 9745614 (24.03%) aligned >1 times 93.30% overall alignment rate Time searching: 03:03:49 Overall time: 03:03:49 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 16 files... [bam_rmdupse_core] 7035152 / 37838995 = 0.1859 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 @ Fri, 10 Nov 2017 23:24:58: # Command line: callpeak -t SRX1056330.bam -f BAM -g 2.15e9 -n SRX1056330.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056330.20 # format = BAM # ChIP-seq file = ['SRX1056330.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 @ Fri, 10 Nov 2017 23:24:58: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:24:58: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:24:58: # Command line: callpeak -t SRX1056330.bam -f BAM -g 2.15e9 -n SRX1056330.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056330.05 # format = BAM # ChIP-seq file = ['SRX1056330.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 @ Fri, 10 Nov 2017 23:24:58: # Command line: callpeak -t SRX1056330.bam -f BAM -g 2.15e9 -n SRX1056330.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056330.10 # format = BAM # ChIP-seq file = ['SRX1056330.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 @ Fri, 10 Nov 2017 23:24:58: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:24:58: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:24:58: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:24:58: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:25:12: 1000000 INFO @ Fri, 10 Nov 2017 23:25:26: 2000000 INFO @ Fri, 10 Nov 2017 23:25:32: 1000000 INFO @ Fri, 10 Nov 2017 23:25:35: 1000000 INFO @ Fri, 10 Nov 2017 23:25:39: 3000000 INFO @ Fri, 10 Nov 2017 23:25:52: 4000000 INFO @ Fri, 10 Nov 2017 23:26:03: 2000000 INFO @ Fri, 10 Nov 2017 23:26:06: 5000000 INFO @ Fri, 10 Nov 2017 23:26:12: 2000000 INFO @ Fri, 10 Nov 2017 23:26:20: 6000000 INFO @ Fri, 10 Nov 2017 23:26:32: 7000000 INFO @ Fri, 10 Nov 2017 23:26:37: 3000000 INFO @ Fri, 10 Nov 2017 23:26:45: 8000000 INFO @ Fri, 10 Nov 2017 23:26:49: 3000000 INFO @ Fri, 10 Nov 2017 23:26:59: 9000000 INFO @ Fri, 10 Nov 2017 23:27:13: 10000000 INFO @ Fri, 10 Nov 2017 23:27:20: 4000000 INFO @ Fri, 10 Nov 2017 23:27:24: 4000000 INFO @ Fri, 10 Nov 2017 23:27:27: 11000000 INFO @ Fri, 10 Nov 2017 23:27:40: 12000000 INFO @ Fri, 10 Nov 2017 23:27:52: 13000000 INFO @ Fri, 10 Nov 2017 23:27:54: 5000000 INFO @ Fri, 10 Nov 2017 23:27:58: 5000000 INFO @ Fri, 10 Nov 2017 23:28:06: 14000000 INFO @ Fri, 10 Nov 2017 23:28:19: 15000000 INFO @ Fri, 10 Nov 2017 23:28:29: 6000000 INFO @ Fri, 10 Nov 2017 23:28:32: 16000000 INFO @ Fri, 10 Nov 2017 23:28:43: 6000000 INFO @ Fri, 10 Nov 2017 23:28:45: 17000000 INFO @ Fri, 10 Nov 2017 23:28:59: 18000000 INFO @ Fri, 10 Nov 2017 23:29:09: 7000000 INFO @ Fri, 10 Nov 2017 23:29:12: 19000000 INFO @ Fri, 10 Nov 2017 23:29:26: 20000000 INFO @ Fri, 10 Nov 2017 23:29:28: 7000000 INFO @ Fri, 10 Nov 2017 23:29:40: 21000000 INFO @ Fri, 10 Nov 2017 23:29:53: 22000000 INFO @ Fri, 10 Nov 2017 23:30:02: 8000000 INFO @ Fri, 10 Nov 2017 23:30:07: 23000000 INFO @ Fri, 10 Nov 2017 23:30:20: 24000000 INFO @ Fri, 10 Nov 2017 23:30:24: 8000000 INFO @ Fri, 10 Nov 2017 23:30:50: 9000000 INFO @ Fri, 10 Nov 2017 23:30:57: 25000000 INFO @ Fri, 10 Nov 2017 23:31:11: 9000000 INFO @ Fri, 10 Nov 2017 23:31:35: 10000000 INFO @ Fri, 10 Nov 2017 23:31:41: 26000000 INFO @ Fri, 10 Nov 2017 23:31:57: 10000000 INFO @ Fri, 10 Nov 2017 23:32:23: 11000000 INFO @ Fri, 10 Nov 2017 23:32:31: 27000000 INFO @ Fri, 10 Nov 2017 23:32:42: 11000000 INFO @ Fri, 10 Nov 2017 23:32:59: 12000000 INFO @ Fri, 10 Nov 2017 23:33:03: 28000000 INFO @ Fri, 10 Nov 2017 23:33:15: 12000000 INFO @ Fri, 10 Nov 2017 23:33:31: 13000000 INFO @ Fri, 10 Nov 2017 23:33:35: 29000000 INFO @ Fri, 10 Nov 2017 23:33:44: 13000000 INFO @ Fri, 10 Nov 2017 23:34:05: 14000000 INFO @ Fri, 10 Nov 2017 23:34:09: 30000000 INFO @ Fri, 10 Nov 2017 23:34:11: 14000000 INFO @ Fri, 10 Nov 2017 23:34:33: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 23:34:33: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 23:34:33: #1 total tags in treatment: 30803843 INFO @ Fri, 10 Nov 2017 23:34:33: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:34:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:34:34: 15000000 INFO @ Fri, 10 Nov 2017 23:34:34: #1 tags after filtering in treatment: 30803749 INFO @ Fri, 10 Nov 2017 23:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:34:34: #1 finished! INFO @ Fri, 10 Nov 2017 23:34:34: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:34:38: #2 number of paired peaks: 7251 INFO @ Fri, 10 Nov 2017 23:34:38: start model_add_line... INFO @ Fri, 10 Nov 2017 23:34:38: start X-correlation... INFO @ Fri, 10 Nov 2017 23:34:38: end of X-cor INFO @ Fri, 10 Nov 2017 23:34:38: #2 finished! INFO @ Fri, 10 Nov 2017 23:34:38: #2 predicted fragment length is 100 bps INFO @ Fri, 10 Nov 2017 23:34:38: #2 alternative fragment length(s) may be 100 bps INFO @ Fri, 10 Nov 2017 23:34:38: #2.2 Generate R script for model : SRX1056330.20_model.r WARNING @ Fri, 10 Nov 2017 23:34:38: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:34:38: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Fri, 10 Nov 2017 23:34:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:34:38: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:34:39: 15000000 INFO @ Fri, 10 Nov 2017 23:34:56: 16000000 INFO @ Fri, 10 Nov 2017 23:35:07: 16000000 INFO @ Fri, 10 Nov 2017 23:35:19: 17000000 INFO @ Fri, 10 Nov 2017 23:35:43: 18000000 INFO @ Fri, 10 Nov 2017 23:35:46: 17000000 INFO @ Fri, 10 Nov 2017 23:36:06: 19000000 INFO @ Fri, 10 Nov 2017 23:36:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:36:19: 18000000 INFO @ Fri, 10 Nov 2017 23:36:29: 20000000 INFO @ Fri, 10 Nov 2017 23:36:47: 19000000 INFO @ Fri, 10 Nov 2017 23:36:53: 21000000 INFO @ Fri, 10 Nov 2017 23:37:04: #4 Write output xls file... SRX1056330.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:37:04: #4 Write peak in narrowPeak format file... SRX1056330.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:37:04: #4 Write summits bed file... SRX1056330.20_summits.bed INFO @ Fri, 10 Nov 2017 23:37:04: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (547 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:37:16: 22000000 INFO @ Fri, 10 Nov 2017 23:37:16: 20000000 INFO @ Fri, 10 Nov 2017 23:37:39: 23000000 INFO @ Fri, 10 Nov 2017 23:37:49: 21000000 INFO @ Fri, 10 Nov 2017 23:38:02: 24000000 INFO @ Fri, 10 Nov 2017 23:38:22: 22000000 INFO @ Fri, 10 Nov 2017 23:38:25: 25000000 INFO @ Fri, 10 Nov 2017 23:38:48: 23000000 INFO @ Fri, 10 Nov 2017 23:38:48: 26000000 INFO @ Fri, 10 Nov 2017 23:39:13: 24000000 INFO @ Fri, 10 Nov 2017 23:39:14: 27000000 INFO @ Fri, 10 Nov 2017 23:39:38: 25000000 INFO @ Fri, 10 Nov 2017 23:39:38: 28000000 INFO @ Fri, 10 Nov 2017 23:40:01: 29000000 INFO @ Fri, 10 Nov 2017 23:40:04: 26000000 INFO @ Fri, 10 Nov 2017 23:40:24: 30000000 INFO @ Fri, 10 Nov 2017 23:40:29: 27000000 INFO @ Fri, 10 Nov 2017 23:40:42: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 23:40:42: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 23:40:42: #1 total tags in treatment: 30803843 INFO @ Fri, 10 Nov 2017 23:40:42: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:40:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:40:43: #1 tags after filtering in treatment: 30803749 INFO @ Fri, 10 Nov 2017 23:40:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:40:43: #1 finished! INFO @ Fri, 10 Nov 2017 23:40:43: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:40:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:40:47: #2 number of paired peaks: 7251 INFO @ Fri, 10 Nov 2017 23:40:47: start model_add_line... INFO @ Fri, 10 Nov 2017 23:40:47: start X-correlation... INFO @ Fri, 10 Nov 2017 23:40:47: end of X-cor INFO @ Fri, 10 Nov 2017 23:40:47: #2 finished! INFO @ Fri, 10 Nov 2017 23:40:47: #2 predicted fragment length is 100 bps INFO @ Fri, 10 Nov 2017 23:40:47: #2 alternative fragment length(s) may be 100 bps INFO @ Fri, 10 Nov 2017 23:40:47: #2.2 Generate R script for model : SRX1056330.05_model.r WARNING @ Fri, 10 Nov 2017 23:40:47: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:40:47: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Fri, 10 Nov 2017 23:40:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:40:47: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:40:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:40:54: 28000000 INFO @ Fri, 10 Nov 2017 23:41:19: 29000000 INFO @ Fri, 10 Nov 2017 23:41:45: 30000000 INFO @ Fri, 10 Nov 2017 23:42:06: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 23:42:06: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 23:42:06: #1 total tags in treatment: 30803843 INFO @ Fri, 10 Nov 2017 23:42:06: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:42:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:42:07: #1 tags after filtering in treatment: 30803749 INFO @ Fri, 10 Nov 2017 23:42:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:42:07: #1 finished! INFO @ Fri, 10 Nov 2017 23:42:07: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:42:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:42:10: #2 number of paired peaks: 7251 INFO @ Fri, 10 Nov 2017 23:42:10: start model_add_line... INFO @ Fri, 10 Nov 2017 23:42:11: start X-correlation... INFO @ Fri, 10 Nov 2017 23:42:11: end of X-cor INFO @ Fri, 10 Nov 2017 23:42:11: #2 finished! INFO @ Fri, 10 Nov 2017 23:42:11: #2 predicted fragment length is 100 bps INFO @ Fri, 10 Nov 2017 23:42:11: #2 alternative fragment length(s) may be 100 bps INFO @ Fri, 10 Nov 2017 23:42:11: #2.2 Generate R script for model : SRX1056330.10_model.r WARNING @ Fri, 10 Nov 2017 23:42:11: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:42:11: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Fri, 10 Nov 2017 23:42:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:42:11: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:42:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:42:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:43:12: #4 Write output xls file... SRX1056330.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:43:12: #4 Write peak in narrowPeak format file... SRX1056330.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:43:12: #4 Write summits bed file... SRX1056330.05_summits.bed INFO @ Fri, 10 Nov 2017 23:43:12: Done! pass1 - making usageList (59 chroms): 2 millis pass2 - checking and writing primary data (2157 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:43:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:44:32: #4 Write output xls file... SRX1056330.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:44:32: #4 Write peak in narrowPeak format file... SRX1056330.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:44:32: #4 Write summits bed file... SRX1056330.10_summits.bed INFO @ Fri, 10 Nov 2017 23:44:32: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (1067 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。