Job ID = 10194840 sra ファイルのダウンロード中... Completed: 1195568K bytes transferred in 28 seconds (342144K 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 57248588 spots for /home/okishinya/chipatlas/results/rn6/SRX1977129/SRR3952261.sra Written 57248588 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:38:29 57248588 reads; of these: 57248588 (100.00%) were unpaired; of these: 10582270 (18.48%) aligned 0 times 23640093 (41.29%) aligned exactly 1 time 23026225 (40.22%) aligned >1 times 81.52% overall alignment rate Time searching: 01:38:32 Overall time: 01:38:32 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 20 files... [bam_rmdupse_core] 4152703 / 46666318 = 0.0890 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 03:41:50: # Command line: callpeak -t SRX1977129.bam -f BAM -g 2.15e9 -n SRX1977129.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977129.05 # format = BAM # ChIP-seq file = ['SRX1977129.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 03:41:50: # Command line: callpeak -t SRX1977129.bam -f BAM -g 2.15e9 -n SRX1977129.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977129.10 # format = BAM # ChIP-seq file = ['SRX1977129.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 03:41:50: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:41:50: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:41:50: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:41:50: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:41:50: # Command line: callpeak -t SRX1977129.bam -f BAM -g 2.15e9 -n SRX1977129.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977129.20 # format = BAM # ChIP-seq file = ['SRX1977129.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 03:41:50: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:41:50: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:41:59: 1000000 INFO @ Sat, 11 Nov 2017 03:41:59: 1000000 INFO @ Sat, 11 Nov 2017 03:41:59: 1000000 INFO @ Sat, 11 Nov 2017 03:42:07: 2000000 INFO @ Sat, 11 Nov 2017 03:42:08: 2000000 INFO @ Sat, 11 Nov 2017 03:42:08: 2000000 INFO @ Sat, 11 Nov 2017 03:42:16: 3000000 INFO @ Sat, 11 Nov 2017 03:42:16: 3000000 INFO @ Sat, 11 Nov 2017 03:42:16: 3000000 INFO @ Sat, 11 Nov 2017 03:42:25: 4000000 INFO @ Sat, 11 Nov 2017 03:42:25: 4000000 INFO @ Sat, 11 Nov 2017 03:42:25: 4000000 INFO @ Sat, 11 Nov 2017 03:42:34: 5000000 INFO @ Sat, 11 Nov 2017 03:42:34: 5000000 INFO @ Sat, 11 Nov 2017 03:42:34: 5000000 INFO @ Sat, 11 Nov 2017 03:42:42: 6000000 INFO @ Sat, 11 Nov 2017 03:42:42: 6000000 INFO @ Sat, 11 Nov 2017 03:42:42: 6000000 INFO @ Sat, 11 Nov 2017 03:42:51: 7000000 INFO @ Sat, 11 Nov 2017 03:42:51: 7000000 INFO @ Sat, 11 Nov 2017 03:42:51: 7000000 INFO @ Sat, 11 Nov 2017 03:42:59: 8000000 INFO @ Sat, 11 Nov 2017 03:43:00: 8000000 INFO @ Sat, 11 Nov 2017 03:43:00: 8000000 INFO @ Sat, 11 Nov 2017 03:43:08: 9000000 INFO @ Sat, 11 Nov 2017 03:43:08: 9000000 INFO @ Sat, 11 Nov 2017 03:43:08: 9000000 INFO @ Sat, 11 Nov 2017 03:43:17: 10000000 INFO @ Sat, 11 Nov 2017 03:43:17: 10000000 INFO @ Sat, 11 Nov 2017 03:43:17: 10000000 INFO @ Sat, 11 Nov 2017 03:43:25: 11000000 INFO @ Sat, 11 Nov 2017 03:43:25: 11000000 INFO @ Sat, 11 Nov 2017 03:43:25: 11000000 INFO @ Sat, 11 Nov 2017 03:43:34: 12000000 INFO @ Sat, 11 Nov 2017 03:43:34: 12000000 INFO @ Sat, 11 Nov 2017 03:43:34: 12000000 INFO @ Sat, 11 Nov 2017 03:43:42: 13000000 INFO @ Sat, 11 Nov 2017 03:43:42: 13000000 INFO @ Sat, 11 Nov 2017 03:43:42: 13000000 INFO @ Sat, 11 Nov 2017 03:43:51: 14000000 INFO @ Sat, 11 Nov 2017 03:43:51: 14000000 INFO @ Sat, 11 Nov 2017 03:43:51: 14000000 INFO @ Sat, 11 Nov 2017 03:43:59: 15000000 INFO @ Sat, 11 Nov 2017 03:43:59: 15000000 INFO @ Sat, 11 Nov 2017 03:43:59: 15000000 INFO @ Sat, 11 Nov 2017 03:44:07: 16000000 INFO @ Sat, 11 Nov 2017 03:44:08: 16000000 INFO @ Sat, 11 Nov 2017 03:44:08: 16000000 INFO @ Sat, 11 Nov 2017 03:44:16: 17000000 INFO @ Sat, 11 Nov 2017 03:44:16: 17000000 INFO @ Sat, 11 Nov 2017 03:44:16: 17000000 INFO @ Sat, 11 Nov 2017 03:44:24: 18000000 INFO @ Sat, 11 Nov 2017 03:44:24: 18000000 INFO @ Sat, 11 Nov 2017 03:44:24: 18000000 INFO @ Sat, 11 Nov 2017 03:44:33: 19000000 INFO @ Sat, 11 Nov 2017 03:44:33: 19000000 INFO @ Sat, 11 Nov 2017 03:44:33: 19000000 INFO @ Sat, 11 Nov 2017 03:44:41: 20000000 INFO @ Sat, 11 Nov 2017 03:44:42: 20000000 INFO @ Sat, 11 Nov 2017 03:44:42: 20000000 INFO @ Sat, 11 Nov 2017 03:44:50: 21000000 INFO @ Sat, 11 Nov 2017 03:44:50: 21000000 INFO @ Sat, 11 Nov 2017 03:44:50: 21000000 INFO @ Sat, 11 Nov 2017 03:44:58: 22000000 INFO @ Sat, 11 Nov 2017 03:44:58: 22000000 INFO @ Sat, 11 Nov 2017 03:44:58: 22000000 INFO @ Sat, 11 Nov 2017 03:45:07: 23000000 INFO @ Sat, 11 Nov 2017 03:45:07: 23000000 INFO @ Sat, 11 Nov 2017 03:45:07: 23000000 INFO @ Sat, 11 Nov 2017 03:45:15: 24000000 INFO @ Sat, 11 Nov 2017 03:45:15: 24000000 INFO @ Sat, 11 Nov 2017 03:45:15: 24000000 INFO @ Sat, 11 Nov 2017 03:45:24: 25000000 INFO @ Sat, 11 Nov 2017 03:45:24: 25000000 INFO @ Sat, 11 Nov 2017 03:45:24: 25000000 INFO @ Sat, 11 Nov 2017 03:45:32: 26000000 INFO @ Sat, 11 Nov 2017 03:45:32: 26000000 INFO @ Sat, 11 Nov 2017 03:45:32: 26000000 INFO @ Sat, 11 Nov 2017 03:45:40: 27000000 INFO @ Sat, 11 Nov 2017 03:45:40: 27000000 INFO @ Sat, 11 Nov 2017 03:45:40: 27000000 INFO @ Sat, 11 Nov 2017 03:45:49: 28000000 INFO @ Sat, 11 Nov 2017 03:45:49: 28000000 INFO @ Sat, 11 Nov 2017 03:45:49: 28000000 INFO @ Sat, 11 Nov 2017 03:45:57: 29000000 INFO @ Sat, 11 Nov 2017 03:45:57: 29000000 INFO @ Sat, 11 Nov 2017 03:45:57: 29000000 INFO @ Sat, 11 Nov 2017 03:46:05: 30000000 INFO @ Sat, 11 Nov 2017 03:46:05: 30000000 INFO @ Sat, 11 Nov 2017 03:46:06: 30000000 INFO @ Sat, 11 Nov 2017 03:46:14: 31000000 INFO @ Sat, 11 Nov 2017 03:46:14: 31000000 INFO @ Sat, 11 Nov 2017 03:46:14: 31000000 INFO @ Sat, 11 Nov 2017 03:46:22: 32000000 INFO @ Sat, 11 Nov 2017 03:46:22: 32000000 INFO @ Sat, 11 Nov 2017 03:46:22: 32000000 INFO @ Sat, 11 Nov 2017 03:46:31: 33000000 INFO @ Sat, 11 Nov 2017 03:46:31: 33000000 INFO @ Sat, 11 Nov 2017 03:46:31: 33000000 INFO @ Sat, 11 Nov 2017 03:46:39: 34000000 INFO @ Sat, 11 Nov 2017 03:46:39: 34000000 INFO @ Sat, 11 Nov 2017 03:46:40: 34000000 INFO @ Sat, 11 Nov 2017 03:46:48: 35000000 INFO @ Sat, 11 Nov 2017 03:46:48: 35000000 INFO @ Sat, 11 Nov 2017 03:46:48: 35000000 INFO @ Sat, 11 Nov 2017 03:46:56: 36000000 INFO @ Sat, 11 Nov 2017 03:46:56: 36000000 INFO @ Sat, 11 Nov 2017 03:46:57: 36000000 INFO @ Sat, 11 Nov 2017 03:47:05: 37000000 INFO @ Sat, 11 Nov 2017 03:47:05: 37000000 INFO @ Sat, 11 Nov 2017 03:47:05: 37000000 INFO @ Sat, 11 Nov 2017 03:47:13: 38000000 INFO @ Sat, 11 Nov 2017 03:47:13: 38000000 INFO @ Sat, 11 Nov 2017 03:47:14: 38000000 INFO @ Sat, 11 Nov 2017 03:47:22: 39000000 INFO @ Sat, 11 Nov 2017 03:47:22: 39000000 INFO @ Sat, 11 Nov 2017 03:47:22: 39000000 INFO @ Sat, 11 Nov 2017 03:47:30: 40000000 INFO @ Sat, 11 Nov 2017 03:47:31: 40000000 INFO @ Sat, 11 Nov 2017 03:47:31: 40000000 INFO @ Sat, 11 Nov 2017 03:47:39: 41000000 INFO @ Sat, 11 Nov 2017 03:47:39: 41000000 INFO @ Sat, 11 Nov 2017 03:47:39: 41000000 INFO @ Sat, 11 Nov 2017 03:47:47: 42000000 INFO @ Sat, 11 Nov 2017 03:47:48: 42000000 INFO @ Sat, 11 Nov 2017 03:47:48: 42000000 INFO @ Sat, 11 Nov 2017 03:47:52: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:47:52: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:47:52: #1 total tags in treatment: 42513615 INFO @ Sat, 11 Nov 2017 03:47:52: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:47:52: #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 03:47:52: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:47:52: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:47:52: #1 total tags in treatment: 42513615 INFO @ Sat, 11 Nov 2017 03:47:52: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:47:52: #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 03:47:53: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:47:53: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:47:53: #1 total tags in treatment: 42513615 INFO @ Sat, 11 Nov 2017 03:47:53: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:47:53: #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 03:47:53: #1 tags after filtering in treatment: 42513551 INFO @ Sat, 11 Nov 2017 03:47:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:47:53: #1 finished! INFO @ Sat, 11 Nov 2017 03:47:53: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:47:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:47:53: #1 tags after filtering in treatment: 42513551 INFO @ Sat, 11 Nov 2017 03:47:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:47:53: #1 finished! INFO @ Sat, 11 Nov 2017 03:47:53: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:47:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:47:54: #1 tags after filtering in treatment: 42513551 INFO @ Sat, 11 Nov 2017 03:47:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:47:54: #1 finished! INFO @ Sat, 11 Nov 2017 03:47:54: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:47:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:47:58: #2 number of paired peaks: 26007 INFO @ Sat, 11 Nov 2017 03:47:58: start model_add_line... INFO @ Sat, 11 Nov 2017 03:47:59: #2 number of paired peaks: 26007 INFO @ Sat, 11 Nov 2017 03:47:59: start model_add_line... INFO @ Sat, 11 Nov 2017 03:47:59: #2 number of paired peaks: 26007 INFO @ Sat, 11 Nov 2017 03:47:59: start model_add_line... INFO @ Sat, 11 Nov 2017 03:47:59: start X-correlation... INFO @ Sat, 11 Nov 2017 03:47:59: end of X-cor INFO @ Sat, 11 Nov 2017 03:47:59: #2 finished! INFO @ Sat, 11 Nov 2017 03:47:59: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Nov 2017 03:47:59: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Nov 2017 03:47:59: #2.2 Generate R script for model : SRX1977129.20_model.r WARNING @ Sat, 11 Nov 2017 03:47:59: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 03:47:59: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Nov 2017 03:47:59: #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 03:47:59: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:47:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:47:59: start X-correlation... INFO @ Sat, 11 Nov 2017 03:47:59: end of X-cor INFO @ Sat, 11 Nov 2017 03:47:59: #2 finished! INFO @ Sat, 11 Nov 2017 03:47:59: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Nov 2017 03:47:59: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Nov 2017 03:47:59: #2.2 Generate R script for model : SRX1977129.10_model.r WARNING @ Sat, 11 Nov 2017 03:47:59: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 03:47:59: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Nov 2017 03:47:59: #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 03:47:59: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:47:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:47:59: start X-correlation... INFO @ Sat, 11 Nov 2017 03:47:59: end of X-cor INFO @ Sat, 11 Nov 2017 03:47:59: #2 finished! INFO @ Sat, 11 Nov 2017 03:47:59: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Nov 2017 03:47:59: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Nov 2017 03:47:59: #2.2 Generate R script for model : SRX1977129.05_model.r WARNING @ Sat, 11 Nov 2017 03:47:59: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 03:47:59: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Nov 2017 03:47:59: #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 03:47:59: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:47:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:49:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:49:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:49:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:50:49: #4 Write output xls file... SRX1977129.10_peaks.xls INFO @ Sat, 11 Nov 2017 03:50:49: #4 Write peak in narrowPeak format file... SRX1977129.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:50:49: #4 Write summits bed file... SRX1977129.10_summits.bed INFO @ Sat, 11 Nov 2017 03:50:49: Done! pass1 - making usageList (81 chroms): 2 millis pass2 - checking and writing primary data (3229 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:51:04: #4 Write output xls file... SRX1977129.05_peaks.xls INFO @ Sat, 11 Nov 2017 03:51:04: #4 Write peak in narrowPeak format file... SRX1977129.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:51:04: #4 Write summits bed file... SRX1977129.05_summits.bed INFO @ Sat, 11 Nov 2017 03:51:04: Done! pass1 - making usageList (144 chroms): 4 millis pass2 - checking and writing primary data (14245 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:51:06: #4 Write output xls file... SRX1977129.20_peaks.xls INFO @ Sat, 11 Nov 2017 03:51:06: #4 Write peak in narrowPeak format file... SRX1977129.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:51:06: #4 Write summits bed file... SRX1977129.20_summits.bed INFO @ Sat, 11 Nov 2017 03:51:06: Done! pass1 - making usageList (59 chroms): 1 millis pass2 - checking and writing primary data (1080 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。