Job ID = 10194724 sra ファイルのダウンロード中... Completed: 7081423K bytes transferred in 82 seconds (706578K 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 118722791 spots for /home/okishinya/chipatlas/results/rn6/SRX1037559/SRR2039163.sra Written 118722791 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 08:08:37 118722791 reads; of these: 118722791 (100.00%) were unpaired; of these: 2843483 (2.40%) aligned 0 times 92471583 (77.89%) aligned exactly 1 time 23407725 (19.72%) aligned >1 times 97.60% overall alignment rate Time searching: 08:08:41 Overall time: 08:08:41 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 48 files... [bam_rmdupse_core] 89437168 / 115879308 = 0.7718 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 04:28:17: # Command line: callpeak -t SRX1037559.bam -f BAM -g 2.15e9 -n SRX1037559.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1037559.05 # format = BAM # ChIP-seq file = ['SRX1037559.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 04:28:17: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:28:17: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:28:17: # Command line: callpeak -t SRX1037559.bam -f BAM -g 2.15e9 -n SRX1037559.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1037559.10 # format = BAM # ChIP-seq file = ['SRX1037559.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 04:28:17: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:28:17: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:28:17: # Command line: callpeak -t SRX1037559.bam -f BAM -g 2.15e9 -n SRX1037559.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1037559.20 # format = BAM # ChIP-seq file = ['SRX1037559.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 04:28:17: #1 read tag files... INFO @ Sat, 11 Nov 2017 04:28:17: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 04:28:27: 1000000 INFO @ Sat, 11 Nov 2017 04:28:28: 1000000 INFO @ Sat, 11 Nov 2017 04:28:36: 1000000 INFO @ Sat, 11 Nov 2017 04:28:38: 2000000 INFO @ Sat, 11 Nov 2017 04:28:40: 2000000 INFO @ Sat, 11 Nov 2017 04:28:48: 3000000 INFO @ Sat, 11 Nov 2017 04:28:51: 3000000 INFO @ Sat, 11 Nov 2017 04:28:53: 2000000 INFO @ Sat, 11 Nov 2017 04:28:57: 4000000 INFO @ Sat, 11 Nov 2017 04:29:01: 4000000 INFO @ Sat, 11 Nov 2017 04:29:08: 5000000 INFO @ Sat, 11 Nov 2017 04:29:09: 3000000 INFO @ Sat, 11 Nov 2017 04:29:12: 5000000 INFO @ Sat, 11 Nov 2017 04:29:18: 6000000 INFO @ Sat, 11 Nov 2017 04:29:23: 4000000 INFO @ Sat, 11 Nov 2017 04:29:23: 6000000 INFO @ Sat, 11 Nov 2017 04:29:28: 7000000 INFO @ Sat, 11 Nov 2017 04:29:34: 7000000 INFO @ Sat, 11 Nov 2017 04:29:37: 5000000 INFO @ Sat, 11 Nov 2017 04:29:40: 8000000 INFO @ Sat, 11 Nov 2017 04:29:49: 8000000 INFO @ Sat, 11 Nov 2017 04:29:51: 9000000 INFO @ Sat, 11 Nov 2017 04:29:53: 6000000 INFO @ Sat, 11 Nov 2017 04:30:01: 10000000 INFO @ Sat, 11 Nov 2017 04:30:01: 9000000 INFO @ Sat, 11 Nov 2017 04:30:08: 7000000 INFO @ Sat, 11 Nov 2017 04:30:11: 11000000 INFO @ Sat, 11 Nov 2017 04:30:12: 10000000 INFO @ Sat, 11 Nov 2017 04:30:21: 12000000 INFO @ Sat, 11 Nov 2017 04:30:22: 8000000 INFO @ Sat, 11 Nov 2017 04:30:23: 11000000 INFO @ Sat, 11 Nov 2017 04:30:30: 13000000 INFO @ Sat, 11 Nov 2017 04:30:34: 12000000 INFO @ Sat, 11 Nov 2017 04:30:38: 9000000 INFO @ Sat, 11 Nov 2017 04:30:40: 14000000 INFO @ Sat, 11 Nov 2017 04:30:45: 13000000 INFO @ Sat, 11 Nov 2017 04:30:50: 15000000 INFO @ Sat, 11 Nov 2017 04:30:54: 10000000 INFO @ Sat, 11 Nov 2017 04:30:55: 14000000 INFO @ Sat, 11 Nov 2017 04:31:00: 16000000 INFO @ Sat, 11 Nov 2017 04:31:06: 15000000 INFO @ Sat, 11 Nov 2017 04:31:08: 11000000 INFO @ Sat, 11 Nov 2017 04:31:09: 17000000 INFO @ Sat, 11 Nov 2017 04:31:18: 16000000 INFO @ Sat, 11 Nov 2017 04:31:19: 18000000 INFO @ Sat, 11 Nov 2017 04:31:22: 12000000 INFO @ Sat, 11 Nov 2017 04:31:30: 19000000 INFO @ Sat, 11 Nov 2017 04:31:33: 17000000 INFO @ Sat, 11 Nov 2017 04:31:37: 13000000 INFO @ Sat, 11 Nov 2017 04:31:40: 20000000 INFO @ Sat, 11 Nov 2017 04:31:48: 18000000 INFO @ Sat, 11 Nov 2017 04:31:50: 21000000 INFO @ Sat, 11 Nov 2017 04:31:52: 14000000 INFO @ Sat, 11 Nov 2017 04:32:00: 22000000 INFO @ Sat, 11 Nov 2017 04:32:05: 19000000 INFO @ Sat, 11 Nov 2017 04:32:07: 15000000 INFO @ Sat, 11 Nov 2017 04:32:11: 23000000 INFO @ Sat, 11 Nov 2017 04:32:19: 16000000 INFO @ Sat, 11 Nov 2017 04:32:21: 20000000 INFO @ Sat, 11 Nov 2017 04:32:22: 24000000 INFO @ Sat, 11 Nov 2017 04:32:30: 17000000 INFO @ Sat, 11 Nov 2017 04:32:36: 25000000 INFO @ Sat, 11 Nov 2017 04:32:39: 21000000 INFO @ Sat, 11 Nov 2017 04:32:42: 18000000 INFO @ Sat, 11 Nov 2017 04:32:47: 26000000 INFO @ Sat, 11 Nov 2017 04:32:54: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 04:32:54: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 04:32:54: #1 total tags in treatment: 26442140 INFO @ Sat, 11 Nov 2017 04:32:54: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:32:54: #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 04:32:54: 19000000 INFO @ Sat, 11 Nov 2017 04:32:55: #1 tags after filtering in treatment: 26441999 INFO @ Sat, 11 Nov 2017 04:32:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:32:55: #1 finished! INFO @ Sat, 11 Nov 2017 04:32:55: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:32:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:32:56: 22000000 INFO @ Sat, 11 Nov 2017 04:33:06: #2 number of paired peaks: 108697 INFO @ Sat, 11 Nov 2017 04:33:06: start model_add_line... INFO @ Sat, 11 Nov 2017 04:33:07: start X-correlation... INFO @ Sat, 11 Nov 2017 04:33:07: end of X-cor INFO @ Sat, 11 Nov 2017 04:33:07: #2 finished! INFO @ Sat, 11 Nov 2017 04:33:07: #2 predicted fragment length is 181 bps INFO @ Sat, 11 Nov 2017 04:33:07: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 11 Nov 2017 04:33:07: #2.2 Generate R script for model : SRX1037559.05_model.r WARNING @ Sat, 11 Nov 2017 04:33:07: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 04:33:07: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Sat, 11 Nov 2017 04:33:07: #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 04:33:07: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:33:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:33:09: 20000000 INFO @ Sat, 11 Nov 2017 04:33:11: 23000000 INFO @ Sat, 11 Nov 2017 04:33:25: 21000000 INFO @ Sat, 11 Nov 2017 04:33:26: 24000000 INFO @ Sat, 11 Nov 2017 04:33:40: 22000000 INFO @ Sat, 11 Nov 2017 04:33:42: 25000000 INFO @ Sat, 11 Nov 2017 04:33:55: 23000000 INFO @ Sat, 11 Nov 2017 04:33:58: 26000000 INFO @ Sat, 11 Nov 2017 04:34:06: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 04:34:06: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 04:34:06: #1 total tags in treatment: 26442140 INFO @ Sat, 11 Nov 2017 04:34:06: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:34:06: #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 04:34:07: #1 tags after filtering in treatment: 26441999 INFO @ Sat, 11 Nov 2017 04:34:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:34:07: #1 finished! INFO @ Sat, 11 Nov 2017 04:34:07: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:34:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:34:10: 24000000 INFO @ Sat, 11 Nov 2017 04:34:16: #2 number of paired peaks: 108697 INFO @ Sat, 11 Nov 2017 04:34:16: start model_add_line... INFO @ Sat, 11 Nov 2017 04:34:17: start X-correlation... INFO @ Sat, 11 Nov 2017 04:34:17: end of X-cor INFO @ Sat, 11 Nov 2017 04:34:17: #2 finished! INFO @ Sat, 11 Nov 2017 04:34:17: #2 predicted fragment length is 181 bps INFO @ Sat, 11 Nov 2017 04:34:17: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 11 Nov 2017 04:34:17: #2.2 Generate R script for model : SRX1037559.10_model.r WARNING @ Sat, 11 Nov 2017 04:34:17: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 04:34:17: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Sat, 11 Nov 2017 04:34:17: #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 04:34:17: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:34:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:34:25: 25000000 INFO @ Sat, 11 Nov 2017 04:34:40: 26000000 INFO @ Sat, 11 Nov 2017 04:34:48: #1 tag size is determined as 100 bps INFO @ Sat, 11 Nov 2017 04:34:48: #1 tag size = 100 INFO @ Sat, 11 Nov 2017 04:34:48: #1 total tags in treatment: 26442140 INFO @ Sat, 11 Nov 2017 04:34:48: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 04:34:48: #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 04:34:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:34:49: #1 tags after filtering in treatment: 26441999 INFO @ Sat, 11 Nov 2017 04:34:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 04:34:49: #1 finished! INFO @ Sat, 11 Nov 2017 04:34:49: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 04:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 04:34:57: #2 number of paired peaks: 108697 INFO @ Sat, 11 Nov 2017 04:34:57: start model_add_line... INFO @ Sat, 11 Nov 2017 04:34:58: start X-correlation... INFO @ Sat, 11 Nov 2017 04:34:58: end of X-cor INFO @ Sat, 11 Nov 2017 04:34:58: #2 finished! INFO @ Sat, 11 Nov 2017 04:34:58: #2 predicted fragment length is 181 bps INFO @ Sat, 11 Nov 2017 04:34:58: #2 alternative fragment length(s) may be 181 bps INFO @ Sat, 11 Nov 2017 04:34:58: #2.2 Generate R script for model : SRX1037559.20_model.r WARNING @ Sat, 11 Nov 2017 04:34:58: #2 Since the d (181) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 04:34:58: #2 You may need to consider one of the other alternative d(s): 181 WARNING @ Sat, 11 Nov 2017 04:34:58: #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 04:34:58: #3 Call peaks... INFO @ Sat, 11 Nov 2017 04:34:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 04:35:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:36:03: #4 Write output xls file... SRX1037559.05_peaks.xls INFO @ Sat, 11 Nov 2017 04:36:03: #4 Write peak in narrowPeak format file... SRX1037559.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:36:04: #4 Write summits bed file... SRX1037559.05_summits.bed INFO @ Sat, 11 Nov 2017 04:36:04: Done! pass1 - making usageList (144 chroms): 11 millis pass2 - checking and writing primary data (33334 records, 4 fields): 107 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 04:36:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 04:36:45: #4 Write output xls file... SRX1037559.10_peaks.xls INFO @ Sat, 11 Nov 2017 04:36:46: #4 Write peak in narrowPeak format file... SRX1037559.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:36:46: #4 Write summits bed file... SRX1037559.10_summits.bed INFO @ Sat, 11 Nov 2017 04:36:46: Done! pass1 - making usageList (99 chroms): 6 millis pass2 - checking and writing primary data (14874 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 04:37:20: #4 Write output xls file... SRX1037559.20_peaks.xls INFO @ Sat, 11 Nov 2017 04:37:20: #4 Write peak in narrowPeak format file... SRX1037559.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 04:37:20: #4 Write summits bed file... SRX1037559.20_summits.bed INFO @ Sat, 11 Nov 2017 04:37:20: Done! pass1 - making usageList (69 chroms): 3 millis pass2 - checking and writing primary data (6545 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。