Job ID = 10487593 sra ファイルのダウンロード中... Completed: 4180463K bytes transferred in 139 seconds (245590K 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 62219293 spots for /home/okishinya/chipatlas/results/rn6/SRX2611116/SRR5311160.sra Written 62219293 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: 00:00:00 Multiseed full-index search: 03:31:33 62219293 reads; of these: 62219293 (100.00%) were unpaired; of these: 13219084 (21.25%) aligned 0 times 41331168 (66.43%) aligned exactly 1 time 7669041 (12.33%) aligned >1 times 78.75% overall alignment rate Time searching: 03:31:35 Overall time: 03:31:35 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 36 files... [bam_rmdupse_core] 17827623 / 49000209 = 0.3638 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 13:44:35: # Command line: callpeak -t SRX2611116.bam -f BAM -g 2.15e9 -n SRX2611116.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611116.05 # format = BAM # ChIP-seq file = ['SRX2611116.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 13:44:35: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:44:35: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:44:35: # Command line: callpeak -t SRX2611116.bam -f BAM -g 2.15e9 -n SRX2611116.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611116.10 # format = BAM # ChIP-seq file = ['SRX2611116.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 13:44:35: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:44:35: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:44:35: # Command line: callpeak -t SRX2611116.bam -f BAM -g 2.15e9 -n SRX2611116.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611116.20 # format = BAM # ChIP-seq file = ['SRX2611116.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 13:44:35: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:44:35: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:44:45: 1000000 INFO @ Sun, 18 Mar 2018 13:44:45: 1000000 INFO @ Sun, 18 Mar 2018 13:44:45: 1000000 INFO @ Sun, 18 Mar 2018 13:44:55: 2000000 INFO @ Sun, 18 Mar 2018 13:44:56: 2000000 INFO @ Sun, 18 Mar 2018 13:44:56: 2000000 INFO @ Sun, 18 Mar 2018 13:45:05: 3000000 INFO @ Sun, 18 Mar 2018 13:45:05: 3000000 INFO @ Sun, 18 Mar 2018 13:45:05: 3000000 INFO @ Sun, 18 Mar 2018 13:45:15: 4000000 INFO @ Sun, 18 Mar 2018 13:45:15: 4000000 INFO @ Sun, 18 Mar 2018 13:45:15: 4000000 INFO @ Sun, 18 Mar 2018 13:45:24: 5000000 INFO @ Sun, 18 Mar 2018 13:45:25: 5000000 INFO @ Sun, 18 Mar 2018 13:45:25: 5000000 INFO @ Sun, 18 Mar 2018 13:45:34: 6000000 INFO @ Sun, 18 Mar 2018 13:45:35: 6000000 INFO @ Sun, 18 Mar 2018 13:45:35: 6000000 INFO @ Sun, 18 Mar 2018 13:45:44: 7000000 INFO @ Sun, 18 Mar 2018 13:45:45: 7000000 INFO @ Sun, 18 Mar 2018 13:45:45: 7000000 INFO @ Sun, 18 Mar 2018 13:45:54: 8000000 INFO @ Sun, 18 Mar 2018 13:45:55: 8000000 INFO @ Sun, 18 Mar 2018 13:45:55: 8000000 INFO @ Sun, 18 Mar 2018 13:46:03: 9000000 INFO @ Sun, 18 Mar 2018 13:46:05: 9000000 INFO @ Sun, 18 Mar 2018 13:46:05: 9000000 INFO @ Sun, 18 Mar 2018 13:46:13: 10000000 INFO @ Sun, 18 Mar 2018 13:46:15: 10000000 INFO @ Sun, 18 Mar 2018 13:46:15: 10000000 INFO @ Sun, 18 Mar 2018 13:46:23: 11000000 INFO @ Sun, 18 Mar 2018 13:46:25: 11000000 INFO @ Sun, 18 Mar 2018 13:46:25: 11000000 INFO @ Sun, 18 Mar 2018 13:46:33: 12000000 INFO @ Sun, 18 Mar 2018 13:46:34: 12000000 INFO @ Sun, 18 Mar 2018 13:46:34: 12000000 INFO @ Sun, 18 Mar 2018 13:46:42: 13000000 INFO @ Sun, 18 Mar 2018 13:46:44: 13000000 INFO @ Sun, 18 Mar 2018 13:46:44: 13000000 INFO @ Sun, 18 Mar 2018 13:46:52: 14000000 INFO @ Sun, 18 Mar 2018 13:46:54: 14000000 INFO @ Sun, 18 Mar 2018 13:46:54: 14000000 INFO @ Sun, 18 Mar 2018 13:47:02: 15000000 INFO @ Sun, 18 Mar 2018 13:47:04: 15000000 INFO @ Sun, 18 Mar 2018 13:47:04: 15000000 INFO @ Sun, 18 Mar 2018 13:47:12: 16000000 INFO @ Sun, 18 Mar 2018 13:47:14: 16000000 INFO @ Sun, 18 Mar 2018 13:47:14: 16000000 INFO @ Sun, 18 Mar 2018 13:47:21: 17000000 INFO @ Sun, 18 Mar 2018 13:47:24: 17000000 INFO @ Sun, 18 Mar 2018 13:47:24: 17000000 INFO @ Sun, 18 Mar 2018 13:47:31: 18000000 INFO @ Sun, 18 Mar 2018 13:47:34: 18000000 INFO @ Sun, 18 Mar 2018 13:47:34: 18000000 INFO @ Sun, 18 Mar 2018 13:47:41: 19000000 INFO @ Sun, 18 Mar 2018 13:47:44: 19000000 INFO @ Sun, 18 Mar 2018 13:47:44: 19000000 INFO @ Sun, 18 Mar 2018 13:47:51: 20000000 INFO @ Sun, 18 Mar 2018 13:47:53: 20000000 INFO @ Sun, 18 Mar 2018 13:47:53: 20000000 INFO @ Sun, 18 Mar 2018 13:48:01: 21000000 INFO @ Sun, 18 Mar 2018 13:48:03: 21000000 INFO @ Sun, 18 Mar 2018 13:48:03: 21000000 INFO @ Sun, 18 Mar 2018 13:48:10: 22000000 INFO @ Sun, 18 Mar 2018 13:48:13: 22000000 INFO @ Sun, 18 Mar 2018 13:48:13: 22000000 INFO @ Sun, 18 Mar 2018 13:48:20: 23000000 INFO @ Sun, 18 Mar 2018 13:48:23: 23000000 INFO @ Sun, 18 Mar 2018 13:48:23: 23000000 INFO @ Sun, 18 Mar 2018 13:48:30: 24000000 INFO @ Sun, 18 Mar 2018 13:48:33: 24000000 INFO @ Sun, 18 Mar 2018 13:48:33: 24000000 INFO @ Sun, 18 Mar 2018 13:48:40: 25000000 INFO @ Sun, 18 Mar 2018 13:48:43: 25000000 INFO @ Sun, 18 Mar 2018 13:48:43: 25000000 INFO @ Sun, 18 Mar 2018 13:48:49: 26000000 INFO @ Sun, 18 Mar 2018 13:48:53: 26000000 INFO @ Sun, 18 Mar 2018 13:48:53: 26000000 INFO @ Sun, 18 Mar 2018 13:48:59: 27000000 INFO @ Sun, 18 Mar 2018 13:49:03: 27000000 INFO @ Sun, 18 Mar 2018 13:49:03: 27000000 INFO @ Sun, 18 Mar 2018 13:49:09: 28000000 INFO @ Sun, 18 Mar 2018 13:49:13: 28000000 INFO @ Sun, 18 Mar 2018 13:49:13: 28000000 INFO @ Sun, 18 Mar 2018 13:49:19: 29000000 INFO @ Sun, 18 Mar 2018 13:49:23: 29000000 INFO @ Sun, 18 Mar 2018 13:49:23: 29000000 INFO @ Sun, 18 Mar 2018 13:49:29: 30000000 INFO @ Sun, 18 Mar 2018 13:49:33: 30000000 INFO @ Sun, 18 Mar 2018 13:49:33: 30000000 INFO @ Sun, 18 Mar 2018 13:49:39: 31000000 INFO @ Sun, 18 Mar 2018 13:49:41: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:49:41: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:49:41: #1 total tags in treatment: 31172586 INFO @ Sun, 18 Mar 2018 13:49:41: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:49:41: #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 13:49:42: #1 tags after filtering in treatment: 31172495 INFO @ Sun, 18 Mar 2018 13:49:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:49:42: #1 finished! INFO @ Sun, 18 Mar 2018 13:49:42: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:49:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:49:43: 31000000 INFO @ Sun, 18 Mar 2018 13:49:43: 31000000 INFO @ Sun, 18 Mar 2018 13:49:45: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:49:45: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:49:45: #1 total tags in treatment: 31172586 INFO @ Sun, 18 Mar 2018 13:49:45: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:49:45: #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 13:49:45: #2 number of paired peaks: 8772 INFO @ Sun, 18 Mar 2018 13:49:45: start model_add_line... INFO @ Sun, 18 Mar 2018 13:49:45: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:49:45: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:49:45: #1 total tags in treatment: 31172586 INFO @ Sun, 18 Mar 2018 13:49:45: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:49:45: #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 13:49:45: start X-correlation... INFO @ Sun, 18 Mar 2018 13:49:45: end of X-cor INFO @ Sun, 18 Mar 2018 13:49:45: #2 finished! INFO @ Sun, 18 Mar 2018 13:49:45: #2 predicted fragment length is 161 bps INFO @ Sun, 18 Mar 2018 13:49:45: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 18 Mar 2018 13:49:45: #2.2 Generate R script for model : SRX2611116.20_model.r WARNING @ Sun, 18 Mar 2018 13:49:45: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:49:45: #2 You may need to consider one of the other alternative d(s): 161 WARNING @ Sun, 18 Mar 2018 13:49:45: #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 13:49:45: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:49:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:49:45: #1 tags after filtering in treatment: 31172495 INFO @ Sun, 18 Mar 2018 13:49:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:49:45: #1 finished! INFO @ Sun, 18 Mar 2018 13:49:45: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:49:46: #1 tags after filtering in treatment: 31172495 INFO @ Sun, 18 Mar 2018 13:49:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:49:46: #1 finished! INFO @ Sun, 18 Mar 2018 13:49:46: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:49:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:49:49: #2 number of paired peaks: 8772 INFO @ Sun, 18 Mar 2018 13:49:49: start model_add_line... INFO @ Sun, 18 Mar 2018 13:49:49: start X-correlation... INFO @ Sun, 18 Mar 2018 13:49:49: end of X-cor INFO @ Sun, 18 Mar 2018 13:49:49: #2 finished! INFO @ Sun, 18 Mar 2018 13:49:49: #2 predicted fragment length is 161 bps INFO @ Sun, 18 Mar 2018 13:49:49: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 18 Mar 2018 13:49:49: #2.2 Generate R script for model : SRX2611116.05_model.r WARNING @ Sun, 18 Mar 2018 13:49:49: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:49:49: #2 You may need to consider one of the other alternative d(s): 161 WARNING @ Sun, 18 Mar 2018 13:49:49: #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 13:49:49: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:49:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:49:49: #2 number of paired peaks: 8772 INFO @ Sun, 18 Mar 2018 13:49:49: start model_add_line... INFO @ Sun, 18 Mar 2018 13:49:49: start X-correlation... INFO @ Sun, 18 Mar 2018 13:49:49: end of X-cor INFO @ Sun, 18 Mar 2018 13:49:49: #2 finished! INFO @ Sun, 18 Mar 2018 13:49:49: #2 predicted fragment length is 161 bps INFO @ Sun, 18 Mar 2018 13:49:49: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 18 Mar 2018 13:49:49: #2.2 Generate R script for model : SRX2611116.10_model.r WARNING @ Sun, 18 Mar 2018 13:49:49: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:49:49: #2 You may need to consider one of the other alternative d(s): 161 WARNING @ Sun, 18 Mar 2018 13:49:49: #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 13:49:49: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:49:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:50:59: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:51:04: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:51:08: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:51:45: #4 Write output xls file... SRX2611116.20_peaks.xls INFO @ Sun, 18 Mar 2018 13:51:45: #4 Write peak in narrowPeak format file... SRX2611116.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:51:45: #4 Write summits bed file... SRX2611116.20_summits.bed INFO @ Sun, 18 Mar 2018 13:51:45: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (466 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:51:47: #4 Write output xls file... SRX2611116.10_peaks.xls INFO @ Sun, 18 Mar 2018 13:51:47: #4 Write peak in narrowPeak format file... SRX2611116.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:51:47: #4 Write summits bed file... SRX2611116.10_summits.bed INFO @ Sun, 18 Mar 2018 13:51:47: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (1126 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:51:53: #4 Write output xls file... SRX2611116.05_peaks.xls INFO @ Sun, 18 Mar 2018 13:51:53: #4 Write peak in narrowPeak format file... SRX2611116.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:51:54: #4 Write summits bed file... SRX2611116.05_summits.bed INFO @ Sun, 18 Mar 2018 13:51:54: Done! pass1 - making usageList (64 chroms): 1 millis pass2 - checking and writing primary data (5215 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。