Job ID = 10487590 sra ファイルのダウンロード中... Completed: 3962059K bytes transferred in 139 seconds (232835K 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 57702646 spots for /home/okishinya/chipatlas/results/rn6/SRX2611113/SRR5311157.sra Written 57702646 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: 03:03:59 57702646 reads; of these: 57702646 (100.00%) were unpaired; of these: 15032932 (26.05%) aligned 0 times 32717057 (56.70%) aligned exactly 1 time 9952657 (17.25%) aligned >1 times 73.95% overall alignment rate Time searching: 03:04:02 Overall time: 03:04:02 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 32 files... [bam_rmdupse_core] 11710353 / 42669714 = 0.2744 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 13:12:54: # Command line: callpeak -t SRX2611113.bam -f BAM -g 2.15e9 -n SRX2611113.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611113.10 # format = BAM # ChIP-seq file = ['SRX2611113.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 13:12:54: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:12:54: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:12:54: # Command line: callpeak -t SRX2611113.bam -f BAM -g 2.15e9 -n SRX2611113.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611113.20 # format = BAM # ChIP-seq file = ['SRX2611113.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 13:12:54: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:12:54: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:12:54: # Command line: callpeak -t SRX2611113.bam -f BAM -g 2.15e9 -n SRX2611113.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611113.05 # format = BAM # ChIP-seq file = ['SRX2611113.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 13:12:54: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:12:54: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:13:05: 1000000 INFO @ Sun, 18 Mar 2018 13:13:05: 1000000 INFO @ Sun, 18 Mar 2018 13:13:05: 1000000 INFO @ Sun, 18 Mar 2018 13:13:16: 2000000 INFO @ Sun, 18 Mar 2018 13:13:16: 2000000 INFO @ Sun, 18 Mar 2018 13:13:16: 2000000 INFO @ Sun, 18 Mar 2018 13:13:27: 3000000 INFO @ Sun, 18 Mar 2018 13:13:27: 3000000 INFO @ Sun, 18 Mar 2018 13:13:27: 3000000 INFO @ Sun, 18 Mar 2018 13:13:38: 4000000 INFO @ Sun, 18 Mar 2018 13:13:38: 4000000 INFO @ Sun, 18 Mar 2018 13:13:39: 4000000 INFO @ Sun, 18 Mar 2018 13:13:48: 5000000 INFO @ Sun, 18 Mar 2018 13:13:49: 5000000 INFO @ Sun, 18 Mar 2018 13:13:50: 5000000 INFO @ Sun, 18 Mar 2018 13:13:59: 6000000 INFO @ Sun, 18 Mar 2018 13:14:00: 6000000 INFO @ Sun, 18 Mar 2018 13:14:01: 6000000 INFO @ Sun, 18 Mar 2018 13:14:10: 7000000 INFO @ Sun, 18 Mar 2018 13:14:11: 7000000 INFO @ Sun, 18 Mar 2018 13:14:12: 7000000 INFO @ Sun, 18 Mar 2018 13:14:20: 8000000 INFO @ Sun, 18 Mar 2018 13:14:22: 8000000 INFO @ Sun, 18 Mar 2018 13:14:24: 8000000 INFO @ Sun, 18 Mar 2018 13:14:31: 9000000 INFO @ Sun, 18 Mar 2018 13:14:34: 9000000 INFO @ Sun, 18 Mar 2018 13:14:35: 9000000 INFO @ Sun, 18 Mar 2018 13:14:42: 10000000 INFO @ Sun, 18 Mar 2018 13:14:45: 10000000 INFO @ Sun, 18 Mar 2018 13:14:47: 10000000 INFO @ Sun, 18 Mar 2018 13:14:53: 11000000 INFO @ Sun, 18 Mar 2018 13:14:56: 11000000 INFO @ Sun, 18 Mar 2018 13:14:58: 11000000 INFO @ Sun, 18 Mar 2018 13:15:04: 12000000 INFO @ Sun, 18 Mar 2018 13:15:07: 12000000 INFO @ Sun, 18 Mar 2018 13:15:09: 12000000 INFO @ Sun, 18 Mar 2018 13:15:14: 13000000 INFO @ Sun, 18 Mar 2018 13:15:18: 13000000 INFO @ Sun, 18 Mar 2018 13:15:20: 13000000 INFO @ Sun, 18 Mar 2018 13:15:25: 14000000 INFO @ Sun, 18 Mar 2018 13:15:29: 14000000 INFO @ Sun, 18 Mar 2018 13:15:31: 14000000 INFO @ Sun, 18 Mar 2018 13:15:35: 15000000 INFO @ Sun, 18 Mar 2018 13:15:40: 15000000 INFO @ Sun, 18 Mar 2018 13:15:43: 15000000 INFO @ Sun, 18 Mar 2018 13:15:46: 16000000 INFO @ Sun, 18 Mar 2018 13:15:51: 16000000 INFO @ Sun, 18 Mar 2018 13:15:54: 16000000 INFO @ Sun, 18 Mar 2018 13:15:56: 17000000 INFO @ Sun, 18 Mar 2018 13:16:02: 17000000 INFO @ Sun, 18 Mar 2018 13:16:05: 17000000 INFO @ Sun, 18 Mar 2018 13:16:08: 18000000 INFO @ Sun, 18 Mar 2018 13:16:12: 18000000 INFO @ Sun, 18 Mar 2018 13:16:16: 18000000 INFO @ Sun, 18 Mar 2018 13:16:19: 19000000 INFO @ Sun, 18 Mar 2018 13:16:22: 19000000 INFO @ Sun, 18 Mar 2018 13:16:28: 19000000 INFO @ Sun, 18 Mar 2018 13:16:32: 20000000 INFO @ Sun, 18 Mar 2018 13:16:33: 20000000 INFO @ Sun, 18 Mar 2018 13:16:40: 20000000 INFO @ Sun, 18 Mar 2018 13:16:43: 21000000 INFO @ Sun, 18 Mar 2018 13:16:43: 21000000 INFO @ Sun, 18 Mar 2018 13:16:51: 21000000 INFO @ Sun, 18 Mar 2018 13:16:53: 22000000 INFO @ Sun, 18 Mar 2018 13:16:54: 22000000 INFO @ Sun, 18 Mar 2018 13:17:02: 22000000 INFO @ Sun, 18 Mar 2018 13:17:04: 23000000 INFO @ Sun, 18 Mar 2018 13:17:05: 23000000 INFO @ Sun, 18 Mar 2018 13:17:13: 23000000 INFO @ Sun, 18 Mar 2018 13:17:15: 24000000 INFO @ Sun, 18 Mar 2018 13:17:16: 24000000 INFO @ Sun, 18 Mar 2018 13:17:24: 24000000 INFO @ Sun, 18 Mar 2018 13:17:26: 25000000 INFO @ Sun, 18 Mar 2018 13:17:27: 25000000 INFO @ Sun, 18 Mar 2018 13:17:35: 25000000 INFO @ Sun, 18 Mar 2018 13:17:36: 26000000 INFO @ Sun, 18 Mar 2018 13:17:37: 26000000 INFO @ Sun, 18 Mar 2018 13:17:46: 26000000 INFO @ Sun, 18 Mar 2018 13:17:47: 27000000 INFO @ Sun, 18 Mar 2018 13:17:48: 27000000 INFO @ Sun, 18 Mar 2018 13:17:57: 28000000 INFO @ Sun, 18 Mar 2018 13:17:58: 27000000 INFO @ Sun, 18 Mar 2018 13:18:01: 28000000 INFO @ Sun, 18 Mar 2018 13:18:08: 29000000 INFO @ Sun, 18 Mar 2018 13:18:10: 28000000 INFO @ Sun, 18 Mar 2018 13:18:11: 29000000 INFO @ Sun, 18 Mar 2018 13:18:19: 30000000 INFO @ Sun, 18 Mar 2018 13:18:21: 29000000 INFO @ Sun, 18 Mar 2018 13:18:23: 30000000 INFO @ Sun, 18 Mar 2018 13:18:29: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:18:29: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:18:29: #1 total tags in treatment: 30959361 INFO @ Sun, 18 Mar 2018 13:18:29: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:18:29: #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 13:18:30: #1 tags after filtering in treatment: 30959255 INFO @ Sun, 18 Mar 2018 13:18:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:18:30: #1 finished! INFO @ Sun, 18 Mar 2018 13:18:30: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:18:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:18:32: 30000000 INFO @ Sun, 18 Mar 2018 13:18:33: #2 number of paired peaks: 6733 INFO @ Sun, 18 Mar 2018 13:18:33: start model_add_line... INFO @ Sun, 18 Mar 2018 13:18:33: start X-correlation... INFO @ Sun, 18 Mar 2018 13:18:33: end of X-cor INFO @ Sun, 18 Mar 2018 13:18:33: #2 finished! INFO @ Sun, 18 Mar 2018 13:18:33: #2 predicted fragment length is 148 bps INFO @ Sun, 18 Mar 2018 13:18:33: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 18 Mar 2018 13:18:33: #2.2 Generate R script for model : SRX2611113.05_model.r WARNING @ Sun, 18 Mar 2018 13:18:33: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:18:33: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 18 Mar 2018 13:18:33: #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 13:18:33: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:18:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:18:34: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:18:34: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:18:34: #1 total tags in treatment: 30959361 INFO @ Sun, 18 Mar 2018 13:18:34: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:18:34: #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 13:18:34: #1 tags after filtering in treatment: 30959255 INFO @ Sun, 18 Mar 2018 13:18:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:18:34: #1 finished! INFO @ Sun, 18 Mar 2018 13:18:34: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:18:37: #2 number of paired peaks: 6733 INFO @ Sun, 18 Mar 2018 13:18:37: start model_add_line... INFO @ Sun, 18 Mar 2018 13:18:38: start X-correlation... INFO @ Sun, 18 Mar 2018 13:18:38: end of X-cor INFO @ Sun, 18 Mar 2018 13:18:38: #2 finished! INFO @ Sun, 18 Mar 2018 13:18:38: #2 predicted fragment length is 148 bps INFO @ Sun, 18 Mar 2018 13:18:38: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 18 Mar 2018 13:18:38: #2.2 Generate R script for model : SRX2611113.10_model.r WARNING @ Sun, 18 Mar 2018 13:18:38: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:18:38: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 18 Mar 2018 13:18:38: #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 13:18:38: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:18:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:18:42: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:18:42: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:18:42: #1 total tags in treatment: 30959361 INFO @ Sun, 18 Mar 2018 13:18:42: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:18:42: #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 13:18:43: #1 tags after filtering in treatment: 30959255 INFO @ Sun, 18 Mar 2018 13:18:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:18:43: #1 finished! INFO @ Sun, 18 Mar 2018 13:18:43: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:18:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:18:46: #2 number of paired peaks: 6733 INFO @ Sun, 18 Mar 2018 13:18:46: start model_add_line... INFO @ Sun, 18 Mar 2018 13:18:47: start X-correlation... INFO @ Sun, 18 Mar 2018 13:18:47: end of X-cor INFO @ Sun, 18 Mar 2018 13:18:47: #2 finished! INFO @ Sun, 18 Mar 2018 13:18:47: #2 predicted fragment length is 148 bps INFO @ Sun, 18 Mar 2018 13:18:47: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 18 Mar 2018 13:18:47: #2.2 Generate R script for model : SRX2611113.20_model.r WARNING @ Sun, 18 Mar 2018 13:18:47: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:18:47: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 18 Mar 2018 13:18:47: #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 13:18:47: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:18:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:19:52: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:19:55: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:20:03: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:20:33: #4 Write output xls file... SRX2611113.10_peaks.xls INFO @ Sun, 18 Mar 2018 13:20:33: #4 Write peak in narrowPeak format file... SRX2611113.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:20:33: #4 Write summits bed file... SRX2611113.10_summits.bed INFO @ Sun, 18 Mar 2018 13:20:33: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1355 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:20:35: #4 Write output xls file... SRX2611113.05_peaks.xls INFO @ Sun, 18 Mar 2018 13:20:35: #4 Write peak in narrowPeak format file... SRX2611113.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:20:35: #4 Write summits bed file... SRX2611113.05_summits.bed INFO @ Sun, 18 Mar 2018 13:20:35: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (3166 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:20:45: #4 Write output xls file... SRX2611113.20_peaks.xls INFO @ Sun, 18 Mar 2018 13:20:45: #4 Write peak in narrowPeak format file... SRX2611113.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:20:45: #4 Write summits bed file... SRX2611113.20_summits.bed INFO @ Sun, 18 Mar 2018 13:20:45: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (612 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。