Job ID = 10487594 sra ファイルのダウンロード中... Completed: 4011538K bytes transferred in 151 seconds (216758K 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 59104347 spots for /home/okishinya/chipatlas/results/rn6/SRX2611117/SRR5311161.sra Written 59104347 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 03:28:04 59104347 reads; of these: 59104347 (100.00%) were unpaired; of these: 13425331 (22.71%) aligned 0 times 39096701 (66.15%) aligned exactly 1 time 6582315 (11.14%) aligned >1 times 77.29% overall alignment rate Time searching: 03:28:09 Overall time: 03:28:09 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] 12973146 / 45679016 = 0.2840 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 13:44:50: # Command line: callpeak -t SRX2611117.bam -f BAM -g 2.15e9 -n SRX2611117.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611117.05 # format = BAM # ChIP-seq file = ['SRX2611117.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 13:44:50: # Command line: callpeak -t SRX2611117.bam -f BAM -g 2.15e9 -n SRX2611117.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611117.10 # format = BAM # ChIP-seq file = ['SRX2611117.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 13:44:50: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:44:50: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:44:50: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:44:50: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:44:50: # Command line: callpeak -t SRX2611117.bam -f BAM -g 2.15e9 -n SRX2611117.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611117.20 # format = BAM # ChIP-seq file = ['SRX2611117.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 13:44:50: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:44:50: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:45:04: 1000000 INFO @ Sun, 18 Mar 2018 13:45:04: 1000000 INFO @ Sun, 18 Mar 2018 13:45:04: 1000000 INFO @ Sun, 18 Mar 2018 13:45:19: 2000000 INFO @ Sun, 18 Mar 2018 13:45:19: 2000000 INFO @ Sun, 18 Mar 2018 13:45:19: 2000000 INFO @ Sun, 18 Mar 2018 13:45:33: 3000000 INFO @ Sun, 18 Mar 2018 13:45:33: 3000000 INFO @ Sun, 18 Mar 2018 13:45:33: 3000000 INFO @ Sun, 18 Mar 2018 13:45:47: 4000000 INFO @ Sun, 18 Mar 2018 13:45:47: 4000000 INFO @ Sun, 18 Mar 2018 13:45:47: 4000000 INFO @ Sun, 18 Mar 2018 13:46:01: 5000000 INFO @ Sun, 18 Mar 2018 13:46:01: 5000000 INFO @ Sun, 18 Mar 2018 13:46:01: 5000000 INFO @ Sun, 18 Mar 2018 13:46:16: 6000000 INFO @ Sun, 18 Mar 2018 13:46:16: 6000000 INFO @ Sun, 18 Mar 2018 13:46:16: 6000000 INFO @ Sun, 18 Mar 2018 13:46:30: 7000000 INFO @ Sun, 18 Mar 2018 13:46:30: 7000000 INFO @ Sun, 18 Mar 2018 13:46:30: 7000000 INFO @ Sun, 18 Mar 2018 13:46:44: 8000000 INFO @ Sun, 18 Mar 2018 13:46:44: 8000000 INFO @ Sun, 18 Mar 2018 13:46:44: 8000000 INFO @ Sun, 18 Mar 2018 13:46:58: 9000000 INFO @ Sun, 18 Mar 2018 13:46:58: 9000000 INFO @ Sun, 18 Mar 2018 13:46:58: 9000000 INFO @ Sun, 18 Mar 2018 13:47:12: 10000000 INFO @ Sun, 18 Mar 2018 13:47:12: 10000000 INFO @ Sun, 18 Mar 2018 13:47:12: 10000000 INFO @ Sun, 18 Mar 2018 13:47:24: 11000000 INFO @ Sun, 18 Mar 2018 13:47:25: 11000000 INFO @ Sun, 18 Mar 2018 13:47:25: 11000000 INFO @ Sun, 18 Mar 2018 13:47:35: 12000000 INFO @ Sun, 18 Mar 2018 13:47:38: 12000000 INFO @ Sun, 18 Mar 2018 13:47:38: 12000000 INFO @ Sun, 18 Mar 2018 13:47:47: 13000000 INFO @ Sun, 18 Mar 2018 13:47:50: 13000000 INFO @ Sun, 18 Mar 2018 13:47:50: 13000000 INFO @ Sun, 18 Mar 2018 13:47:58: 14000000 INFO @ Sun, 18 Mar 2018 13:48:03: 14000000 INFO @ Sun, 18 Mar 2018 13:48:03: 14000000 INFO @ Sun, 18 Mar 2018 13:48:10: 15000000 INFO @ Sun, 18 Mar 2018 13:48:16: 15000000 INFO @ Sun, 18 Mar 2018 13:48:16: 15000000 INFO @ Sun, 18 Mar 2018 13:48:21: 16000000 INFO @ Sun, 18 Mar 2018 13:48:29: 16000000 INFO @ Sun, 18 Mar 2018 13:48:29: 16000000 INFO @ Sun, 18 Mar 2018 13:48:33: 17000000 INFO @ Sun, 18 Mar 2018 13:48:41: 17000000 INFO @ Sun, 18 Mar 2018 13:48:41: 17000000 INFO @ Sun, 18 Mar 2018 13:48:44: 18000000 INFO @ Sun, 18 Mar 2018 13:48:54: 18000000 INFO @ Sun, 18 Mar 2018 13:48:54: 18000000 INFO @ Sun, 18 Mar 2018 13:48:56: 19000000 INFO @ Sun, 18 Mar 2018 13:49:07: 19000000 INFO @ Sun, 18 Mar 2018 13:49:07: 19000000 INFO @ Sun, 18 Mar 2018 13:49:07: 20000000 INFO @ Sun, 18 Mar 2018 13:49:19: 21000000 INFO @ Sun, 18 Mar 2018 13:49:20: 20000000 INFO @ Sun, 18 Mar 2018 13:49:20: 20000000 INFO @ Sun, 18 Mar 2018 13:49:30: 22000000 INFO @ Sun, 18 Mar 2018 13:49:32: 21000000 INFO @ Sun, 18 Mar 2018 13:49:32: 21000000 INFO @ Sun, 18 Mar 2018 13:49:42: 23000000 INFO @ Sun, 18 Mar 2018 13:49:45: 22000000 INFO @ Sun, 18 Mar 2018 13:49:45: 22000000 INFO @ Sun, 18 Mar 2018 13:49:53: 24000000 INFO @ Sun, 18 Mar 2018 13:49:58: 23000000 INFO @ Sun, 18 Mar 2018 13:49:58: 23000000 INFO @ Sun, 18 Mar 2018 13:50:05: 25000000 INFO @ Sun, 18 Mar 2018 13:50:10: 24000000 INFO @ Sun, 18 Mar 2018 13:50:10: 24000000 INFO @ Sun, 18 Mar 2018 13:50:16: 26000000 INFO @ Sun, 18 Mar 2018 13:50:23: 25000000 INFO @ Sun, 18 Mar 2018 13:50:23: 25000000 INFO @ Sun, 18 Mar 2018 13:50:28: 27000000 INFO @ Sun, 18 Mar 2018 13:50:36: 26000000 INFO @ Sun, 18 Mar 2018 13:50:36: 26000000 INFO @ Sun, 18 Mar 2018 13:50:39: 28000000 INFO @ Sun, 18 Mar 2018 13:50:49: 27000000 INFO @ Sun, 18 Mar 2018 13:50:49: 27000000 INFO @ Sun, 18 Mar 2018 13:50:51: 29000000 INFO @ Sun, 18 Mar 2018 13:51:02: 30000000 INFO @ Sun, 18 Mar 2018 13:51:02: 28000000 INFO @ Sun, 18 Mar 2018 13:51:02: 28000000 INFO @ Sun, 18 Mar 2018 13:51:13: 31000000 INFO @ Sun, 18 Mar 2018 13:51:16: 29000000 INFO @ Sun, 18 Mar 2018 13:51:16: 29000000 INFO @ Sun, 18 Mar 2018 13:51:25: 32000000 INFO @ Sun, 18 Mar 2018 13:51:29: 30000000 INFO @ Sun, 18 Mar 2018 13:51:29: 30000000 INFO @ Sun, 18 Mar 2018 13:51:33: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:51:33: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:51:33: #1 total tags in treatment: 32705870 INFO @ Sun, 18 Mar 2018 13:51:33: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:51:33: #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 13:51:34: #1 tags after filtering in treatment: 32705764 INFO @ Sun, 18 Mar 2018 13:51:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:51:34: #1 finished! INFO @ Sun, 18 Mar 2018 13:51:34: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:51:37: #2 number of paired peaks: 6814 INFO @ Sun, 18 Mar 2018 13:51:37: start model_add_line... INFO @ Sun, 18 Mar 2018 13:51:38: start X-correlation... INFO @ Sun, 18 Mar 2018 13:51:38: end of X-cor INFO @ Sun, 18 Mar 2018 13:51:38: #2 finished! INFO @ Sun, 18 Mar 2018 13:51:38: #2 predicted fragment length is 156 bps INFO @ Sun, 18 Mar 2018 13:51:38: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 18 Mar 2018 13:51:38: #2.2 Generate R script for model : SRX2611117.20_model.r WARNING @ Sun, 18 Mar 2018 13:51:38: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:51:38: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sun, 18 Mar 2018 13:51:38: #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 13:51:38: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:51:42: 31000000 INFO @ Sun, 18 Mar 2018 13:51:42: 31000000 INFO @ Sun, 18 Mar 2018 13:51:55: 32000000 INFO @ Sun, 18 Mar 2018 13:51:55: 32000000 INFO @ Sun, 18 Mar 2018 13:52:05: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:52:05: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:52:05: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:52:05: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:52:05: #1 total tags in treatment: 32705870 INFO @ Sun, 18 Mar 2018 13:52:05: #1 total tags in treatment: 32705870 INFO @ Sun, 18 Mar 2018 13:52:05: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:52:05: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:52:05: #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 13:52:05: #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 13:52:06: #1 tags after filtering in treatment: 32705764 INFO @ Sun, 18 Mar 2018 13:52:06: #1 tags after filtering in treatment: 32705764 INFO @ Sun, 18 Mar 2018 13:52:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:52:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:52:06: #1 finished! INFO @ Sun, 18 Mar 2018 13:52:06: #1 finished! INFO @ Sun, 18 Mar 2018 13:52:06: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:52:06: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:52:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:52:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:52:09: #2 number of paired peaks: 6814 INFO @ Sun, 18 Mar 2018 13:52:09: start model_add_line... INFO @ Sun, 18 Mar 2018 13:52:09: start X-correlation... INFO @ Sun, 18 Mar 2018 13:52:09: end of X-cor INFO @ Sun, 18 Mar 2018 13:52:09: #2 finished! INFO @ Sun, 18 Mar 2018 13:52:09: #2 predicted fragment length is 156 bps INFO @ Sun, 18 Mar 2018 13:52:09: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 18 Mar 2018 13:52:09: #2.2 Generate R script for model : SRX2611117.10_model.r WARNING @ Sun, 18 Mar 2018 13:52:09: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:52:09: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sun, 18 Mar 2018 13:52:09: #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 13:52:09: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:52:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:52:09: #2 number of paired peaks: 6814 INFO @ Sun, 18 Mar 2018 13:52:09: start model_add_line... INFO @ Sun, 18 Mar 2018 13:52:10: start X-correlation... INFO @ Sun, 18 Mar 2018 13:52:10: end of X-cor INFO @ Sun, 18 Mar 2018 13:52:10: #2 finished! INFO @ Sun, 18 Mar 2018 13:52:10: #2 predicted fragment length is 156 bps INFO @ Sun, 18 Mar 2018 13:52:10: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 18 Mar 2018 13:52:10: #2.2 Generate R script for model : SRX2611117.05_model.r WARNING @ Sun, 18 Mar 2018 13:52:10: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:52:10: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sun, 18 Mar 2018 13:52:10: #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 13:52:10: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:52:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:52:58: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:53:33: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:53:35: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:53:47: #4 Write output xls file... SRX2611117.20_peaks.xls INFO @ Sun, 18 Mar 2018 13:53:47: #4 Write peak in narrowPeak format file... SRX2611117.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:53:47: #4 Write summits bed file... SRX2611117.20_summits.bed INFO @ Sun, 18 Mar 2018 13:53:47: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (408 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:54:20: #4 Write output xls file... SRX2611117.10_peaks.xls INFO @ Sun, 18 Mar 2018 13:54:20: #4 Write peak in narrowPeak format file... SRX2611117.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:54:20: #4 Write summits bed file... SRX2611117.10_summits.bed INFO @ Sun, 18 Mar 2018 13:54:20: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (886 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:54:26: #4 Write output xls file... SRX2611117.05_peaks.xls INFO @ Sun, 18 Mar 2018 13:54:26: #4 Write peak in narrowPeak format file... SRX2611117.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:54:26: #4 Write summits bed file... SRX2611117.05_summits.bed INFO @ Sun, 18 Mar 2018 13:54:26: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (2249 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。