Job ID = 10487577 sra ファイルのダウンロード中... Completed: 4419877K bytes transferred in 164 seconds (220243K 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 65305667 spots for /home/okishinya/chipatlas/results/rn6/SRX2611107/SRR5311151.sra Written 65305667 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: 03:43:51 65305667 reads; of these: 65305667 (100.00%) were unpaired; of these: 18592648 (28.47%) aligned 0 times 40417423 (61.89%) aligned exactly 1 time 6295596 (9.64%) aligned >1 times 71.53% overall alignment rate Time searching: 03:43:54 Overall time: 03:43:54 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] 12337455 / 46713019 = 0.2641 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 13:47:31: # Command line: callpeak -t SRX2611107.bam -f BAM -g 2.15e9 -n SRX2611107.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611107.05 # format = BAM # ChIP-seq file = ['SRX2611107.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 13:47:31: # Command line: callpeak -t SRX2611107.bam -f BAM -g 2.15e9 -n SRX2611107.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611107.20 # format = BAM # ChIP-seq file = ['SRX2611107.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 13:47:31: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:47:31: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:47:31: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:47:31: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:47:31: # Command line: callpeak -t SRX2611107.bam -f BAM -g 2.15e9 -n SRX2611107.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611107.10 # format = BAM # ChIP-seq file = ['SRX2611107.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 13:47:31: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:47:31: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:47:41: 1000000 INFO @ Sun, 18 Mar 2018 13:47:41: 1000000 INFO @ Sun, 18 Mar 2018 13:47:41: 1000000 INFO @ Sun, 18 Mar 2018 13:47:51: 2000000 INFO @ Sun, 18 Mar 2018 13:47:51: 2000000 INFO @ Sun, 18 Mar 2018 13:47:51: 2000000 INFO @ Sun, 18 Mar 2018 13:48:01: 3000000 INFO @ Sun, 18 Mar 2018 13:48:01: 3000000 INFO @ Sun, 18 Mar 2018 13:48:01: 3000000 INFO @ Sun, 18 Mar 2018 13:48:11: 4000000 INFO @ Sun, 18 Mar 2018 13:48:12: 4000000 INFO @ Sun, 18 Mar 2018 13:48:12: 4000000 INFO @ Sun, 18 Mar 2018 13:48:21: 5000000 INFO @ Sun, 18 Mar 2018 13:48:22: 5000000 INFO @ Sun, 18 Mar 2018 13:48:23: 5000000 INFO @ Sun, 18 Mar 2018 13:48:31: 6000000 INFO @ Sun, 18 Mar 2018 13:48:33: 6000000 INFO @ Sun, 18 Mar 2018 13:48:34: 6000000 INFO @ Sun, 18 Mar 2018 13:48:40: 7000000 INFO @ Sun, 18 Mar 2018 13:48:43: 7000000 INFO @ Sun, 18 Mar 2018 13:48:45: 7000000 INFO @ Sun, 18 Mar 2018 13:48:50: 8000000 INFO @ Sun, 18 Mar 2018 13:48:54: 8000000 INFO @ Sun, 18 Mar 2018 13:48:55: 8000000 INFO @ Sun, 18 Mar 2018 13:49:00: 9000000 INFO @ Sun, 18 Mar 2018 13:49:05: 9000000 INFO @ Sun, 18 Mar 2018 13:49:06: 9000000 INFO @ Sun, 18 Mar 2018 13:49:10: 10000000 INFO @ Sun, 18 Mar 2018 13:49:15: 10000000 INFO @ Sun, 18 Mar 2018 13:49:17: 10000000 INFO @ Sun, 18 Mar 2018 13:49:20: 11000000 INFO @ Sun, 18 Mar 2018 13:49:26: 11000000 INFO @ Sun, 18 Mar 2018 13:49:28: 11000000 INFO @ Sun, 18 Mar 2018 13:49:30: 12000000 INFO @ Sun, 18 Mar 2018 13:49:37: 12000000 INFO @ Sun, 18 Mar 2018 13:49:39: 12000000 INFO @ Sun, 18 Mar 2018 13:49:39: 13000000 INFO @ Sun, 18 Mar 2018 13:49:48: 13000000 INFO @ Sun, 18 Mar 2018 13:49:49: 14000000 INFO @ Sun, 18 Mar 2018 13:49:50: 13000000 INFO @ Sun, 18 Mar 2018 13:49:58: 14000000 INFO @ Sun, 18 Mar 2018 13:49:59: 15000000 INFO @ Sun, 18 Mar 2018 13:50:01: 14000000 INFO @ Sun, 18 Mar 2018 13:50:09: 15000000 INFO @ Sun, 18 Mar 2018 13:50:09: 16000000 INFO @ Sun, 18 Mar 2018 13:50:12: 15000000 INFO @ Sun, 18 Mar 2018 13:50:19: 17000000 INFO @ Sun, 18 Mar 2018 13:50:19: 16000000 INFO @ Sun, 18 Mar 2018 13:50:23: 16000000 INFO @ Sun, 18 Mar 2018 13:50:29: 18000000 INFO @ Sun, 18 Mar 2018 13:50:30: 17000000 INFO @ Sun, 18 Mar 2018 13:50:34: 17000000 INFO @ Sun, 18 Mar 2018 13:50:38: 19000000 INFO @ Sun, 18 Mar 2018 13:50:41: 18000000 INFO @ Sun, 18 Mar 2018 13:50:45: 18000000 INFO @ Sun, 18 Mar 2018 13:50:48: 20000000 INFO @ Sun, 18 Mar 2018 13:50:51: 19000000 INFO @ Sun, 18 Mar 2018 13:50:56: 19000000 INFO @ Sun, 18 Mar 2018 13:50:58: 21000000 INFO @ Sun, 18 Mar 2018 13:51:02: 20000000 INFO @ Sun, 18 Mar 2018 13:51:06: 20000000 INFO @ Sun, 18 Mar 2018 13:51:08: 22000000 INFO @ Sun, 18 Mar 2018 13:51:13: 21000000 INFO @ Sun, 18 Mar 2018 13:51:17: 21000000 INFO @ Sun, 18 Mar 2018 13:51:18: 23000000 INFO @ Sun, 18 Mar 2018 13:51:23: 22000000 INFO @ Sun, 18 Mar 2018 13:51:27: 24000000 INFO @ Sun, 18 Mar 2018 13:51:28: 22000000 INFO @ Sun, 18 Mar 2018 13:51:34: 23000000 INFO @ Sun, 18 Mar 2018 13:51:37: 25000000 INFO @ Sun, 18 Mar 2018 13:51:39: 23000000 INFO @ Sun, 18 Mar 2018 13:51:44: 24000000 INFO @ Sun, 18 Mar 2018 13:51:47: 26000000 INFO @ Sun, 18 Mar 2018 13:51:50: 24000000 INFO @ Sun, 18 Mar 2018 13:51:55: 25000000 INFO @ Sun, 18 Mar 2018 13:51:57: 27000000 INFO @ Sun, 18 Mar 2018 13:52:01: 25000000 INFO @ Sun, 18 Mar 2018 13:52:06: 26000000 INFO @ Sun, 18 Mar 2018 13:52:07: 28000000 INFO @ Sun, 18 Mar 2018 13:52:12: 26000000 INFO @ Sun, 18 Mar 2018 13:52:16: 27000000 INFO @ Sun, 18 Mar 2018 13:52:16: 29000000 INFO @ Sun, 18 Mar 2018 13:52:23: 27000000 INFO @ Sun, 18 Mar 2018 13:52:26: 30000000 INFO @ Sun, 18 Mar 2018 13:52:27: 28000000 INFO @ Sun, 18 Mar 2018 13:52:34: 28000000 INFO @ Sun, 18 Mar 2018 13:52:36: 31000000 INFO @ Sun, 18 Mar 2018 13:52:37: 29000000 INFO @ Sun, 18 Mar 2018 13:52:45: 29000000 INFO @ Sun, 18 Mar 2018 13:52:46: 32000000 INFO @ Sun, 18 Mar 2018 13:52:48: 30000000 INFO @ Sun, 18 Mar 2018 13:52:56: 30000000 INFO @ Sun, 18 Mar 2018 13:52:56: 33000000 INFO @ Sun, 18 Mar 2018 13:52:59: 31000000 INFO @ Sun, 18 Mar 2018 13:53:06: 34000000 INFO @ Sun, 18 Mar 2018 13:53:06: 31000000 INFO @ Sun, 18 Mar 2018 13:53:09: 32000000 INFO @ Sun, 18 Mar 2018 13:53:10: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:53:10: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:53:10: #1 total tags in treatment: 34375564 INFO @ Sun, 18 Mar 2018 13:53:10: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:53:10: #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 13:53:11: #1 tags after filtering in treatment: 34375460 INFO @ Sun, 18 Mar 2018 13:53:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:53:11: #1 finished! INFO @ Sun, 18 Mar 2018 13:53:11: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:53:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:53:14: #2 number of paired peaks: 10369 INFO @ Sun, 18 Mar 2018 13:53:14: start model_add_line... INFO @ Sun, 18 Mar 2018 13:53:15: start X-correlation... INFO @ Sun, 18 Mar 2018 13:53:15: end of X-cor INFO @ Sun, 18 Mar 2018 13:53:15: #2 finished! INFO @ Sun, 18 Mar 2018 13:53:15: #2 predicted fragment length is 156 bps INFO @ Sun, 18 Mar 2018 13:53:15: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 18 Mar 2018 13:53:15: #2.2 Generate R script for model : SRX2611107.20_model.r WARNING @ Sun, 18 Mar 2018 13:53:15: #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 13:53:15: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sun, 18 Mar 2018 13:53:15: #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 13:53:15: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:53:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:53:17: 32000000 INFO @ Sun, 18 Mar 2018 13:53:20: 33000000 INFO @ Sun, 18 Mar 2018 13:53:28: 33000000 INFO @ Sun, 18 Mar 2018 13:53:31: 34000000 INFO @ Sun, 18 Mar 2018 13:53:35: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:53:35: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:53:35: #1 total tags in treatment: 34375564 INFO @ Sun, 18 Mar 2018 13:53:35: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:53:35: #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 13:53:36: #1 tags after filtering in treatment: 34375460 INFO @ Sun, 18 Mar 2018 13:53:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:53:36: #1 finished! INFO @ Sun, 18 Mar 2018 13:53:36: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:53:39: 34000000 INFO @ Sun, 18 Mar 2018 13:53:39: #2 number of paired peaks: 10369 INFO @ Sun, 18 Mar 2018 13:53:39: start model_add_line... INFO @ Sun, 18 Mar 2018 13:53:40: start X-correlation... INFO @ Sun, 18 Mar 2018 13:53:40: end of X-cor INFO @ Sun, 18 Mar 2018 13:53:40: #2 finished! INFO @ Sun, 18 Mar 2018 13:53:40: #2 predicted fragment length is 156 bps INFO @ Sun, 18 Mar 2018 13:53:40: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 18 Mar 2018 13:53:40: #2.2 Generate R script for model : SRX2611107.10_model.r WARNING @ Sun, 18 Mar 2018 13:53:40: #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 13:53:40: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sun, 18 Mar 2018 13:53:40: #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 13:53:40: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:53:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:53:43: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:53:43: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:53:43: #1 total tags in treatment: 34375564 INFO @ Sun, 18 Mar 2018 13:53:43: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:53:43: #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 13:53:43: #1 tags after filtering in treatment: 34375460 INFO @ Sun, 18 Mar 2018 13:53:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:53:43: #1 finished! INFO @ Sun, 18 Mar 2018 13:53:43: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:53:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:53:47: #2 number of paired peaks: 10369 INFO @ Sun, 18 Mar 2018 13:53:47: start model_add_line... INFO @ Sun, 18 Mar 2018 13:53:47: start X-correlation... INFO @ Sun, 18 Mar 2018 13:53:47: end of X-cor INFO @ Sun, 18 Mar 2018 13:53:47: #2 finished! INFO @ Sun, 18 Mar 2018 13:53:47: #2 predicted fragment length is 156 bps INFO @ Sun, 18 Mar 2018 13:53:47: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 18 Mar 2018 13:53:47: #2.2 Generate R script for model : SRX2611107.05_model.r WARNING @ Sun, 18 Mar 2018 13:53:47: #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 13:53:47: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sun, 18 Mar 2018 13:53:47: #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 13:53:47: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:53:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:54:41: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:55:09: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:55:10: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:55:32: #4 Write output xls file... SRX2611107.20_peaks.xls INFO @ Sun, 18 Mar 2018 13:55:32: #4 Write peak in narrowPeak format file... SRX2611107.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:55:32: #4 Write summits bed file... SRX2611107.20_summits.bed INFO @ Sun, 18 Mar 2018 13:55:32: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (394 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:55:56: #4 Write output xls file... SRX2611107.05_peaks.xls INFO @ Sun, 18 Mar 2018 13:55:56: #4 Write peak in narrowPeak format file... SRX2611107.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:55:56: #4 Write summits bed file... SRX2611107.05_summits.bed INFO @ Sun, 18 Mar 2018 13:55:56: Done! pass1 - making usageList (52 chroms): 2 millis pass2 - checking and writing primary data (4621 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:55:58: #4 Write output xls file... SRX2611107.10_peaks.xls INFO @ Sun, 18 Mar 2018 13:55:58: #4 Write peak in narrowPeak format file... SRX2611107.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:55:58: #4 Write summits bed file... SRX2611107.10_summits.bed INFO @ Sun, 18 Mar 2018 13:55:58: Done! pass1 - making usageList (35 chroms): 0 millis pass2 - checking and writing primary data (1161 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。