Job ID = 10487588 sra ファイルのダウンロード中... Completed: 4123591K bytes transferred in 72 seconds (463827K 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 60796884 spots for /home/okishinya/chipatlas/results/rn6/SRX2611111/SRR5311155.sra Written 60796884 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: 03:32:34 60796884 reads; of these: 60796884 (100.00%) were unpaired; of these: 11929981 (19.62%) aligned 0 times 41637477 (68.49%) aligned exactly 1 time 7229426 (11.89%) aligned >1 times 80.38% overall alignment rate Time searching: 03:32:37 Overall time: 03:32:37 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] 12879079 / 48866903 = 0.2636 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 13:43:13: # Command line: callpeak -t SRX2611111.bam -f BAM -g 2.15e9 -n SRX2611111.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611111.20 # format = BAM # ChIP-seq file = ['SRX2611111.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 13:43:13: # Command line: callpeak -t SRX2611111.bam -f BAM -g 2.15e9 -n SRX2611111.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611111.10 # format = BAM # ChIP-seq file = ['SRX2611111.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 13:43:13: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:43:13: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:43:13: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:43:13: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:43:13: # Command line: callpeak -t SRX2611111.bam -f BAM -g 2.15e9 -n SRX2611111.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611111.05 # format = BAM # ChIP-seq file = ['SRX2611111.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 13:43:13: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:43:13: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:43:23: 1000000 INFO @ Sun, 18 Mar 2018 13:43:23: 1000000 INFO @ Sun, 18 Mar 2018 13:43:23: 1000000 INFO @ Sun, 18 Mar 2018 13:43:33: 2000000 INFO @ Sun, 18 Mar 2018 13:43:33: 2000000 INFO @ Sun, 18 Mar 2018 13:43:33: 2000000 INFO @ Sun, 18 Mar 2018 13:43:43: 3000000 INFO @ Sun, 18 Mar 2018 13:43:43: 3000000 INFO @ Sun, 18 Mar 2018 13:43:43: 3000000 INFO @ Sun, 18 Mar 2018 13:43:53: 4000000 INFO @ Sun, 18 Mar 2018 13:43:53: 4000000 INFO @ Sun, 18 Mar 2018 13:43:53: 4000000 INFO @ Sun, 18 Mar 2018 13:44:03: 5000000 INFO @ Sun, 18 Mar 2018 13:44:03: 5000000 INFO @ Sun, 18 Mar 2018 13:44:03: 5000000 INFO @ Sun, 18 Mar 2018 13:44:13: 6000000 INFO @ Sun, 18 Mar 2018 13:44:13: 6000000 INFO @ Sun, 18 Mar 2018 13:44:13: 6000000 INFO @ Sun, 18 Mar 2018 13:44:23: 7000000 INFO @ Sun, 18 Mar 2018 13:44:23: 7000000 INFO @ Sun, 18 Mar 2018 13:44:24: 7000000 INFO @ Sun, 18 Mar 2018 13:44:33: 8000000 INFO @ Sun, 18 Mar 2018 13:44:33: 8000000 INFO @ Sun, 18 Mar 2018 13:44:34: 8000000 INFO @ Sun, 18 Mar 2018 13:44:43: 9000000 INFO @ Sun, 18 Mar 2018 13:44:44: 9000000 INFO @ Sun, 18 Mar 2018 13:44:45: 9000000 INFO @ Sun, 18 Mar 2018 13:44:53: 10000000 INFO @ Sun, 18 Mar 2018 13:44:54: 10000000 INFO @ Sun, 18 Mar 2018 13:44:56: 10000000 INFO @ Sun, 18 Mar 2018 13:45:02: 11000000 INFO @ Sun, 18 Mar 2018 13:45:04: 11000000 INFO @ Sun, 18 Mar 2018 13:45:06: 11000000 INFO @ Sun, 18 Mar 2018 13:45:12: 12000000 INFO @ Sun, 18 Mar 2018 13:45:14: 12000000 INFO @ Sun, 18 Mar 2018 13:45:17: 12000000 INFO @ Sun, 18 Mar 2018 13:45:22: 13000000 INFO @ Sun, 18 Mar 2018 13:45:24: 13000000 INFO @ Sun, 18 Mar 2018 13:45:27: 13000000 INFO @ Sun, 18 Mar 2018 13:45:32: 14000000 INFO @ Sun, 18 Mar 2018 13:45:34: 14000000 INFO @ Sun, 18 Mar 2018 13:45:37: 14000000 INFO @ Sun, 18 Mar 2018 13:45:43: 15000000 INFO @ Sun, 18 Mar 2018 13:45:45: 15000000 INFO @ Sun, 18 Mar 2018 13:45:48: 15000000 INFO @ Sun, 18 Mar 2018 13:45:53: 16000000 INFO @ Sun, 18 Mar 2018 13:45:55: 16000000 INFO @ Sun, 18 Mar 2018 13:45:59: 16000000 INFO @ Sun, 18 Mar 2018 13:46:04: 17000000 INFO @ Sun, 18 Mar 2018 13:46:06: 17000000 INFO @ Sun, 18 Mar 2018 13:46:11: 17000000 INFO @ Sun, 18 Mar 2018 13:46:14: 18000000 INFO @ Sun, 18 Mar 2018 13:46:16: 18000000 INFO @ Sun, 18 Mar 2018 13:46:21: 18000000 INFO @ Sun, 18 Mar 2018 13:46:24: 19000000 INFO @ Sun, 18 Mar 2018 13:46:27: 19000000 INFO @ Sun, 18 Mar 2018 13:46:32: 19000000 INFO @ Sun, 18 Mar 2018 13:46:34: 20000000 INFO @ Sun, 18 Mar 2018 13:46:36: 20000000 INFO @ Sun, 18 Mar 2018 13:46:43: 20000000 INFO @ Sun, 18 Mar 2018 13:46:45: 21000000 INFO @ Sun, 18 Mar 2018 13:46:47: 21000000 INFO @ Sun, 18 Mar 2018 13:46:53: 21000000 INFO @ Sun, 18 Mar 2018 13:46:54: 22000000 INFO @ Sun, 18 Mar 2018 13:46:57: 22000000 INFO @ Sun, 18 Mar 2018 13:47:04: 22000000 INFO @ Sun, 18 Mar 2018 13:47:04: 23000000 INFO @ Sun, 18 Mar 2018 13:47:07: 23000000 INFO @ Sun, 18 Mar 2018 13:47:14: 23000000 INFO @ Sun, 18 Mar 2018 13:47:14: 24000000 INFO @ Sun, 18 Mar 2018 13:47:17: 24000000 INFO @ Sun, 18 Mar 2018 13:47:25: 25000000 INFO @ Sun, 18 Mar 2018 13:47:25: 24000000 INFO @ Sun, 18 Mar 2018 13:47:28: 25000000 INFO @ Sun, 18 Mar 2018 13:47:35: 26000000 INFO @ Sun, 18 Mar 2018 13:47:35: 25000000 INFO @ Sun, 18 Mar 2018 13:47:38: 26000000 INFO @ Sun, 18 Mar 2018 13:47:45: 27000000 INFO @ Sun, 18 Mar 2018 13:47:45: 26000000 INFO @ Sun, 18 Mar 2018 13:47:48: 27000000 INFO @ Sun, 18 Mar 2018 13:47:56: 28000000 INFO @ Sun, 18 Mar 2018 13:47:56: 27000000 INFO @ Sun, 18 Mar 2018 13:47:59: 28000000 INFO @ Sun, 18 Mar 2018 13:48:05: 29000000 INFO @ Sun, 18 Mar 2018 13:48:07: 28000000 INFO @ Sun, 18 Mar 2018 13:48:09: 29000000 INFO @ Sun, 18 Mar 2018 13:48:15: 30000000 INFO @ Sun, 18 Mar 2018 13:48:17: 29000000 INFO @ Sun, 18 Mar 2018 13:48:19: 30000000 INFO @ Sun, 18 Mar 2018 13:48:26: 31000000 INFO @ Sun, 18 Mar 2018 13:48:28: 30000000 INFO @ Sun, 18 Mar 2018 13:48:29: 31000000 INFO @ Sun, 18 Mar 2018 13:48:36: 32000000 INFO @ Sun, 18 Mar 2018 13:48:37: 31000000 INFO @ Sun, 18 Mar 2018 13:48:39: 32000000 INFO @ Sun, 18 Mar 2018 13:48:46: 33000000 INFO @ Sun, 18 Mar 2018 13:48:47: 32000000 INFO @ Sun, 18 Mar 2018 13:48:50: 33000000 INFO @ Sun, 18 Mar 2018 13:48:57: 34000000 INFO @ Sun, 18 Mar 2018 13:48:58: 33000000 INFO @ Sun, 18 Mar 2018 13:49:01: 34000000 INFO @ Sun, 18 Mar 2018 13:49:08: 35000000 INFO @ Sun, 18 Mar 2018 13:49:10: 34000000 INFO @ Sun, 18 Mar 2018 13:49:11: 35000000 INFO @ Sun, 18 Mar 2018 13:49:18: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:49:18: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:49:18: #1 total tags in treatment: 35987824 INFO @ Sun, 18 Mar 2018 13:49:18: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:49:18: #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 13:49:19: #1 tags after filtering in treatment: 35987709 INFO @ Sun, 18 Mar 2018 13:49:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:49:19: #1 finished! INFO @ Sun, 18 Mar 2018 13:49:19: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:49:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:49:21: 35000000 INFO @ Sun, 18 Mar 2018 13:49:22: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:49:22: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:49:22: #1 total tags in treatment: 35987824 INFO @ Sun, 18 Mar 2018 13:49:22: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:49:22: #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 13:49:23: #1 tags after filtering in treatment: 35987709 INFO @ Sun, 18 Mar 2018 13:49:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:49:23: #1 finished! INFO @ Sun, 18 Mar 2018 13:49:23: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:49:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:49:23: #2 number of paired peaks: 9314 INFO @ Sun, 18 Mar 2018 13:49:23: start model_add_line... INFO @ Sun, 18 Mar 2018 13:49:23: start X-correlation... INFO @ Sun, 18 Mar 2018 13:49:23: end of X-cor INFO @ Sun, 18 Mar 2018 13:49:23: #2 finished! INFO @ Sun, 18 Mar 2018 13:49:23: #2 predicted fragment length is 164 bps INFO @ Sun, 18 Mar 2018 13:49:23: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 18 Mar 2018 13:49:23: #2.2 Generate R script for model : SRX2611111.05_model.r WARNING @ Sun, 18 Mar 2018 13:49:23: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:49:23: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Sun, 18 Mar 2018 13:49:23: #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 13:49:23: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:49:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:49:27: #2 number of paired peaks: 9314 INFO @ Sun, 18 Mar 2018 13:49:27: start model_add_line... INFO @ Sun, 18 Mar 2018 13:49:27: start X-correlation... INFO @ Sun, 18 Mar 2018 13:49:27: end of X-cor INFO @ Sun, 18 Mar 2018 13:49:27: #2 finished! INFO @ Sun, 18 Mar 2018 13:49:27: #2 predicted fragment length is 164 bps INFO @ Sun, 18 Mar 2018 13:49:27: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 18 Mar 2018 13:49:27: #2.2 Generate R script for model : SRX2611111.20_model.r WARNING @ Sun, 18 Mar 2018 13:49:27: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:49:27: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Sun, 18 Mar 2018 13:49:27: #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 13:49:27: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:49:30: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:49:30: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:49:30: #1 total tags in treatment: 35987824 INFO @ Sun, 18 Mar 2018 13:49:30: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:49:30: #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 13:49:31: #1 tags after filtering in treatment: 35987709 INFO @ Sun, 18 Mar 2018 13:49:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:49:31: #1 finished! INFO @ Sun, 18 Mar 2018 13:49:31: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:49:35: #2 number of paired peaks: 9314 INFO @ Sun, 18 Mar 2018 13:49:35: start model_add_line... INFO @ Sun, 18 Mar 2018 13:49:36: start X-correlation... INFO @ Sun, 18 Mar 2018 13:49:36: end of X-cor INFO @ Sun, 18 Mar 2018 13:49:36: #2 finished! INFO @ Sun, 18 Mar 2018 13:49:36: #2 predicted fragment length is 164 bps INFO @ Sun, 18 Mar 2018 13:49:36: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 18 Mar 2018 13:49:36: #2.2 Generate R script for model : SRX2611111.10_model.r WARNING @ Sun, 18 Mar 2018 13:49:36: #2 Since the d (164) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:49:36: #2 You may need to consider one of the other alternative d(s): 164 WARNING @ Sun, 18 Mar 2018 13:49:36: #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 13:49:36: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:49:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:50:49: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:51:01: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:51:07: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:51:44: #4 Write output xls file... SRX2611111.05_peaks.xls INFO @ Sun, 18 Mar 2018 13:51:44: #4 Write peak in narrowPeak format file... SRX2611111.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:51:44: #4 Write summits bed file... SRX2611111.05_summits.bed INFO @ Sun, 18 Mar 2018 13:51:44: Done! pass1 - making usageList (54 chroms): 12 millis pass2 - checking and writing primary data (4740 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:51:52: #4 Write output xls file... SRX2611111.20_peaks.xls INFO @ Sun, 18 Mar 2018 13:51:52: #4 Write peak in narrowPeak format file... SRX2611111.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:51:52: #4 Write summits bed file... SRX2611111.20_summits.bed INFO @ Sun, 18 Mar 2018 13:51:52: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (404 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:51:55: #4 Write output xls file... SRX2611111.10_peaks.xls INFO @ Sun, 18 Mar 2018 13:51:55: #4 Write peak in narrowPeak format file... SRX2611111.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:51:55: #4 Write summits bed file... SRX2611111.10_summits.bed INFO @ Sun, 18 Mar 2018 13:51:55: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (1104 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。