Job ID = 11192585 sra ファイルのダウンロード中... Completed: 538710K bytes transferred in 8 seconds (494208K 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... Read 42390579 spots for /home/okishinya/chipatlas/results/rn6/SRX4014805/SRR7085054.sra Written 42390579 spots for /home/okishinya/chipatlas/results/rn6/SRX4014805/SRR7085054.sra 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: 00:34:09 42390579 reads; of these: 42390579 (100.00%) were unpaired; of these: 1378448 (3.25%) aligned 0 times 35758679 (84.36%) aligned exactly 1 time 5253452 (12.39%) aligned >1 times 96.75% overall alignment rate Time searching: 00:34:13 Overall time: 00:34:13 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 20 files... [bam_rmdupse_core] 11232955 / 41012131 = 0.2739 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 @ Sat, 15 Sep 2018 11:41:18: # Command line: callpeak -t SRX4014805.bam -f BAM -g 2.15e9 -n SRX4014805.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014805.05 # format = BAM # ChIP-seq file = ['SRX4014805.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 @ Sat, 15 Sep 2018 11:41:18: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:41:18: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:41:18: # Command line: callpeak -t SRX4014805.bam -f BAM -g 2.15e9 -n SRX4014805.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014805.20 # format = BAM # ChIP-seq file = ['SRX4014805.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 @ Sat, 15 Sep 2018 11:41:18: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:41:18: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:41:18: # Command line: callpeak -t SRX4014805.bam -f BAM -g 2.15e9 -n SRX4014805.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014805.10 # format = BAM # ChIP-seq file = ['SRX4014805.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 @ Sat, 15 Sep 2018 11:41:18: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:41:18: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:41:25: 1000000 INFO @ Sat, 15 Sep 2018 11:41:26: 1000000 INFO @ Sat, 15 Sep 2018 11:41:26: 1000000 INFO @ Sat, 15 Sep 2018 11:41:32: 2000000 INFO @ Sat, 15 Sep 2018 11:41:34: 2000000 INFO @ Sat, 15 Sep 2018 11:41:34: 2000000 INFO @ Sat, 15 Sep 2018 11:41:40: 3000000 INFO @ Sat, 15 Sep 2018 11:41:41: 3000000 INFO @ Sat, 15 Sep 2018 11:41:41: 3000000 INFO @ Sat, 15 Sep 2018 11:41:48: 4000000 INFO @ Sat, 15 Sep 2018 11:41:48: 4000000 INFO @ Sat, 15 Sep 2018 11:41:49: 4000000 INFO @ Sat, 15 Sep 2018 11:41:55: 5000000 INFO @ Sat, 15 Sep 2018 11:41:56: 5000000 INFO @ Sat, 15 Sep 2018 11:41:56: 5000000 INFO @ Sat, 15 Sep 2018 11:42:03: 6000000 INFO @ Sat, 15 Sep 2018 11:42:03: 6000000 INFO @ Sat, 15 Sep 2018 11:42:03: 6000000 INFO @ Sat, 15 Sep 2018 11:42:11: 7000000 INFO @ Sat, 15 Sep 2018 11:42:11: 7000000 INFO @ Sat, 15 Sep 2018 11:42:11: 7000000 INFO @ Sat, 15 Sep 2018 11:42:18: 8000000 INFO @ Sat, 15 Sep 2018 11:42:19: 8000000 INFO @ Sat, 15 Sep 2018 11:42:19: 8000000 INFO @ Sat, 15 Sep 2018 11:42:25: 9000000 INFO @ Sat, 15 Sep 2018 11:42:26: 9000000 INFO @ Sat, 15 Sep 2018 11:42:27: 9000000 INFO @ Sat, 15 Sep 2018 11:42:33: 10000000 INFO @ Sat, 15 Sep 2018 11:42:34: 10000000 INFO @ Sat, 15 Sep 2018 11:42:34: 10000000 INFO @ Sat, 15 Sep 2018 11:42:41: 11000000 INFO @ Sat, 15 Sep 2018 11:42:42: 11000000 INFO @ Sat, 15 Sep 2018 11:42:43: 11000000 INFO @ Sat, 15 Sep 2018 11:42:49: 12000000 INFO @ Sat, 15 Sep 2018 11:42:50: 12000000 INFO @ Sat, 15 Sep 2018 11:42:51: 12000000 INFO @ Sat, 15 Sep 2018 11:42:56: 13000000 INFO @ Sat, 15 Sep 2018 11:42:58: 13000000 INFO @ Sat, 15 Sep 2018 11:42:59: 13000000 INFO @ Sat, 15 Sep 2018 11:43:04: 14000000 INFO @ Sat, 15 Sep 2018 11:43:06: 14000000 INFO @ Sat, 15 Sep 2018 11:43:07: 14000000 INFO @ Sat, 15 Sep 2018 11:43:12: 15000000 INFO @ Sat, 15 Sep 2018 11:43:13: 15000000 INFO @ Sat, 15 Sep 2018 11:43:15: 15000000 INFO @ Sat, 15 Sep 2018 11:43:20: 16000000 INFO @ Sat, 15 Sep 2018 11:43:21: 16000000 INFO @ Sat, 15 Sep 2018 11:43:22: 16000000 INFO @ Sat, 15 Sep 2018 11:43:27: 17000000 INFO @ Sat, 15 Sep 2018 11:43:28: 17000000 INFO @ Sat, 15 Sep 2018 11:43:30: 17000000 INFO @ Sat, 15 Sep 2018 11:43:35: 18000000 INFO @ Sat, 15 Sep 2018 11:43:36: 18000000 INFO @ Sat, 15 Sep 2018 11:43:38: 18000000 INFO @ Sat, 15 Sep 2018 11:43:43: 19000000 INFO @ Sat, 15 Sep 2018 11:43:43: 19000000 INFO @ Sat, 15 Sep 2018 11:43:45: 19000000 INFO @ Sat, 15 Sep 2018 11:43:50: 20000000 INFO @ Sat, 15 Sep 2018 11:43:51: 20000000 INFO @ Sat, 15 Sep 2018 11:43:53: 20000000 INFO @ Sat, 15 Sep 2018 11:43:58: 21000000 INFO @ Sat, 15 Sep 2018 11:43:58: 21000000 INFO @ Sat, 15 Sep 2018 11:44:00: 21000000 INFO @ Sat, 15 Sep 2018 11:44:06: 22000000 INFO @ Sat, 15 Sep 2018 11:44:06: 22000000 INFO @ Sat, 15 Sep 2018 11:44:08: 22000000 INFO @ Sat, 15 Sep 2018 11:44:14: 23000000 INFO @ Sat, 15 Sep 2018 11:44:14: 23000000 INFO @ Sat, 15 Sep 2018 11:44:16: 23000000 INFO @ Sat, 15 Sep 2018 11:44:21: 24000000 INFO @ Sat, 15 Sep 2018 11:44:21: 24000000 INFO @ Sat, 15 Sep 2018 11:44:23: 24000000 INFO @ Sat, 15 Sep 2018 11:44:29: 25000000 INFO @ Sat, 15 Sep 2018 11:44:29: 25000000 INFO @ Sat, 15 Sep 2018 11:44:31: 25000000 INFO @ Sat, 15 Sep 2018 11:44:36: 26000000 INFO @ Sat, 15 Sep 2018 11:44:37: 26000000 INFO @ Sat, 15 Sep 2018 11:44:39: 26000000 INFO @ Sat, 15 Sep 2018 11:44:44: 27000000 INFO @ Sat, 15 Sep 2018 11:44:45: 27000000 INFO @ Sat, 15 Sep 2018 11:44:46: 27000000 INFO @ Sat, 15 Sep 2018 11:44:51: 28000000 INFO @ Sat, 15 Sep 2018 11:44:52: 28000000 INFO @ Sat, 15 Sep 2018 11:44:54: 28000000 INFO @ Sat, 15 Sep 2018 11:44:59: 29000000 INFO @ Sat, 15 Sep 2018 11:45:00: 29000000 INFO @ Sat, 15 Sep 2018 11:45:02: 29000000 INFO @ Sat, 15 Sep 2018 11:45:06: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:45:06: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:45:06: #1 total tags in treatment: 29779176 INFO @ Sat, 15 Sep 2018 11:45:06: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:45:06: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:45:06: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:45:06: #1 total tags in treatment: 29779176 INFO @ Sat, 15 Sep 2018 11:45:06: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:45:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:45:06: #1 tags after filtering in treatment: 29778997 INFO @ Sat, 15 Sep 2018 11:45:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:45:06: #1 finished! INFO @ Sat, 15 Sep 2018 11:45:06: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:45:07: #1 tags after filtering in treatment: 29778997 INFO @ Sat, 15 Sep 2018 11:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:45:07: #1 finished! INFO @ Sat, 15 Sep 2018 11:45:07: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:45:09: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:45:09: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:45:09: #1 total tags in treatment: 29779176 INFO @ Sat, 15 Sep 2018 11:45:09: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:45:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:45:09: #1 tags after filtering in treatment: 29778997 INFO @ Sat, 15 Sep 2018 11:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:45:09: #1 finished! INFO @ Sat, 15 Sep 2018 11:45:09: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:45:14: #2 number of paired peaks: 93516 INFO @ Sat, 15 Sep 2018 11:45:14: start model_add_line... INFO @ Sat, 15 Sep 2018 11:45:14: #2 number of paired peaks: 93516 INFO @ Sat, 15 Sep 2018 11:45:14: start model_add_line... INFO @ Sat, 15 Sep 2018 11:45:15: start X-correlation... INFO @ Sat, 15 Sep 2018 11:45:15: end of X-cor INFO @ Sat, 15 Sep 2018 11:45:15: #2 finished! INFO @ Sat, 15 Sep 2018 11:45:15: #2 predicted fragment length is 317 bps INFO @ Sat, 15 Sep 2018 11:45:15: #2 alternative fragment length(s) may be 4,317 bps INFO @ Sat, 15 Sep 2018 11:45:15: #2.2 Generate R script for model : SRX4014805.10_model.r INFO @ Sat, 15 Sep 2018 11:45:15: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:45:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:45:15: start X-correlation... INFO @ Sat, 15 Sep 2018 11:45:15: end of X-cor INFO @ Sat, 15 Sep 2018 11:45:15: #2 finished! INFO @ Sat, 15 Sep 2018 11:45:15: #2 predicted fragment length is 317 bps INFO @ Sat, 15 Sep 2018 11:45:15: #2 alternative fragment length(s) may be 4,317 bps INFO @ Sat, 15 Sep 2018 11:45:15: #2.2 Generate R script for model : SRX4014805.20_model.r INFO @ Sat, 15 Sep 2018 11:45:15: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:45:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:45:17: #2 number of paired peaks: 93516 INFO @ Sat, 15 Sep 2018 11:45:17: start model_add_line... INFO @ Sat, 15 Sep 2018 11:45:17: start X-correlation... INFO @ Sat, 15 Sep 2018 11:45:17: end of X-cor INFO @ Sat, 15 Sep 2018 11:45:17: #2 finished! INFO @ Sat, 15 Sep 2018 11:45:17: #2 predicted fragment length is 317 bps INFO @ Sat, 15 Sep 2018 11:45:17: #2 alternative fragment length(s) may be 4,317 bps INFO @ Sat, 15 Sep 2018 11:45:17: #2.2 Generate R script for model : SRX4014805.05_model.r INFO @ Sat, 15 Sep 2018 11:45:17: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:45:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:47:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:47:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:47:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:47:55: #4 Write output xls file... SRX4014805.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:47:55: #4 Write peak in narrowPeak format file... SRX4014805.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:47:55: #4 Write summits bed file... SRX4014805.10_summits.bed INFO @ Sat, 15 Sep 2018 11:47:55: Done! pass1 - making usageList (120 chroms): 6 millis pass2 - checking and writing primary data (32095 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:47:58: #4 Write output xls file... SRX4014805.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:47:59: #4 Write peak in narrowPeak format file... SRX4014805.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:47:59: #4 Write summits bed file... SRX4014805.05_summits.bed INFO @ Sat, 15 Sep 2018 11:47:59: Done! pass1 - making usageList (139 chroms): 8 millis pass2 - checking and writing primary data (41996 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:48:00: #4 Write output xls file... SRX4014805.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:48:00: #4 Write peak in narrowPeak format file... SRX4014805.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:48:01: #4 Write summits bed file... SRX4014805.20_summits.bed INFO @ Sat, 15 Sep 2018 11:48:01: Done! pass1 - making usageList (92 chroms): 4 millis pass2 - checking and writing primary data (22211 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。