Job ID = 11192591 sra ファイルのダウンロード中... Completed: 585611K bytes transferred in 57 seconds (83158K 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 47838230 spots for /home/okishinya/chipatlas/results/rn6/SRX4014811/SRR7085060.sra Written 47838230 spots for /home/okishinya/chipatlas/results/rn6/SRX4014811/SRR7085060.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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:41:14 47838230 reads; of these: 47838230 (100.00%) were unpaired; of these: 1390476 (2.91%) aligned 0 times 41290829 (86.31%) aligned exactly 1 time 5156925 (10.78%) aligned >1 times 97.09% overall alignment rate Time searching: 00:41:18 Overall time: 00:41:18 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] 10346595 / 46447754 = 0.2228 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 11:44:43: # Command line: callpeak -t SRX4014811.bam -f BAM -g 2.15e9 -n SRX4014811.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014811.20 # format = BAM # ChIP-seq file = ['SRX4014811.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 11:44:43: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:44:43: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:44:43: # Command line: callpeak -t SRX4014811.bam -f BAM -g 2.15e9 -n SRX4014811.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014811.10 # format = BAM # ChIP-seq file = ['SRX4014811.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 11:44:43: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:44:43: # Command line: callpeak -t SRX4014811.bam -f BAM -g 2.15e9 -n SRX4014811.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014811.05 # format = BAM # ChIP-seq file = ['SRX4014811.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 11:44:43: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:44:43: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:44:43: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:44:50: 1000000 INFO @ Sat, 15 Sep 2018 11:44:50: 1000000 INFO @ Sat, 15 Sep 2018 11:44:50: 1000000 INFO @ Sat, 15 Sep 2018 11:44:57: 2000000 INFO @ Sat, 15 Sep 2018 11:44:57: 2000000 INFO @ Sat, 15 Sep 2018 11:44:57: 2000000 INFO @ Sat, 15 Sep 2018 11:45:04: 3000000 INFO @ Sat, 15 Sep 2018 11:45:04: 3000000 INFO @ Sat, 15 Sep 2018 11:45:04: 3000000 INFO @ Sat, 15 Sep 2018 11:45:10: 4000000 INFO @ Sat, 15 Sep 2018 11:45:11: 4000000 INFO @ Sat, 15 Sep 2018 11:45:11: 4000000 INFO @ Sat, 15 Sep 2018 11:45:18: 5000000 INFO @ Sat, 15 Sep 2018 11:45:18: 5000000 INFO @ Sat, 15 Sep 2018 11:45:18: 5000000 INFO @ Sat, 15 Sep 2018 11:45:25: 6000000 INFO @ Sat, 15 Sep 2018 11:45:25: 6000000 INFO @ Sat, 15 Sep 2018 11:45:26: 6000000 INFO @ Sat, 15 Sep 2018 11:45:32: 7000000 INFO @ Sat, 15 Sep 2018 11:45:32: 7000000 INFO @ Sat, 15 Sep 2018 11:45:34: 7000000 INFO @ Sat, 15 Sep 2018 11:45:39: 8000000 INFO @ Sat, 15 Sep 2018 11:45:40: 8000000 INFO @ Sat, 15 Sep 2018 11:45:42: 8000000 INFO @ Sat, 15 Sep 2018 11:45:47: 9000000 INFO @ Sat, 15 Sep 2018 11:45:47: 9000000 INFO @ Sat, 15 Sep 2018 11:45:50: 9000000 INFO @ Sat, 15 Sep 2018 11:45:54: 10000000 INFO @ Sat, 15 Sep 2018 11:45:54: 10000000 INFO @ Sat, 15 Sep 2018 11:45:58: 10000000 INFO @ Sat, 15 Sep 2018 11:46:01: 11000000 INFO @ Sat, 15 Sep 2018 11:46:01: 11000000 INFO @ Sat, 15 Sep 2018 11:46:06: 11000000 INFO @ Sat, 15 Sep 2018 11:46:08: 12000000 INFO @ Sat, 15 Sep 2018 11:46:09: 12000000 INFO @ Sat, 15 Sep 2018 11:46:14: 12000000 INFO @ Sat, 15 Sep 2018 11:46:16: 13000000 INFO @ Sat, 15 Sep 2018 11:46:16: 13000000 INFO @ Sat, 15 Sep 2018 11:46:22: 13000000 INFO @ Sat, 15 Sep 2018 11:46:23: 14000000 INFO @ Sat, 15 Sep 2018 11:46:23: 14000000 INFO @ Sat, 15 Sep 2018 11:46:30: 14000000 INFO @ Sat, 15 Sep 2018 11:46:30: 15000000 INFO @ Sat, 15 Sep 2018 11:46:31: 15000000 INFO @ Sat, 15 Sep 2018 11:46:38: 16000000 INFO @ Sat, 15 Sep 2018 11:46:38: 15000000 INFO @ Sat, 15 Sep 2018 11:46:38: 16000000 INFO @ Sat, 15 Sep 2018 11:46:45: 17000000 INFO @ Sat, 15 Sep 2018 11:46:46: 16000000 INFO @ Sat, 15 Sep 2018 11:46:46: 17000000 INFO @ Sat, 15 Sep 2018 11:46:53: 18000000 INFO @ Sat, 15 Sep 2018 11:46:54: 18000000 INFO @ Sat, 15 Sep 2018 11:46:54: 17000000 INFO @ Sat, 15 Sep 2018 11:47:01: 19000000 INFO @ Sat, 15 Sep 2018 11:47:02: 19000000 INFO @ Sat, 15 Sep 2018 11:47:03: 18000000 INFO @ Sat, 15 Sep 2018 11:47:09: 20000000 INFO @ Sat, 15 Sep 2018 11:47:10: 20000000 INFO @ Sat, 15 Sep 2018 11:47:11: 19000000 INFO @ Sat, 15 Sep 2018 11:47:16: 21000000 INFO @ Sat, 15 Sep 2018 11:47:18: 21000000 INFO @ Sat, 15 Sep 2018 11:47:20: 20000000 INFO @ Sat, 15 Sep 2018 11:47:24: 22000000 INFO @ Sat, 15 Sep 2018 11:47:25: 22000000 INFO @ Sat, 15 Sep 2018 11:47:28: 21000000 INFO @ Sat, 15 Sep 2018 11:47:32: 23000000 INFO @ Sat, 15 Sep 2018 11:47:33: 23000000 INFO @ Sat, 15 Sep 2018 11:47:36: 22000000 INFO @ Sat, 15 Sep 2018 11:47:39: 24000000 INFO @ Sat, 15 Sep 2018 11:47:41: 24000000 INFO @ Sat, 15 Sep 2018 11:47:45: 23000000 INFO @ Sat, 15 Sep 2018 11:47:47: 25000000 INFO @ Sat, 15 Sep 2018 11:47:48: 25000000 INFO @ Sat, 15 Sep 2018 11:47:53: 24000000 INFO @ Sat, 15 Sep 2018 11:47:54: 26000000 INFO @ Sat, 15 Sep 2018 11:47:56: 26000000 INFO @ Sat, 15 Sep 2018 11:48:01: 25000000 INFO @ Sat, 15 Sep 2018 11:48:02: 27000000 INFO @ Sat, 15 Sep 2018 11:48:03: 27000000 INFO @ Sat, 15 Sep 2018 11:48:09: 26000000 INFO @ Sat, 15 Sep 2018 11:48:09: 28000000 INFO @ Sat, 15 Sep 2018 11:48:11: 28000000 INFO @ Sat, 15 Sep 2018 11:48:17: 29000000 INFO @ Sat, 15 Sep 2018 11:48:17: 27000000 INFO @ Sat, 15 Sep 2018 11:48:19: 29000000 INFO @ Sat, 15 Sep 2018 11:48:24: 30000000 INFO @ Sat, 15 Sep 2018 11:48:25: 28000000 INFO @ Sat, 15 Sep 2018 11:48:26: 30000000 INFO @ Sat, 15 Sep 2018 11:48:32: 31000000 INFO @ Sat, 15 Sep 2018 11:48:34: 29000000 INFO @ Sat, 15 Sep 2018 11:48:34: 31000000 INFO @ Sat, 15 Sep 2018 11:48:39: 32000000 INFO @ Sat, 15 Sep 2018 11:48:42: 32000000 INFO @ Sat, 15 Sep 2018 11:48:42: 30000000 INFO @ Sat, 15 Sep 2018 11:48:47: 33000000 INFO @ Sat, 15 Sep 2018 11:48:50: 33000000 INFO @ Sat, 15 Sep 2018 11:48:51: 31000000 INFO @ Sat, 15 Sep 2018 11:48:55: 34000000 INFO @ Sat, 15 Sep 2018 11:48:58: 34000000 INFO @ Sat, 15 Sep 2018 11:49:00: 32000000 INFO @ Sat, 15 Sep 2018 11:49:04: 35000000 INFO @ Sat, 15 Sep 2018 11:49:07: 35000000 INFO @ Sat, 15 Sep 2018 11:49:10: 33000000 INFO @ Sat, 15 Sep 2018 11:49:12: 36000000 INFO @ Sat, 15 Sep 2018 11:49:13: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:49:13: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:49:13: #1 total tags in treatment: 36101159 INFO @ Sat, 15 Sep 2018 11:49:13: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:49:13: #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 11:49:14: #1 tags after filtering in treatment: 36100952 INFO @ Sat, 15 Sep 2018 11:49:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:49:14: #1 finished! INFO @ Sat, 15 Sep 2018 11:49:14: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:49:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:49:15: 36000000 INFO @ Sat, 15 Sep 2018 11:49:16: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:49:16: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:49:16: #1 total tags in treatment: 36101159 INFO @ Sat, 15 Sep 2018 11:49:16: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:49:16: #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 11:49:17: #1 tags after filtering in treatment: 36100952 INFO @ Sat, 15 Sep 2018 11:49:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:49:17: #1 finished! INFO @ Sat, 15 Sep 2018 11:49:17: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:49:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:49:18: 34000000 INFO @ Sat, 15 Sep 2018 11:49:24: #2 number of paired peaks: 141966 INFO @ Sat, 15 Sep 2018 11:49:24: start model_add_line... INFO @ Sat, 15 Sep 2018 11:49:25: 35000000 INFO @ Sat, 15 Sep 2018 11:49:25: start X-correlation... INFO @ Sat, 15 Sep 2018 11:49:25: end of X-cor INFO @ Sat, 15 Sep 2018 11:49:25: #2 finished! INFO @ Sat, 15 Sep 2018 11:49:25: #2 predicted fragment length is 266 bps INFO @ Sat, 15 Sep 2018 11:49:25: #2 alternative fragment length(s) may be 4,266 bps INFO @ Sat, 15 Sep 2018 11:49:25: #2.2 Generate R script for model : SRX4014811.20_model.r INFO @ Sat, 15 Sep 2018 11:49:25: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:49:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:49:27: #2 number of paired peaks: 141966 INFO @ Sat, 15 Sep 2018 11:49:27: start model_add_line... INFO @ Sat, 15 Sep 2018 11:49:28: start X-correlation... INFO @ Sat, 15 Sep 2018 11:49:28: end of X-cor INFO @ Sat, 15 Sep 2018 11:49:28: #2 finished! INFO @ Sat, 15 Sep 2018 11:49:28: #2 predicted fragment length is 266 bps INFO @ Sat, 15 Sep 2018 11:49:28: #2 alternative fragment length(s) may be 4,266 bps INFO @ Sat, 15 Sep 2018 11:49:28: #2.2 Generate R script for model : SRX4014811.05_model.r INFO @ Sat, 15 Sep 2018 11:49:28: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:49:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:49:32: 36000000 INFO @ Sat, 15 Sep 2018 11:49:34: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:49:34: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:49:34: #1 total tags in treatment: 36101159 INFO @ Sat, 15 Sep 2018 11:49:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:49:34: #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 11:49:34: #1 tags after filtering in treatment: 36100952 INFO @ Sat, 15 Sep 2018 11:49:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:49:34: #1 finished! INFO @ Sat, 15 Sep 2018 11:49:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:49:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:49:44: #2 number of paired peaks: 141966 INFO @ Sat, 15 Sep 2018 11:49:44: start model_add_line... INFO @ Sat, 15 Sep 2018 11:49:45: start X-correlation... INFO @ Sat, 15 Sep 2018 11:49:45: end of X-cor INFO @ Sat, 15 Sep 2018 11:49:45: #2 finished! INFO @ Sat, 15 Sep 2018 11:49:45: #2 predicted fragment length is 266 bps INFO @ Sat, 15 Sep 2018 11:49:45: #2 alternative fragment length(s) may be 4,266 bps INFO @ Sat, 15 Sep 2018 11:49:45: #2.2 Generate R script for model : SRX4014811.10_model.r INFO @ Sat, 15 Sep 2018 11:49:45: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:49:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:51:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:51:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:51:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:52:22: #4 Write output xls file... SRX4014811.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:52:22: #4 Write peak in narrowPeak format file... SRX4014811.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:52:22: #4 Write summits bed file... SRX4014811.20_summits.bed INFO @ Sat, 15 Sep 2018 11:52:22: Done! pass1 - making usageList (66 chroms): 11 millis pass2 - checking and writing primary data (8939 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:52:23: #4 Write output xls file... SRX4014811.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:52:23: #4 Write peak in narrowPeak format file... SRX4014811.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:52:23: #4 Write summits bed file... SRX4014811.05_summits.bed INFO @ Sat, 15 Sep 2018 11:52:23: Done! pass1 - making usageList (121 chroms): 6 millis pass2 - checking and writing primary data (26307 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:52:51: #4 Write output xls file... SRX4014811.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:52:51: #4 Write peak in narrowPeak format file... SRX4014811.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:52:51: #4 Write summits bed file... SRX4014811.10_summits.bed INFO @ Sat, 15 Sep 2018 11:52:51: Done! pass1 - making usageList (97 chroms): 3 millis pass2 - checking and writing primary data (16883 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。