Job ID = 11632684 sra ファイルのダウンロード中... Completed: 980606K bytes transferred in 12 seconds (641120K 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 63084351 spots for /home/okishinya/chipatlas/results/rn6/SRX3782444/SRR6826262.sra Written 63084351 spots for /home/okishinya/chipatlas/results/rn6/SRX3782444/SRR6826262.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:23:27 63084351 reads; of these: 63084351 (100.00%) were unpaired; of these: 4206578 (6.67%) aligned 0 times 49560635 (78.56%) aligned exactly 1 time 9317138 (14.77%) aligned >1 times 93.33% overall alignment rate Time searching: 00:23:30 Overall time: 00:23:30 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 16 files... [bam_rmdupse_core] 9001912 / 58877773 = 0.1529 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 @ Fri, 15 Feb 2019 06:53:28: # Command line: callpeak -t SRX3782444.bam -f BAM -g 2.15e9 -n SRX3782444.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782444.10 # format = BAM # ChIP-seq file = ['SRX3782444.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 @ Fri, 15 Feb 2019 06:53:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:53:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:53:28: # Command line: callpeak -t SRX3782444.bam -f BAM -g 2.15e9 -n SRX3782444.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782444.05 # format = BAM # ChIP-seq file = ['SRX3782444.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 @ Fri, 15 Feb 2019 06:53:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:53:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:53:28: # Command line: callpeak -t SRX3782444.bam -f BAM -g 2.15e9 -n SRX3782444.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782444.20 # format = BAM # ChIP-seq file = ['SRX3782444.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 @ Fri, 15 Feb 2019 06:53:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:53:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:53:34: 1000000 INFO @ Fri, 15 Feb 2019 06:53:34: 1000000 INFO @ Fri, 15 Feb 2019 06:53:34: 1000000 INFO @ Fri, 15 Feb 2019 06:53:40: 2000000 INFO @ Fri, 15 Feb 2019 06:53:40: 2000000 INFO @ Fri, 15 Feb 2019 06:53:40: 2000000 INFO @ Fri, 15 Feb 2019 06:53:45: 3000000 INFO @ Fri, 15 Feb 2019 06:53:46: 3000000 INFO @ Fri, 15 Feb 2019 06:53:47: 3000000 INFO @ Fri, 15 Feb 2019 06:53:51: 4000000 INFO @ Fri, 15 Feb 2019 06:53:53: 4000000 INFO @ Fri, 15 Feb 2019 06:53:53: 4000000 INFO @ Fri, 15 Feb 2019 06:53:56: 5000000 INFO @ Fri, 15 Feb 2019 06:53:59: 5000000 INFO @ Fri, 15 Feb 2019 06:54:00: 5000000 INFO @ Fri, 15 Feb 2019 06:54:02: 6000000 INFO @ Fri, 15 Feb 2019 06:54:05: 6000000 INFO @ Fri, 15 Feb 2019 06:54:06: 6000000 INFO @ Fri, 15 Feb 2019 06:54:07: 7000000 INFO @ Fri, 15 Feb 2019 06:54:11: 7000000 INFO @ Fri, 15 Feb 2019 06:54:13: 7000000 INFO @ Fri, 15 Feb 2019 06:54:13: 8000000 INFO @ Fri, 15 Feb 2019 06:54:17: 8000000 INFO @ Fri, 15 Feb 2019 06:54:18: 9000000 INFO @ Fri, 15 Feb 2019 06:54:19: 8000000 INFO @ Fri, 15 Feb 2019 06:54:23: 9000000 INFO @ Fri, 15 Feb 2019 06:54:24: 10000000 INFO @ Fri, 15 Feb 2019 06:54:25: 9000000 INFO @ Fri, 15 Feb 2019 06:54:29: 10000000 INFO @ Fri, 15 Feb 2019 06:54:29: 11000000 INFO @ Fri, 15 Feb 2019 06:54:31: 10000000 INFO @ Fri, 15 Feb 2019 06:54:35: 11000000 INFO @ Fri, 15 Feb 2019 06:54:35: 12000000 INFO @ Fri, 15 Feb 2019 06:54:37: 11000000 INFO @ Fri, 15 Feb 2019 06:54:40: 13000000 INFO @ Fri, 15 Feb 2019 06:54:40: 12000000 INFO @ Fri, 15 Feb 2019 06:54:43: 12000000 INFO @ Fri, 15 Feb 2019 06:54:46: 14000000 INFO @ Fri, 15 Feb 2019 06:54:46: 13000000 INFO @ Fri, 15 Feb 2019 06:54:49: 13000000 INFO @ Fri, 15 Feb 2019 06:54:51: 15000000 INFO @ Fri, 15 Feb 2019 06:54:52: 14000000 INFO @ Fri, 15 Feb 2019 06:54:55: 14000000 INFO @ Fri, 15 Feb 2019 06:54:57: 16000000 INFO @ Fri, 15 Feb 2019 06:54:58: 15000000 INFO @ Fri, 15 Feb 2019 06:55:01: 15000000 INFO @ Fri, 15 Feb 2019 06:55:02: 17000000 INFO @ Fri, 15 Feb 2019 06:55:03: 16000000 INFO @ Fri, 15 Feb 2019 06:55:07: 16000000 INFO @ Fri, 15 Feb 2019 06:55:08: 18000000 INFO @ Fri, 15 Feb 2019 06:55:09: 17000000 INFO @ Fri, 15 Feb 2019 06:55:13: 17000000 INFO @ Fri, 15 Feb 2019 06:55:13: 19000000 INFO @ Fri, 15 Feb 2019 06:55:16: 18000000 INFO @ Fri, 15 Feb 2019 06:55:19: 20000000 INFO @ Fri, 15 Feb 2019 06:55:19: 18000000 INFO @ Fri, 15 Feb 2019 06:55:21: 19000000 INFO @ Fri, 15 Feb 2019 06:55:24: 21000000 INFO @ Fri, 15 Feb 2019 06:55:25: 19000000 INFO @ Fri, 15 Feb 2019 06:55:27: 20000000 INFO @ Fri, 15 Feb 2019 06:55:30: 22000000 INFO @ Fri, 15 Feb 2019 06:55:31: 20000000 INFO @ Fri, 15 Feb 2019 06:55:33: 21000000 INFO @ Fri, 15 Feb 2019 06:55:36: 23000000 INFO @ Fri, 15 Feb 2019 06:55:37: 21000000 INFO @ Fri, 15 Feb 2019 06:55:38: 22000000 INFO @ Fri, 15 Feb 2019 06:55:41: 24000000 INFO @ Fri, 15 Feb 2019 06:55:43: 22000000 INFO @ Fri, 15 Feb 2019 06:55:44: 23000000 INFO @ Fri, 15 Feb 2019 06:55:47: 25000000 INFO @ Fri, 15 Feb 2019 06:55:49: 23000000 INFO @ Fri, 15 Feb 2019 06:55:50: 24000000 INFO @ Fri, 15 Feb 2019 06:55:53: 26000000 INFO @ Fri, 15 Feb 2019 06:55:55: 24000000 INFO @ Fri, 15 Feb 2019 06:55:56: 25000000 INFO @ Fri, 15 Feb 2019 06:55:59: 27000000 INFO @ Fri, 15 Feb 2019 06:56:01: 25000000 INFO @ Fri, 15 Feb 2019 06:56:01: 26000000 INFO @ Fri, 15 Feb 2019 06:56:05: 28000000 INFO @ Fri, 15 Feb 2019 06:56:07: 26000000 INFO @ Fri, 15 Feb 2019 06:56:07: 27000000 INFO @ Fri, 15 Feb 2019 06:56:11: 29000000 INFO @ Fri, 15 Feb 2019 06:56:13: 28000000 INFO @ Fri, 15 Feb 2019 06:56:13: 27000000 INFO @ Fri, 15 Feb 2019 06:56:16: 30000000 INFO @ Fri, 15 Feb 2019 06:56:18: 29000000 INFO @ Fri, 15 Feb 2019 06:56:19: 28000000 INFO @ Fri, 15 Feb 2019 06:56:22: 31000000 INFO @ Fri, 15 Feb 2019 06:56:24: 30000000 INFO @ Fri, 15 Feb 2019 06:56:25: 29000000 INFO @ Fri, 15 Feb 2019 06:56:27: 32000000 INFO @ Fri, 15 Feb 2019 06:56:30: 31000000 INFO @ Fri, 15 Feb 2019 06:56:30: 30000000 INFO @ Fri, 15 Feb 2019 06:56:33: 33000000 INFO @ Fri, 15 Feb 2019 06:56:36: 32000000 INFO @ Fri, 15 Feb 2019 06:56:36: 31000000 INFO @ Fri, 15 Feb 2019 06:56:38: 34000000 INFO @ Fri, 15 Feb 2019 06:56:41: 33000000 INFO @ Fri, 15 Feb 2019 06:56:42: 32000000 INFO @ Fri, 15 Feb 2019 06:56:44: 35000000 INFO @ Fri, 15 Feb 2019 06:56:47: 34000000 INFO @ Fri, 15 Feb 2019 06:56:48: 33000000 INFO @ Fri, 15 Feb 2019 06:56:49: 36000000 INFO @ Fri, 15 Feb 2019 06:56:53: 35000000 INFO @ Fri, 15 Feb 2019 06:56:54: 34000000 INFO @ Fri, 15 Feb 2019 06:56:55: 37000000 INFO @ Fri, 15 Feb 2019 06:56:58: 36000000 INFO @ Fri, 15 Feb 2019 06:57:00: 35000000 INFO @ Fri, 15 Feb 2019 06:57:00: 38000000 INFO @ Fri, 15 Feb 2019 06:57:04: 37000000 INFO @ Fri, 15 Feb 2019 06:57:06: 36000000 INFO @ Fri, 15 Feb 2019 06:57:06: 39000000 INFO @ Fri, 15 Feb 2019 06:57:10: 38000000 INFO @ Fri, 15 Feb 2019 06:57:12: 40000000 INFO @ Fri, 15 Feb 2019 06:57:12: 37000000 INFO @ Fri, 15 Feb 2019 06:57:16: 39000000 INFO @ Fri, 15 Feb 2019 06:57:17: 41000000 INFO @ Fri, 15 Feb 2019 06:57:18: 38000000 INFO @ Fri, 15 Feb 2019 06:57:21: 40000000 INFO @ Fri, 15 Feb 2019 06:57:23: 42000000 INFO @ Fri, 15 Feb 2019 06:57:24: 39000000 INFO @ Fri, 15 Feb 2019 06:57:27: 41000000 INFO @ Fri, 15 Feb 2019 06:57:28: 43000000 INFO @ Fri, 15 Feb 2019 06:57:30: 40000000 INFO @ Fri, 15 Feb 2019 06:57:33: 42000000 INFO @ Fri, 15 Feb 2019 06:57:34: 44000000 INFO @ Fri, 15 Feb 2019 06:57:36: 41000000 INFO @ Fri, 15 Feb 2019 06:57:38: 43000000 INFO @ Fri, 15 Feb 2019 06:57:40: 45000000 INFO @ Fri, 15 Feb 2019 06:57:42: 42000000 INFO @ Fri, 15 Feb 2019 06:57:44: 44000000 INFO @ Fri, 15 Feb 2019 06:57:45: 46000000 INFO @ Fri, 15 Feb 2019 06:57:47: 43000000 INFO @ Fri, 15 Feb 2019 06:57:50: 45000000 INFO @ Fri, 15 Feb 2019 06:57:51: 47000000 INFO @ Fri, 15 Feb 2019 06:57:53: 44000000 INFO @ Fri, 15 Feb 2019 06:57:56: 46000000 INFO @ Fri, 15 Feb 2019 06:57:57: 48000000 INFO @ Fri, 15 Feb 2019 06:57:59: 45000000 INFO @ Fri, 15 Feb 2019 06:58:02: 47000000 INFO @ Fri, 15 Feb 2019 06:58:03: 49000000 INFO @ Fri, 15 Feb 2019 06:58:05: 46000000 INFO @ Fri, 15 Feb 2019 06:58:07: 48000000 INFO @ Fri, 15 Feb 2019 06:58:09: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 06:58:09: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 06:58:09: #1 total tags in treatment: 49875861 INFO @ Fri, 15 Feb 2019 06:58:09: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:58:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:58:10: #1 tags after filtering in treatment: 49875720 INFO @ Fri, 15 Feb 2019 06:58:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:58:10: #1 finished! INFO @ Fri, 15 Feb 2019 06:58:10: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:58:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:58:11: 47000000 INFO @ Fri, 15 Feb 2019 06:58:13: 49000000 INFO @ Fri, 15 Feb 2019 06:58:17: 48000000 INFO @ Fri, 15 Feb 2019 06:58:19: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 06:58:19: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 06:58:19: #1 total tags in treatment: 49875861 INFO @ Fri, 15 Feb 2019 06:58:19: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:58:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:58:20: #1 tags after filtering in treatment: 49875720 INFO @ Fri, 15 Feb 2019 06:58:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:58:20: #1 finished! INFO @ Fri, 15 Feb 2019 06:58:20: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:58:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:58:20: #2 number of paired peaks: 112251 INFO @ Fri, 15 Feb 2019 06:58:20: start model_add_line... INFO @ Fri, 15 Feb 2019 06:58:22: start X-correlation... INFO @ Fri, 15 Feb 2019 06:58:22: end of X-cor INFO @ Fri, 15 Feb 2019 06:58:22: #2 finished! INFO @ Fri, 15 Feb 2019 06:58:22: #2 predicted fragment length is 258 bps INFO @ Fri, 15 Feb 2019 06:58:22: #2 alternative fragment length(s) may be 258 bps INFO @ Fri, 15 Feb 2019 06:58:22: #2.2 Generate R script for model : SRX3782444.10_model.r INFO @ Fri, 15 Feb 2019 06:58:22: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:58:23: 49000000 INFO @ Fri, 15 Feb 2019 06:58:28: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 06:58:28: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 06:58:28: #1 total tags in treatment: 49875861 INFO @ Fri, 15 Feb 2019 06:58:28: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:58:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:58:29: #1 tags after filtering in treatment: 49875720 INFO @ Fri, 15 Feb 2019 06:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:58:29: #1 finished! INFO @ Fri, 15 Feb 2019 06:58:29: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:58:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:58:31: #2 number of paired peaks: 112251 INFO @ Fri, 15 Feb 2019 06:58:31: start model_add_line... INFO @ Fri, 15 Feb 2019 06:58:32: start X-correlation... INFO @ Fri, 15 Feb 2019 06:58:32: end of X-cor INFO @ Fri, 15 Feb 2019 06:58:32: #2 finished! INFO @ Fri, 15 Feb 2019 06:58:32: #2 predicted fragment length is 258 bps INFO @ Fri, 15 Feb 2019 06:58:32: #2 alternative fragment length(s) may be 258 bps INFO @ Fri, 15 Feb 2019 06:58:32: #2.2 Generate R script for model : SRX3782444.20_model.r INFO @ Fri, 15 Feb 2019 06:58:32: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:58:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:58:40: #2 number of paired peaks: 112251 INFO @ Fri, 15 Feb 2019 06:58:40: start model_add_line... INFO @ Fri, 15 Feb 2019 06:58:41: start X-correlation... INFO @ Fri, 15 Feb 2019 06:58:41: end of X-cor INFO @ Fri, 15 Feb 2019 06:58:41: #2 finished! INFO @ Fri, 15 Feb 2019 06:58:41: #2 predicted fragment length is 258 bps INFO @ Fri, 15 Feb 2019 06:58:41: #2 alternative fragment length(s) may be 258 bps INFO @ Fri, 15 Feb 2019 06:58:41: #2.2 Generate R script for model : SRX3782444.05_model.r INFO @ Fri, 15 Feb 2019 06:58:41: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:58:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:00:39: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:00:56: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:01:01: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:02:04: #4 Write output xls file... SRX3782444.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:02:04: #4 Write peak in narrowPeak format file... SRX3782444.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:02:05: #4 Write summits bed file... SRX3782444.10_summits.bed INFO @ Fri, 15 Feb 2019 07:02:05: Done! pass1 - making usageList (127 chroms): 10 millis pass2 - checking and writing primary data (42210 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:02:17: #4 Write output xls file... SRX3782444.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:02:17: #4 Write peak in narrowPeak format file... SRX3782444.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:02:18: #4 Write summits bed file... SRX3782444.20_summits.bed INFO @ Fri, 15 Feb 2019 07:02:18: Done! pass1 - making usageList (101 chroms): 6 millis pass2 - checking and writing primary data (27685 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:02:31: #4 Write output xls file... SRX3782444.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:02:33: #4 Write peak in narrowPeak format file... SRX3782444.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:02:33: #4 Write summits bed file... SRX3782444.05_summits.bed INFO @ Fri, 15 Feb 2019 07:02:33: Done! pass1 - making usageList (144 chroms): 11 millis pass2 - checking and writing primary data (56528 records, 4 fields): 72 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。