Job ID = 11632704 sra ファイルのダウンロード中... Completed: 1378567K bytes transferred in 14 seconds (773516K 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 52560443 spots for /home/okishinya/chipatlas/results/rn6/SRX3782463/SRR6826281.sra Written 52560443 spots for /home/okishinya/chipatlas/results/rn6/SRX3782463/SRR6826281.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: 00:00:03 Multiseed full-index search: 00:20:50 52560443 reads; of these: 52560443 (100.00%) were unpaired; of these: 6323445 (12.03%) aligned 0 times 37456068 (71.26%) aligned exactly 1 time 8780930 (16.71%) aligned >1 times 87.97% overall alignment rate Time searching: 00:20:57 Overall time: 00:20:57 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 12 files... [bam_rmdupse_core] 8421396 / 46236998 = 0.1821 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 06:55:16: # Command line: callpeak -t SRX3782463.bam -f BAM -g 2.15e9 -n SRX3782463.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782463.10 # format = BAM # ChIP-seq file = ['SRX3782463.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 06:55:16: # Command line: callpeak -t SRX3782463.bam -f BAM -g 2.15e9 -n SRX3782463.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782463.05 # format = BAM # ChIP-seq file = ['SRX3782463.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 06:55:16: # Command line: callpeak -t SRX3782463.bam -f BAM -g 2.15e9 -n SRX3782463.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782463.20 # format = BAM # ChIP-seq file = ['SRX3782463.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 06:55:16: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:55:16: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:55:16: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:55:16: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:55:16: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:55:16: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:55:22: 1000000 INFO @ Fri, 15 Feb 2019 06:55:24: 1000000 INFO @ Fri, 15 Feb 2019 06:55:24: 1000000 INFO @ Fri, 15 Feb 2019 06:55:29: 2000000 INFO @ Fri, 15 Feb 2019 06:55:32: 2000000 INFO @ Fri, 15 Feb 2019 06:55:32: 2000000 INFO @ Fri, 15 Feb 2019 06:55:35: 3000000 INFO @ Fri, 15 Feb 2019 06:55:39: 3000000 INFO @ Fri, 15 Feb 2019 06:55:39: 3000000 INFO @ Fri, 15 Feb 2019 06:55:42: 4000000 INFO @ Fri, 15 Feb 2019 06:55:47: 4000000 INFO @ Fri, 15 Feb 2019 06:55:47: 4000000 INFO @ Fri, 15 Feb 2019 06:55:48: 5000000 INFO @ Fri, 15 Feb 2019 06:55:54: 5000000 INFO @ Fri, 15 Feb 2019 06:55:54: 5000000 INFO @ Fri, 15 Feb 2019 06:55:55: 6000000 INFO @ Fri, 15 Feb 2019 06:56:01: 6000000 INFO @ Fri, 15 Feb 2019 06:56:01: 6000000 INFO @ Fri, 15 Feb 2019 06:56:01: 7000000 INFO @ Fri, 15 Feb 2019 06:56:08: 8000000 INFO @ Fri, 15 Feb 2019 06:56:08: 7000000 INFO @ Fri, 15 Feb 2019 06:56:08: 7000000 INFO @ Fri, 15 Feb 2019 06:56:14: 9000000 INFO @ Fri, 15 Feb 2019 06:56:16: 8000000 INFO @ Fri, 15 Feb 2019 06:56:16: 8000000 INFO @ Fri, 15 Feb 2019 06:56:21: 10000000 INFO @ Fri, 15 Feb 2019 06:56:23: 9000000 INFO @ Fri, 15 Feb 2019 06:56:23: 9000000 INFO @ Fri, 15 Feb 2019 06:56:27: 11000000 INFO @ Fri, 15 Feb 2019 06:56:30: 10000000 INFO @ Fri, 15 Feb 2019 06:56:30: 10000000 INFO @ Fri, 15 Feb 2019 06:56:34: 12000000 INFO @ Fri, 15 Feb 2019 06:56:37: 11000000 INFO @ Fri, 15 Feb 2019 06:56:37: 11000000 INFO @ Fri, 15 Feb 2019 06:56:40: 13000000 INFO @ Fri, 15 Feb 2019 06:56:44: 12000000 INFO @ Fri, 15 Feb 2019 06:56:44: 12000000 INFO @ Fri, 15 Feb 2019 06:56:47: 14000000 INFO @ Fri, 15 Feb 2019 06:56:52: 13000000 INFO @ Fri, 15 Feb 2019 06:56:52: 13000000 INFO @ Fri, 15 Feb 2019 06:56:53: 15000000 INFO @ Fri, 15 Feb 2019 06:57:00: 16000000 INFO @ Fri, 15 Feb 2019 06:57:00: 14000000 INFO @ Fri, 15 Feb 2019 06:57:00: 14000000 INFO @ Fri, 15 Feb 2019 06:57:06: 17000000 INFO @ Fri, 15 Feb 2019 06:57:08: 15000000 INFO @ Fri, 15 Feb 2019 06:57:08: 15000000 INFO @ Fri, 15 Feb 2019 06:57:13: 18000000 INFO @ Fri, 15 Feb 2019 06:57:15: 16000000 INFO @ Fri, 15 Feb 2019 06:57:15: 16000000 INFO @ Fri, 15 Feb 2019 06:57:19: 19000000 INFO @ Fri, 15 Feb 2019 06:57:21: 17000000 INFO @ Fri, 15 Feb 2019 06:57:21: 17000000 INFO @ Fri, 15 Feb 2019 06:57:26: 20000000 INFO @ Fri, 15 Feb 2019 06:57:28: 18000000 INFO @ Fri, 15 Feb 2019 06:57:28: 18000000 INFO @ Fri, 15 Feb 2019 06:57:33: 21000000 INFO @ Fri, 15 Feb 2019 06:57:36: 19000000 INFO @ Fri, 15 Feb 2019 06:57:36: 19000000 INFO @ Fri, 15 Feb 2019 06:57:39: 22000000 INFO @ Fri, 15 Feb 2019 06:57:43: 20000000 INFO @ Fri, 15 Feb 2019 06:57:43: 20000000 INFO @ Fri, 15 Feb 2019 06:57:46: 23000000 INFO @ Fri, 15 Feb 2019 06:57:49: 21000000 INFO @ Fri, 15 Feb 2019 06:57:49: 21000000 INFO @ Fri, 15 Feb 2019 06:57:52: 24000000 INFO @ Fri, 15 Feb 2019 06:57:56: 22000000 INFO @ Fri, 15 Feb 2019 06:57:56: 22000000 INFO @ Fri, 15 Feb 2019 06:57:59: 25000000 INFO @ Fri, 15 Feb 2019 06:58:03: 23000000 INFO @ Fri, 15 Feb 2019 06:58:03: 23000000 INFO @ Fri, 15 Feb 2019 06:58:05: 26000000 INFO @ Fri, 15 Feb 2019 06:58:11: 24000000 INFO @ Fri, 15 Feb 2019 06:58:11: 24000000 INFO @ Fri, 15 Feb 2019 06:58:12: 27000000 INFO @ Fri, 15 Feb 2019 06:58:18: 25000000 INFO @ Fri, 15 Feb 2019 06:58:18: 25000000 INFO @ Fri, 15 Feb 2019 06:58:18: 28000000 INFO @ Fri, 15 Feb 2019 06:58:25: 29000000 INFO @ Fri, 15 Feb 2019 06:58:26: 26000000 INFO @ Fri, 15 Feb 2019 06:58:26: 26000000 INFO @ Fri, 15 Feb 2019 06:58:31: 30000000 INFO @ Fri, 15 Feb 2019 06:58:33: 27000000 INFO @ Fri, 15 Feb 2019 06:58:33: 27000000 INFO @ Fri, 15 Feb 2019 06:58:38: 31000000 INFO @ Fri, 15 Feb 2019 06:58:40: 28000000 INFO @ Fri, 15 Feb 2019 06:58:40: 28000000 INFO @ Fri, 15 Feb 2019 06:58:44: 32000000 INFO @ Fri, 15 Feb 2019 06:58:46: 29000000 INFO @ Fri, 15 Feb 2019 06:58:46: 29000000 INFO @ Fri, 15 Feb 2019 06:58:50: 33000000 INFO @ Fri, 15 Feb 2019 06:58:53: 30000000 INFO @ Fri, 15 Feb 2019 06:58:53: 30000000 INFO @ Fri, 15 Feb 2019 06:58:57: 34000000 INFO @ Fri, 15 Feb 2019 06:59:00: 31000000 INFO @ Fri, 15 Feb 2019 06:59:00: 31000000 INFO @ Fri, 15 Feb 2019 06:59:04: 35000000 INFO @ Fri, 15 Feb 2019 06:59:07: 32000000 INFO @ Fri, 15 Feb 2019 06:59:07: 32000000 INFO @ Fri, 15 Feb 2019 06:59:10: 36000000 INFO @ Fri, 15 Feb 2019 06:59:13: 33000000 INFO @ Fri, 15 Feb 2019 06:59:13: 33000000 INFO @ Fri, 15 Feb 2019 06:59:17: 37000000 INFO @ Fri, 15 Feb 2019 06:59:20: 34000000 INFO @ Fri, 15 Feb 2019 06:59:20: 34000000 INFO @ Fri, 15 Feb 2019 06:59:23: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 06:59:23: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 06:59:23: #1 total tags in treatment: 37815602 INFO @ Fri, 15 Feb 2019 06:59:23: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:59:23: #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 06:59:24: #1 tags after filtering in treatment: 37815493 INFO @ Fri, 15 Feb 2019 06:59:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:59:24: #1 finished! INFO @ Fri, 15 Feb 2019 06:59:24: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:59:27: 35000000 INFO @ Fri, 15 Feb 2019 06:59:27: 35000000 INFO @ Fri, 15 Feb 2019 06:59:29: #2 number of paired peaks: 61371 INFO @ Fri, 15 Feb 2019 06:59:29: start model_add_line... INFO @ Fri, 15 Feb 2019 06:59:30: start X-correlation... INFO @ Fri, 15 Feb 2019 06:59:30: end of X-cor INFO @ Fri, 15 Feb 2019 06:59:30: #2 finished! INFO @ Fri, 15 Feb 2019 06:59:30: #2 predicted fragment length is 309 bps INFO @ Fri, 15 Feb 2019 06:59:30: #2 alternative fragment length(s) may be 309 bps INFO @ Fri, 15 Feb 2019 06:59:30: #2.2 Generate R script for model : SRX3782463.05_model.r INFO @ Fri, 15 Feb 2019 06:59:30: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:59:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:59:34: 36000000 INFO @ Fri, 15 Feb 2019 06:59:34: 36000000 INFO @ Fri, 15 Feb 2019 06:59:42: 37000000 INFO @ Fri, 15 Feb 2019 06:59:42: 37000000 INFO @ Fri, 15 Feb 2019 06:59:49: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 06:59:49: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 06:59:49: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 06:59:49: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 06:59:49: #1 total tags in treatment: 37815602 INFO @ Fri, 15 Feb 2019 06:59:49: #1 total tags in treatment: 37815602 INFO @ Fri, 15 Feb 2019 06:59:49: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:59:49: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:59:49: #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 06:59:49: #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 06:59:50: #1 tags after filtering in treatment: 37815493 INFO @ Fri, 15 Feb 2019 06:59:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:59:50: #1 finished! INFO @ Fri, 15 Feb 2019 06:59:50: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:59:50: #1 tags after filtering in treatment: 37815493 INFO @ Fri, 15 Feb 2019 06:59:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:59:50: #1 finished! INFO @ Fri, 15 Feb 2019 06:59:50: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:59:56: #2 number of paired peaks: 61371 INFO @ Fri, 15 Feb 2019 06:59:56: start model_add_line... INFO @ Fri, 15 Feb 2019 06:59:56: #2 number of paired peaks: 61371 INFO @ Fri, 15 Feb 2019 06:59:56: start model_add_line... INFO @ Fri, 15 Feb 2019 06:59:56: start X-correlation... INFO @ Fri, 15 Feb 2019 06:59:56: end of X-cor INFO @ Fri, 15 Feb 2019 06:59:56: #2 finished! INFO @ Fri, 15 Feb 2019 06:59:56: #2 predicted fragment length is 309 bps INFO @ Fri, 15 Feb 2019 06:59:56: #2 alternative fragment length(s) may be 309 bps INFO @ Fri, 15 Feb 2019 06:59:56: #2.2 Generate R script for model : SRX3782463.10_model.r INFO @ Fri, 15 Feb 2019 06:59:56: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:59:56: start X-correlation... INFO @ Fri, 15 Feb 2019 06:59:56: end of X-cor INFO @ Fri, 15 Feb 2019 06:59:56: #2 finished! INFO @ Fri, 15 Feb 2019 06:59:56: #2 predicted fragment length is 309 bps INFO @ Fri, 15 Feb 2019 06:59:56: #2 alternative fragment length(s) may be 309 bps INFO @ Fri, 15 Feb 2019 06:59:56: #2.2 Generate R script for model : SRX3782463.20_model.r INFO @ Fri, 15 Feb 2019 06:59:56: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:01:10: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:01:39: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:01:41: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:02:10: #4 Write output xls file... SRX3782463.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:02:10: #4 Write peak in narrowPeak format file... SRX3782463.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:02:10: #4 Write summits bed file... SRX3782463.05_summits.bed INFO @ Fri, 15 Feb 2019 07:02:10: Done! pass1 - making usageList (108 chroms): 7 millis pass2 - checking and writing primary data (26592 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:02:37: #4 Write output xls file... SRX3782463.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:02:38: #4 Write peak in narrowPeak format file... SRX3782463.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:02:38: #4 Write summits bed file... SRX3782463.20_summits.bed INFO @ Fri, 15 Feb 2019 07:02:38: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (4878 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:02:39: #4 Write output xls file... SRX3782463.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:02:39: #4 Write peak in narrowPeak format file... SRX3782463.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:02:39: #4 Write summits bed file... SRX3782463.10_summits.bed INFO @ Fri, 15 Feb 2019 07:02:40: Done! pass1 - making usageList (75 chroms): 4 millis pass2 - checking and writing primary data (14486 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。