Job ID = 10487601 sra ファイルのダウンロード中... Completed: 1362258K bytes transferred in 78 seconds (141508K 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 49567711 spots for /home/okishinya/chipatlas/results/rn6/SRX3087681/SRR5927317.sra Written 49567711 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:59:08 49567711 reads; of these: 49567711 (100.00%) were unpaired; of these: 1804804 (3.64%) aligned 0 times 40376677 (81.46%) aligned exactly 1 time 7386230 (14.90%) aligned >1 times 96.36% overall alignment rate Time searching: 00:59:09 Overall time: 00:59:09 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] 4917983 / 47762907 = 0.1030 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 11:03:04: # Command line: callpeak -t SRX3087681.bam -f BAM -g 2.15e9 -n SRX3087681.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087681.05 # format = BAM # ChIP-seq file = ['SRX3087681.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 11:03:04: # Command line: callpeak -t SRX3087681.bam -f BAM -g 2.15e9 -n SRX3087681.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087681.10 # format = BAM # ChIP-seq file = ['SRX3087681.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 11:03:04: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:03:04: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:03:04: # Command line: callpeak -t SRX3087681.bam -f BAM -g 2.15e9 -n SRX3087681.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087681.20 # format = BAM # ChIP-seq file = ['SRX3087681.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 11:03:04: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:03:04: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:03:04: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:03:04: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:03:12: 1000000 INFO @ Sun, 18 Mar 2018 11:03:12: 1000000 INFO @ Sun, 18 Mar 2018 11:03:12: 1000000 INFO @ Sun, 18 Mar 2018 11:03:20: 2000000 INFO @ Sun, 18 Mar 2018 11:03:20: 2000000 INFO @ Sun, 18 Mar 2018 11:03:20: 2000000 INFO @ Sun, 18 Mar 2018 11:03:27: 3000000 INFO @ Sun, 18 Mar 2018 11:03:28: 3000000 INFO @ Sun, 18 Mar 2018 11:03:28: 3000000 INFO @ Sun, 18 Mar 2018 11:03:35: 4000000 INFO @ Sun, 18 Mar 2018 11:03:35: 4000000 INFO @ Sun, 18 Mar 2018 11:03:35: 4000000 INFO @ Sun, 18 Mar 2018 11:03:43: 5000000 INFO @ Sun, 18 Mar 2018 11:03:43: 5000000 INFO @ Sun, 18 Mar 2018 11:03:43: 5000000 INFO @ Sun, 18 Mar 2018 11:03:50: 6000000 INFO @ Sun, 18 Mar 2018 11:03:50: 6000000 INFO @ Sun, 18 Mar 2018 11:03:51: 6000000 INFO @ Sun, 18 Mar 2018 11:03:58: 7000000 INFO @ Sun, 18 Mar 2018 11:03:58: 7000000 INFO @ Sun, 18 Mar 2018 11:03:59: 7000000 INFO @ Sun, 18 Mar 2018 11:04:05: 8000000 INFO @ Sun, 18 Mar 2018 11:04:05: 8000000 INFO @ Sun, 18 Mar 2018 11:04:07: 8000000 INFO @ Sun, 18 Mar 2018 11:04:13: 9000000 INFO @ Sun, 18 Mar 2018 11:04:13: 9000000 INFO @ Sun, 18 Mar 2018 11:04:15: 9000000 INFO @ Sun, 18 Mar 2018 11:04:20: 10000000 INFO @ Sun, 18 Mar 2018 11:04:20: 10000000 INFO @ Sun, 18 Mar 2018 11:04:23: 10000000 INFO @ Sun, 18 Mar 2018 11:04:28: 11000000 INFO @ Sun, 18 Mar 2018 11:04:28: 11000000 INFO @ Sun, 18 Mar 2018 11:04:31: 11000000 INFO @ Sun, 18 Mar 2018 11:04:35: 12000000 INFO @ Sun, 18 Mar 2018 11:04:35: 12000000 INFO @ Sun, 18 Mar 2018 11:04:39: 12000000 INFO @ Sun, 18 Mar 2018 11:04:43: 13000000 INFO @ Sun, 18 Mar 2018 11:04:43: 13000000 INFO @ Sun, 18 Mar 2018 11:04:47: 13000000 INFO @ Sun, 18 Mar 2018 11:04:50: 14000000 INFO @ Sun, 18 Mar 2018 11:04:50: 14000000 INFO @ Sun, 18 Mar 2018 11:04:55: 14000000 INFO @ Sun, 18 Mar 2018 11:04:58: 15000000 INFO @ Sun, 18 Mar 2018 11:04:58: 15000000 INFO @ Sun, 18 Mar 2018 11:05:03: 15000000 INFO @ Sun, 18 Mar 2018 11:05:05: 16000000 INFO @ Sun, 18 Mar 2018 11:05:05: 16000000 INFO @ Sun, 18 Mar 2018 11:05:11: 16000000 INFO @ Sun, 18 Mar 2018 11:05:12: 17000000 INFO @ Sun, 18 Mar 2018 11:05:12: 17000000 INFO @ Sun, 18 Mar 2018 11:05:20: 17000000 INFO @ Sun, 18 Mar 2018 11:05:20: 18000000 INFO @ Sun, 18 Mar 2018 11:05:20: 18000000 INFO @ Sun, 18 Mar 2018 11:05:27: 19000000 INFO @ Sun, 18 Mar 2018 11:05:27: 19000000 INFO @ Sun, 18 Mar 2018 11:05:28: 18000000 INFO @ Sun, 18 Mar 2018 11:05:35: 20000000 INFO @ Sun, 18 Mar 2018 11:05:35: 20000000 INFO @ Sun, 18 Mar 2018 11:05:36: 19000000 INFO @ Sun, 18 Mar 2018 11:05:42: 21000000 INFO @ Sun, 18 Mar 2018 11:05:42: 21000000 INFO @ Sun, 18 Mar 2018 11:05:44: 20000000 INFO @ Sun, 18 Mar 2018 11:05:50: 22000000 INFO @ Sun, 18 Mar 2018 11:05:50: 22000000 INFO @ Sun, 18 Mar 2018 11:05:52: 21000000 INFO @ Sun, 18 Mar 2018 11:05:58: 23000000 INFO @ Sun, 18 Mar 2018 11:05:58: 23000000 INFO @ Sun, 18 Mar 2018 11:05:59: 22000000 INFO @ Sun, 18 Mar 2018 11:06:05: 24000000 INFO @ Sun, 18 Mar 2018 11:06:05: 24000000 INFO @ Sun, 18 Mar 2018 11:06:07: 23000000 INFO @ Sun, 18 Mar 2018 11:06:13: 25000000 INFO @ Sun, 18 Mar 2018 11:06:13: 25000000 INFO @ Sun, 18 Mar 2018 11:06:14: 24000000 INFO @ Sun, 18 Mar 2018 11:06:21: 26000000 INFO @ Sun, 18 Mar 2018 11:06:21: 26000000 INFO @ Sun, 18 Mar 2018 11:06:22: 25000000 INFO @ Sun, 18 Mar 2018 11:06:29: 27000000 INFO @ Sun, 18 Mar 2018 11:06:29: 27000000 INFO @ Sun, 18 Mar 2018 11:06:30: 26000000 INFO @ Sun, 18 Mar 2018 11:06:36: 28000000 INFO @ Sun, 18 Mar 2018 11:06:36: 28000000 INFO @ Sun, 18 Mar 2018 11:06:38: 27000000 INFO @ Sun, 18 Mar 2018 11:06:44: 29000000 INFO @ Sun, 18 Mar 2018 11:06:44: 29000000 INFO @ Sun, 18 Mar 2018 11:06:46: 28000000 INFO @ Sun, 18 Mar 2018 11:06:51: 30000000 INFO @ Sun, 18 Mar 2018 11:06:51: 30000000 INFO @ Sun, 18 Mar 2018 11:06:54: 29000000 INFO @ Sun, 18 Mar 2018 11:06:58: 31000000 INFO @ Sun, 18 Mar 2018 11:06:58: 31000000 INFO @ Sun, 18 Mar 2018 11:07:02: 30000000 INFO @ Sun, 18 Mar 2018 11:07:06: 32000000 INFO @ Sun, 18 Mar 2018 11:07:06: 32000000 INFO @ Sun, 18 Mar 2018 11:07:09: 31000000 INFO @ Sun, 18 Mar 2018 11:07:14: 33000000 INFO @ Sun, 18 Mar 2018 11:07:14: 33000000 INFO @ Sun, 18 Mar 2018 11:07:17: 32000000 INFO @ Sun, 18 Mar 2018 11:07:22: 34000000 INFO @ Sun, 18 Mar 2018 11:07:22: 34000000 INFO @ Sun, 18 Mar 2018 11:07:25: 33000000 INFO @ Sun, 18 Mar 2018 11:07:30: 35000000 INFO @ Sun, 18 Mar 2018 11:07:30: 35000000 INFO @ Sun, 18 Mar 2018 11:07:32: 34000000 INFO @ Sun, 18 Mar 2018 11:07:38: 36000000 INFO @ Sun, 18 Mar 2018 11:07:38: 36000000 INFO @ Sun, 18 Mar 2018 11:07:40: 35000000 INFO @ Sun, 18 Mar 2018 11:07:45: 37000000 INFO @ Sun, 18 Mar 2018 11:07:45: 37000000 INFO @ Sun, 18 Mar 2018 11:07:48: 36000000 INFO @ Sun, 18 Mar 2018 11:07:53: 38000000 INFO @ Sun, 18 Mar 2018 11:07:53: 38000000 INFO @ Sun, 18 Mar 2018 11:07:55: 37000000 INFO @ Sun, 18 Mar 2018 11:08:01: 39000000 INFO @ Sun, 18 Mar 2018 11:08:01: 39000000 INFO @ Sun, 18 Mar 2018 11:08:03: 38000000 INFO @ Sun, 18 Mar 2018 11:08:09: 40000000 INFO @ Sun, 18 Mar 2018 11:08:09: 40000000 INFO @ Sun, 18 Mar 2018 11:08:11: 39000000 INFO @ Sun, 18 Mar 2018 11:08:17: 41000000 INFO @ Sun, 18 Mar 2018 11:08:17: 41000000 INFO @ Sun, 18 Mar 2018 11:08:18: 40000000 INFO @ Sun, 18 Mar 2018 11:08:25: 42000000 INFO @ Sun, 18 Mar 2018 11:08:25: 42000000 INFO @ Sun, 18 Mar 2018 11:08:26: 41000000 INFO @ Sun, 18 Mar 2018 11:08:32: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:08:32: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:08:32: #1 total tags in treatment: 42844924 INFO @ Sun, 18 Mar 2018 11:08:32: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:08:32: #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 11:08:32: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:08:32: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:08:32: #1 total tags in treatment: 42844924 INFO @ Sun, 18 Mar 2018 11:08:32: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:08:32: #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 11:08:33: #1 tags after filtering in treatment: 42844802 INFO @ Sun, 18 Mar 2018 11:08:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:08:33: #1 finished! INFO @ Sun, 18 Mar 2018 11:08:33: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:08:33: #1 tags after filtering in treatment: 42844802 INFO @ Sun, 18 Mar 2018 11:08:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:08:33: #1 finished! INFO @ Sun, 18 Mar 2018 11:08:33: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:08:34: 42000000 INFO @ Sun, 18 Mar 2018 11:08:40: #2 number of paired peaks: 77858 INFO @ Sun, 18 Mar 2018 11:08:40: start model_add_line... INFO @ Sun, 18 Mar 2018 11:08:40: #2 number of paired peaks: 77858 INFO @ Sun, 18 Mar 2018 11:08:40: start model_add_line... INFO @ Sun, 18 Mar 2018 11:08:40: start X-correlation... INFO @ Sun, 18 Mar 2018 11:08:40: end of X-cor INFO @ Sun, 18 Mar 2018 11:08:40: #2 finished! INFO @ Sun, 18 Mar 2018 11:08:40: #2 predicted fragment length is 271 bps INFO @ Sun, 18 Mar 2018 11:08:40: #2 alternative fragment length(s) may be 271 bps INFO @ Sun, 18 Mar 2018 11:08:40: #2.2 Generate R script for model : SRX3087681.05_model.r INFO @ Sun, 18 Mar 2018 11:08:40: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:08:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:08:41: start X-correlation... INFO @ Sun, 18 Mar 2018 11:08:41: end of X-cor INFO @ Sun, 18 Mar 2018 11:08:41: #2 finished! INFO @ Sun, 18 Mar 2018 11:08:41: #2 predicted fragment length is 271 bps INFO @ Sun, 18 Mar 2018 11:08:41: #2 alternative fragment length(s) may be 271 bps INFO @ Sun, 18 Mar 2018 11:08:41: #2.2 Generate R script for model : SRX3087681.10_model.r INFO @ Sun, 18 Mar 2018 11:08:41: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:08:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:08:42: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:08:42: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:08:42: #1 total tags in treatment: 42844924 INFO @ Sun, 18 Mar 2018 11:08:42: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:08:42: #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 11:08:43: #1 tags after filtering in treatment: 42844802 INFO @ Sun, 18 Mar 2018 11:08:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:08:43: #1 finished! INFO @ Sun, 18 Mar 2018 11:08:43: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:08:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:08:50: #2 number of paired peaks: 77858 INFO @ Sun, 18 Mar 2018 11:08:50: start model_add_line... INFO @ Sun, 18 Mar 2018 11:08:51: start X-correlation... INFO @ Sun, 18 Mar 2018 11:08:51: end of X-cor INFO @ Sun, 18 Mar 2018 11:08:51: #2 finished! INFO @ Sun, 18 Mar 2018 11:08:51: #2 predicted fragment length is 271 bps INFO @ Sun, 18 Mar 2018 11:08:51: #2 alternative fragment length(s) may be 271 bps INFO @ Sun, 18 Mar 2018 11:08:51: #2.2 Generate R script for model : SRX3087681.20_model.r INFO @ Sun, 18 Mar 2018 11:08:51: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:08:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:10:31: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:10:33: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:10:43: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:11:37: #4 Write output xls file... SRX3087681.10_peaks.xls INFO @ Sun, 18 Mar 2018 11:11:38: #4 Write peak in narrowPeak format file... SRX3087681.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:11:38: #4 Write summits bed file... SRX3087681.10_summits.bed INFO @ Sun, 18 Mar 2018 11:11:38: Done! pass1 - making usageList (95 chroms): 4 millis pass2 - checking and writing primary data (15744 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:11:44: #4 Write output xls file... SRX3087681.05_peaks.xls INFO @ Sun, 18 Mar 2018 11:11:44: #4 Write peak in narrowPeak format file... SRX3087681.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:11:45: #4 Write summits bed file... SRX3087681.05_summits.bed INFO @ Sun, 18 Mar 2018 11:11:45: Done! pass1 - making usageList (135 chroms): 7 millis pass2 - checking and writing primary data (29972 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:11:49: #4 Write output xls file... SRX3087681.20_peaks.xls INFO @ Sun, 18 Mar 2018 11:11:49: #4 Write peak in narrowPeak format file... SRX3087681.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:11:49: #4 Write summits bed file... SRX3087681.20_summits.bed INFO @ Sun, 18 Mar 2018 11:11:49: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (7623 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。