Job ID = 10487605 sra ファイルのダウンロード中... Completed: 1326323K bytes transferred in 102 seconds (106437K 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 48370312 spots for /home/okishinya/chipatlas/results/rn6/SRX3087685/SRR5927321.sra Written 48370312 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:00:14 48370312 reads; of these: 48370312 (100.00%) were unpaired; of these: 1689366 (3.49%) aligned 0 times 39599874 (81.87%) aligned exactly 1 time 7081072 (14.64%) aligned >1 times 96.51% overall alignment rate Time searching: 01:00:17 Overall time: 01:00:17 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] 5220749 / 46680946 = 0.1118 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 11:08:27: # Command line: callpeak -t SRX3087685.bam -f BAM -g 2.15e9 -n SRX3087685.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087685.20 # format = BAM # ChIP-seq file = ['SRX3087685.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 11:08:27: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:08:27: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:08:27: # Command line: callpeak -t SRX3087685.bam -f BAM -g 2.15e9 -n SRX3087685.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087685.05 # format = BAM # ChIP-seq file = ['SRX3087685.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 11:08:27: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:08:27: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:08:27: # Command line: callpeak -t SRX3087685.bam -f BAM -g 2.15e9 -n SRX3087685.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087685.10 # format = BAM # ChIP-seq file = ['SRX3087685.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 11:08:27: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:08:27: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:08:34: 1000000 INFO @ Sun, 18 Mar 2018 11:08:34: 1000000 INFO @ Sun, 18 Mar 2018 11:08:34: 1000000 INFO @ Sun, 18 Mar 2018 11:08:41: 2000000 INFO @ Sun, 18 Mar 2018 11:08:41: 2000000 INFO @ Sun, 18 Mar 2018 11:08:41: 2000000 INFO @ Sun, 18 Mar 2018 11:08:48: 3000000 INFO @ Sun, 18 Mar 2018 11:08:48: 3000000 INFO @ Sun, 18 Mar 2018 11:08:48: 3000000 INFO @ Sun, 18 Mar 2018 11:08:55: 4000000 INFO @ Sun, 18 Mar 2018 11:08:55: 4000000 INFO @ Sun, 18 Mar 2018 11:08:55: 4000000 INFO @ Sun, 18 Mar 2018 11:09:01: 5000000 INFO @ Sun, 18 Mar 2018 11:09:01: 5000000 INFO @ Sun, 18 Mar 2018 11:09:01: 5000000 INFO @ Sun, 18 Mar 2018 11:09:08: 6000000 INFO @ Sun, 18 Mar 2018 11:09:08: 6000000 INFO @ Sun, 18 Mar 2018 11:09:08: 6000000 INFO @ Sun, 18 Mar 2018 11:09:15: 7000000 INFO @ Sun, 18 Mar 2018 11:09:16: 7000000 INFO @ Sun, 18 Mar 2018 11:09:16: 7000000 INFO @ Sun, 18 Mar 2018 11:09:23: 8000000 INFO @ Sun, 18 Mar 2018 11:09:23: 8000000 INFO @ Sun, 18 Mar 2018 11:09:23: 8000000 INFO @ Sun, 18 Mar 2018 11:09:30: 9000000 INFO @ Sun, 18 Mar 2018 11:09:31: 9000000 INFO @ Sun, 18 Mar 2018 11:09:31: 9000000 INFO @ Sun, 18 Mar 2018 11:09:37: 10000000 INFO @ Sun, 18 Mar 2018 11:09:38: 10000000 INFO @ Sun, 18 Mar 2018 11:09:38: 10000000 INFO @ Sun, 18 Mar 2018 11:09:44: 11000000 INFO @ Sun, 18 Mar 2018 11:09:45: 11000000 INFO @ Sun, 18 Mar 2018 11:09:45: 11000000 INFO @ Sun, 18 Mar 2018 11:09:51: 12000000 INFO @ Sun, 18 Mar 2018 11:09:53: 12000000 INFO @ Sun, 18 Mar 2018 11:09:53: 12000000 INFO @ Sun, 18 Mar 2018 11:09:58: 13000000 INFO @ Sun, 18 Mar 2018 11:10:00: 13000000 INFO @ Sun, 18 Mar 2018 11:10:00: 13000000 INFO @ Sun, 18 Mar 2018 11:10:05: 14000000 INFO @ Sun, 18 Mar 2018 11:10:08: 14000000 INFO @ Sun, 18 Mar 2018 11:10:08: 14000000 INFO @ Sun, 18 Mar 2018 11:10:12: 15000000 INFO @ Sun, 18 Mar 2018 11:10:15: 15000000 INFO @ Sun, 18 Mar 2018 11:10:15: 15000000 INFO @ Sun, 18 Mar 2018 11:10:19: 16000000 INFO @ Sun, 18 Mar 2018 11:10:23: 16000000 INFO @ Sun, 18 Mar 2018 11:10:23: 16000000 INFO @ Sun, 18 Mar 2018 11:10:26: 17000000 INFO @ Sun, 18 Mar 2018 11:10:30: 17000000 INFO @ Sun, 18 Mar 2018 11:10:30: 17000000 INFO @ Sun, 18 Mar 2018 11:10:33: 18000000 INFO @ Sun, 18 Mar 2018 11:10:38: 18000000 INFO @ Sun, 18 Mar 2018 11:10:38: 18000000 INFO @ Sun, 18 Mar 2018 11:10:40: 19000000 INFO @ Sun, 18 Mar 2018 11:10:45: 19000000 INFO @ Sun, 18 Mar 2018 11:10:45: 19000000 INFO @ Sun, 18 Mar 2018 11:10:47: 20000000 INFO @ Sun, 18 Mar 2018 11:10:53: 20000000 INFO @ Sun, 18 Mar 2018 11:10:53: 20000000 INFO @ Sun, 18 Mar 2018 11:10:54: 21000000 INFO @ Sun, 18 Mar 2018 11:11:00: 21000000 INFO @ Sun, 18 Mar 2018 11:11:00: 21000000 INFO @ Sun, 18 Mar 2018 11:11:01: 22000000 INFO @ Sun, 18 Mar 2018 11:11:07: 22000000 INFO @ Sun, 18 Mar 2018 11:11:07: 22000000 INFO @ Sun, 18 Mar 2018 11:11:08: 23000000 INFO @ Sun, 18 Mar 2018 11:11:14: 23000000 INFO @ Sun, 18 Mar 2018 11:11:14: 23000000 INFO @ Sun, 18 Mar 2018 11:11:15: 24000000 INFO @ Sun, 18 Mar 2018 11:11:21: 24000000 INFO @ Sun, 18 Mar 2018 11:11:21: 24000000 INFO @ Sun, 18 Mar 2018 11:11:22: 25000000 INFO @ Sun, 18 Mar 2018 11:11:28: 25000000 INFO @ Sun, 18 Mar 2018 11:11:28: 25000000 INFO @ Sun, 18 Mar 2018 11:11:29: 26000000 INFO @ Sun, 18 Mar 2018 11:11:35: 26000000 INFO @ Sun, 18 Mar 2018 11:11:35: 26000000 INFO @ Sun, 18 Mar 2018 11:11:37: 27000000 INFO @ Sun, 18 Mar 2018 11:11:42: 27000000 INFO @ Sun, 18 Mar 2018 11:11:42: 27000000 INFO @ Sun, 18 Mar 2018 11:11:44: 28000000 INFO @ Sun, 18 Mar 2018 11:11:49: 28000000 INFO @ Sun, 18 Mar 2018 11:11:50: 28000000 INFO @ Sun, 18 Mar 2018 11:11:52: 29000000 INFO @ Sun, 18 Mar 2018 11:11:57: 29000000 INFO @ Sun, 18 Mar 2018 11:11:57: 29000000 INFO @ Sun, 18 Mar 2018 11:11:59: 30000000 INFO @ Sun, 18 Mar 2018 11:12:04: 30000000 INFO @ Sun, 18 Mar 2018 11:12:05: 30000000 INFO @ Sun, 18 Mar 2018 11:12:08: 31000000 INFO @ Sun, 18 Mar 2018 11:12:12: 31000000 INFO @ Sun, 18 Mar 2018 11:12:12: 31000000 INFO @ Sun, 18 Mar 2018 11:12:17: 32000000 INFO @ Sun, 18 Mar 2018 11:12:20: 32000000 INFO @ Sun, 18 Mar 2018 11:12:20: 32000000 INFO @ Sun, 18 Mar 2018 11:12:25: 33000000 INFO @ Sun, 18 Mar 2018 11:12:27: 33000000 INFO @ Sun, 18 Mar 2018 11:12:28: 33000000 INFO @ Sun, 18 Mar 2018 11:12:32: 34000000 INFO @ Sun, 18 Mar 2018 11:12:35: 34000000 INFO @ Sun, 18 Mar 2018 11:12:35: 34000000 INFO @ Sun, 18 Mar 2018 11:12:40: 35000000 INFO @ Sun, 18 Mar 2018 11:12:42: 35000000 INFO @ Sun, 18 Mar 2018 11:12:42: 35000000 INFO @ Sun, 18 Mar 2018 11:12:48: 36000000 INFO @ Sun, 18 Mar 2018 11:12:50: 36000000 INFO @ Sun, 18 Mar 2018 11:12:50: 36000000 INFO @ Sun, 18 Mar 2018 11:12:55: 37000000 INFO @ Sun, 18 Mar 2018 11:12:57: 37000000 INFO @ Sun, 18 Mar 2018 11:12:57: 37000000 INFO @ Sun, 18 Mar 2018 11:13:03: 38000000 INFO @ Sun, 18 Mar 2018 11:13:04: 38000000 INFO @ Sun, 18 Mar 2018 11:13:04: 38000000 INFO @ Sun, 18 Mar 2018 11:13:10: 39000000 INFO @ Sun, 18 Mar 2018 11:13:11: 39000000 INFO @ Sun, 18 Mar 2018 11:13:11: 39000000 INFO @ Sun, 18 Mar 2018 11:13:17: 40000000 INFO @ Sun, 18 Mar 2018 11:13:18: 40000000 INFO @ Sun, 18 Mar 2018 11:13:19: 40000000 INFO @ Sun, 18 Mar 2018 11:13:24: 41000000 INFO @ Sun, 18 Mar 2018 11:13:26: 41000000 INFO @ Sun, 18 Mar 2018 11:13:26: 41000000 INFO @ Sun, 18 Mar 2018 11:13:28: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:13:28: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:13:28: #1 total tags in treatment: 41460197 INFO @ Sun, 18 Mar 2018 11:13:28: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:13:28: #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 11:13:29: #1 tags after filtering in treatment: 41460046 INFO @ Sun, 18 Mar 2018 11:13:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:13:29: #1 finished! INFO @ Sun, 18 Mar 2018 11:13:29: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:13:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:13:29: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:13:29: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:13:29: #1 total tags in treatment: 41460197 INFO @ Sun, 18 Mar 2018 11:13:29: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:13:29: #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 11:13:30: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:13:30: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:13:30: #1 total tags in treatment: 41460197 INFO @ Sun, 18 Mar 2018 11:13:30: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:13:30: #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 11:13:31: #1 tags after filtering in treatment: 41460046 INFO @ Sun, 18 Mar 2018 11:13:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:13:31: #1 finished! INFO @ Sun, 18 Mar 2018 11:13:31: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:13:31: #1 tags after filtering in treatment: 41460046 INFO @ Sun, 18 Mar 2018 11:13:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:13:31: #1 finished! INFO @ Sun, 18 Mar 2018 11:13:31: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:13:37: #2 number of paired peaks: 96678 INFO @ Sun, 18 Mar 2018 11:13:37: start model_add_line... INFO @ Sun, 18 Mar 2018 11:13:37: start X-correlation... INFO @ Sun, 18 Mar 2018 11:13:37: end of X-cor INFO @ Sun, 18 Mar 2018 11:13:37: #2 finished! INFO @ Sun, 18 Mar 2018 11:13:37: #2 predicted fragment length is 271 bps INFO @ Sun, 18 Mar 2018 11:13:37: #2 alternative fragment length(s) may be 271 bps INFO @ Sun, 18 Mar 2018 11:13:37: #2.2 Generate R script for model : SRX3087685.10_model.r INFO @ Sun, 18 Mar 2018 11:13:37: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:13:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:13:38: #2 number of paired peaks: 96678 INFO @ Sun, 18 Mar 2018 11:13:38: start model_add_line... INFO @ Sun, 18 Mar 2018 11:13:38: #2 number of paired peaks: 96678 INFO @ Sun, 18 Mar 2018 11:13:38: start model_add_line... INFO @ Sun, 18 Mar 2018 11:13:39: start X-correlation... INFO @ Sun, 18 Mar 2018 11:13:39: end of X-cor INFO @ Sun, 18 Mar 2018 11:13:39: #2 finished! INFO @ Sun, 18 Mar 2018 11:13:39: #2 predicted fragment length is 271 bps INFO @ Sun, 18 Mar 2018 11:13:39: #2 alternative fragment length(s) may be 271 bps INFO @ Sun, 18 Mar 2018 11:13:39: #2.2 Generate R script for model : SRX3087685.20_model.r INFO @ Sun, 18 Mar 2018 11:13:39: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:13:39: start X-correlation... INFO @ Sun, 18 Mar 2018 11:13:39: end of X-cor INFO @ Sun, 18 Mar 2018 11:13:39: #2 finished! INFO @ Sun, 18 Mar 2018 11:13:39: #2 predicted fragment length is 271 bps INFO @ Sun, 18 Mar 2018 11:13:39: #2 alternative fragment length(s) may be 271 bps INFO @ Sun, 18 Mar 2018 11:13:39: #2.2 Generate R script for model : SRX3087685.05_model.r INFO @ Sun, 18 Mar 2018 11:13:39: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:15:18: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:15:23: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:15:37: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:16:22: #4 Write output xls file... SRX3087685.10_peaks.xls INFO @ Sun, 18 Mar 2018 11:16:23: #4 Write peak in narrowPeak format file... SRX3087685.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:16:23: #4 Write summits bed file... SRX3087685.10_summits.bed INFO @ Sun, 18 Mar 2018 11:16:23: Done! pass1 - making usageList (103 chroms): 4 millis pass2 - checking and writing primary data (21167 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:16:30: #4 Write output xls file... SRX3087685.05_peaks.xls INFO @ Sun, 18 Mar 2018 11:16:31: #4 Write peak in narrowPeak format file... SRX3087685.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:16:31: #4 Write summits bed file... SRX3087685.05_summits.bed INFO @ Sun, 18 Mar 2018 11:16:31: Done! pass1 - making usageList (133 chroms): 8 millis pass2 - checking and writing primary data (39512 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:16:45: #4 Write output xls file... SRX3087685.20_peaks.xls INFO @ Sun, 18 Mar 2018 11:16:45: #4 Write peak in narrowPeak format file... SRX3087685.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:16:45: #4 Write summits bed file... SRX3087685.20_summits.bed INFO @ Sun, 18 Mar 2018 11:16:45: Done! pass1 - making usageList (52 chroms): 3 millis pass2 - checking and writing primary data (8757 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。