Job ID = 10487604 sra ファイルのダウンロード中... Completed: 1268420K bytes transferred in 91 seconds (113671K 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 46351664 spots for /home/okishinya/chipatlas/results/rn6/SRX3087684/SRR5927320.sra Written 46351664 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: 00:00:01 Multiseed full-index search: 00:56:24 46351664 reads; of these: 46351664 (100.00%) were unpaired; of these: 1431361 (3.09%) aligned 0 times 38322718 (82.68%) aligned exactly 1 time 6597585 (14.23%) aligned >1 times 96.91% overall alignment rate Time searching: 00:56:26 Overall time: 00:56:26 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] 9017313 / 44920303 = 0.2007 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 11:01:40: # Command line: callpeak -t SRX3087684.bam -f BAM -g 2.15e9 -n SRX3087684.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087684.05 # format = BAM # ChIP-seq file = ['SRX3087684.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 11:01:40: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:01:40: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:01:40: # Command line: callpeak -t SRX3087684.bam -f BAM -g 2.15e9 -n SRX3087684.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087684.10 # format = BAM # ChIP-seq file = ['SRX3087684.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 11:01:40: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:01:40: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:01:40: # Command line: callpeak -t SRX3087684.bam -f BAM -g 2.15e9 -n SRX3087684.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087684.20 # format = BAM # ChIP-seq file = ['SRX3087684.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 11:01:40: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:01:40: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:01:48: 1000000 INFO @ Sun, 18 Mar 2018 11:01:49: 1000000 INFO @ Sun, 18 Mar 2018 11:01:49: 1000000 INFO @ Sun, 18 Mar 2018 11:01:55: 2000000 INFO @ Sun, 18 Mar 2018 11:01:58: 2000000 INFO @ Sun, 18 Mar 2018 11:01:58: 2000000 INFO @ Sun, 18 Mar 2018 11:02:03: 3000000 INFO @ Sun, 18 Mar 2018 11:02:06: 3000000 INFO @ Sun, 18 Mar 2018 11:02:06: 3000000 INFO @ Sun, 18 Mar 2018 11:02:10: 4000000 INFO @ Sun, 18 Mar 2018 11:02:15: 4000000 INFO @ Sun, 18 Mar 2018 11:02:15: 4000000 INFO @ Sun, 18 Mar 2018 11:02:18: 5000000 INFO @ Sun, 18 Mar 2018 11:02:24: 5000000 INFO @ Sun, 18 Mar 2018 11:02:24: 5000000 INFO @ Sun, 18 Mar 2018 11:02:25: 6000000 INFO @ Sun, 18 Mar 2018 11:02:32: 6000000 INFO @ Sun, 18 Mar 2018 11:02:32: 6000000 INFO @ Sun, 18 Mar 2018 11:02:33: 7000000 INFO @ Sun, 18 Mar 2018 11:02:40: 8000000 INFO @ Sun, 18 Mar 2018 11:02:41: 7000000 INFO @ Sun, 18 Mar 2018 11:02:41: 7000000 INFO @ Sun, 18 Mar 2018 11:02:48: 9000000 INFO @ Sun, 18 Mar 2018 11:02:50: 8000000 INFO @ Sun, 18 Mar 2018 11:02:50: 8000000 INFO @ Sun, 18 Mar 2018 11:02:55: 10000000 INFO @ Sun, 18 Mar 2018 11:02:58: 9000000 INFO @ Sun, 18 Mar 2018 11:02:58: 9000000 INFO @ Sun, 18 Mar 2018 11:03:02: 11000000 INFO @ Sun, 18 Mar 2018 11:03:07: 10000000 INFO @ Sun, 18 Mar 2018 11:03:07: 10000000 INFO @ Sun, 18 Mar 2018 11:03:10: 12000000 INFO @ Sun, 18 Mar 2018 11:03:16: 11000000 INFO @ Sun, 18 Mar 2018 11:03:16: 11000000 INFO @ Sun, 18 Mar 2018 11:03:17: 13000000 INFO @ Sun, 18 Mar 2018 11:03:24: 12000000 INFO @ Sun, 18 Mar 2018 11:03:24: 12000000 INFO @ Sun, 18 Mar 2018 11:03:25: 14000000 INFO @ Sun, 18 Mar 2018 11:03:32: 15000000 INFO @ Sun, 18 Mar 2018 11:03:33: 13000000 INFO @ Sun, 18 Mar 2018 11:03:33: 13000000 INFO @ Sun, 18 Mar 2018 11:03:40: 16000000 INFO @ Sun, 18 Mar 2018 11:03:42: 14000000 INFO @ Sun, 18 Mar 2018 11:03:42: 14000000 INFO @ Sun, 18 Mar 2018 11:03:47: 17000000 INFO @ Sun, 18 Mar 2018 11:03:51: 15000000 INFO @ Sun, 18 Mar 2018 11:03:51: 15000000 INFO @ Sun, 18 Mar 2018 11:03:55: 18000000 INFO @ Sun, 18 Mar 2018 11:03:59: 16000000 INFO @ Sun, 18 Mar 2018 11:03:59: 16000000 INFO @ Sun, 18 Mar 2018 11:04:02: 19000000 INFO @ Sun, 18 Mar 2018 11:04:08: 17000000 INFO @ Sun, 18 Mar 2018 11:04:08: 17000000 INFO @ Sun, 18 Mar 2018 11:04:10: 20000000 INFO @ Sun, 18 Mar 2018 11:04:16: 18000000 INFO @ Sun, 18 Mar 2018 11:04:16: 18000000 INFO @ Sun, 18 Mar 2018 11:04:17: 21000000 INFO @ Sun, 18 Mar 2018 11:04:25: 22000000 INFO @ Sun, 18 Mar 2018 11:04:25: 19000000 INFO @ Sun, 18 Mar 2018 11:04:25: 19000000 INFO @ Sun, 18 Mar 2018 11:04:32: 23000000 INFO @ Sun, 18 Mar 2018 11:04:34: 20000000 INFO @ Sun, 18 Mar 2018 11:04:34: 20000000 INFO @ Sun, 18 Mar 2018 11:04:39: 24000000 INFO @ Sun, 18 Mar 2018 11:04:42: 21000000 INFO @ Sun, 18 Mar 2018 11:04:42: 21000000 INFO @ Sun, 18 Mar 2018 11:04:47: 25000000 INFO @ Sun, 18 Mar 2018 11:04:51: 22000000 INFO @ Sun, 18 Mar 2018 11:04:51: 22000000 INFO @ Sun, 18 Mar 2018 11:04:54: 26000000 INFO @ Sun, 18 Mar 2018 11:04:59: 23000000 INFO @ Sun, 18 Mar 2018 11:04:59: 23000000 INFO @ Sun, 18 Mar 2018 11:05:02: 27000000 INFO @ Sun, 18 Mar 2018 11:05:08: 24000000 INFO @ Sun, 18 Mar 2018 11:05:08: 24000000 INFO @ Sun, 18 Mar 2018 11:05:09: 28000000 INFO @ Sun, 18 Mar 2018 11:05:16: 25000000 INFO @ Sun, 18 Mar 2018 11:05:16: 25000000 INFO @ Sun, 18 Mar 2018 11:05:17: 29000000 INFO @ Sun, 18 Mar 2018 11:05:24: 30000000 INFO @ Sun, 18 Mar 2018 11:05:25: 26000000 INFO @ Sun, 18 Mar 2018 11:05:25: 26000000 INFO @ Sun, 18 Mar 2018 11:05:32: 31000000 INFO @ Sun, 18 Mar 2018 11:05:34: 27000000 INFO @ Sun, 18 Mar 2018 11:05:34: 27000000 INFO @ Sun, 18 Mar 2018 11:05:39: 32000000 INFO @ Sun, 18 Mar 2018 11:05:42: 28000000 INFO @ Sun, 18 Mar 2018 11:05:42: 28000000 INFO @ Sun, 18 Mar 2018 11:05:47: 33000000 INFO @ Sun, 18 Mar 2018 11:05:51: 29000000 INFO @ Sun, 18 Mar 2018 11:05:51: 29000000 INFO @ Sun, 18 Mar 2018 11:05:54: 34000000 INFO @ Sun, 18 Mar 2018 11:05:59: 30000000 INFO @ Sun, 18 Mar 2018 11:05:59: 30000000 INFO @ Sun, 18 Mar 2018 11:06:01: 35000000 INFO @ Sun, 18 Mar 2018 11:06:08: 31000000 INFO @ Sun, 18 Mar 2018 11:06:08: 31000000 INFO @ Sun, 18 Mar 2018 11:06:09: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:06:09: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:06:09: #1 total tags in treatment: 35902990 INFO @ Sun, 18 Mar 2018 11:06:09: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:06:09: #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 11:06:10: #1 tags after filtering in treatment: 35902842 INFO @ Sun, 18 Mar 2018 11:06:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:06:10: #1 finished! INFO @ Sun, 18 Mar 2018 11:06:10: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:06:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:06:17: #2 number of paired peaks: 104134 INFO @ Sun, 18 Mar 2018 11:06:17: start model_add_line... INFO @ Sun, 18 Mar 2018 11:06:17: 32000000 INFO @ Sun, 18 Mar 2018 11:06:17: 32000000 INFO @ Sun, 18 Mar 2018 11:06:18: start X-correlation... INFO @ Sun, 18 Mar 2018 11:06:18: end of X-cor INFO @ Sun, 18 Mar 2018 11:06:18: #2 finished! INFO @ Sun, 18 Mar 2018 11:06:18: #2 predicted fragment length is 272 bps INFO @ Sun, 18 Mar 2018 11:06:18: #2 alternative fragment length(s) may be 272 bps INFO @ Sun, 18 Mar 2018 11:06:18: #2.2 Generate R script for model : SRX3087684.05_model.r INFO @ Sun, 18 Mar 2018 11:06:18: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:06:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:06:26: 33000000 INFO @ Sun, 18 Mar 2018 11:06:26: 33000000 INFO @ Sun, 18 Mar 2018 11:06:33: 34000000 INFO @ Sun, 18 Mar 2018 11:06:33: 34000000 INFO @ Sun, 18 Mar 2018 11:06:41: 35000000 INFO @ Sun, 18 Mar 2018 11:06:41: 35000000 INFO @ Sun, 18 Mar 2018 11:06:49: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:06:49: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:06:49: #1 total tags in treatment: 35902990 INFO @ Sun, 18 Mar 2018 11:06:49: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:06:49: #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 11:06:49: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:06:49: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:06:49: #1 total tags in treatment: 35902990 INFO @ Sun, 18 Mar 2018 11:06:49: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:06:49: #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 11:06:50: #1 tags after filtering in treatment: 35902842 INFO @ Sun, 18 Mar 2018 11:06:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:06:50: #1 finished! INFO @ Sun, 18 Mar 2018 11:06:50: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:06:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:06:50: #1 tags after filtering in treatment: 35902842 INFO @ Sun, 18 Mar 2018 11:06:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:06:50: #1 finished! INFO @ Sun, 18 Mar 2018 11:06:50: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:06:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:06:57: #2 number of paired peaks: 104134 INFO @ Sun, 18 Mar 2018 11:06:57: start model_add_line... INFO @ Sun, 18 Mar 2018 11:06:58: #2 number of paired peaks: 104134 INFO @ Sun, 18 Mar 2018 11:06:58: start model_add_line... INFO @ Sun, 18 Mar 2018 11:06:58: start X-correlation... INFO @ Sun, 18 Mar 2018 11:06:58: end of X-cor INFO @ Sun, 18 Mar 2018 11:06:58: #2 finished! INFO @ Sun, 18 Mar 2018 11:06:58: #2 predicted fragment length is 272 bps INFO @ Sun, 18 Mar 2018 11:06:58: #2 alternative fragment length(s) may be 272 bps INFO @ Sun, 18 Mar 2018 11:06:58: #2.2 Generate R script for model : SRX3087684.20_model.r INFO @ Sun, 18 Mar 2018 11:06:58: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:06:58: start X-correlation... INFO @ Sun, 18 Mar 2018 11:06:58: end of X-cor INFO @ Sun, 18 Mar 2018 11:06:58: #2 finished! INFO @ Sun, 18 Mar 2018 11:06:58: #2 predicted fragment length is 272 bps INFO @ Sun, 18 Mar 2018 11:06:58: #2 alternative fragment length(s) may be 272 bps INFO @ Sun, 18 Mar 2018 11:06:58: #2.2 Generate R script for model : SRX3087684.10_model.r INFO @ Sun, 18 Mar 2018 11:06:58: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:07:50: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:08:30: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:08:32: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:08:46: #4 Write output xls file... SRX3087684.05_peaks.xls INFO @ Sun, 18 Mar 2018 11:08:47: #4 Write peak in narrowPeak format file... SRX3087684.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:08:47: #4 Write summits bed file... SRX3087684.05_summits.bed INFO @ Sun, 18 Mar 2018 11:08:47: Done! pass1 - making usageList (134 chroms): 8 millis pass2 - checking and writing primary data (40277 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:09:26: #4 Write output xls file... SRX3087684.20_peaks.xls INFO @ Sun, 18 Mar 2018 11:09:26: #4 Write peak in narrowPeak format file... SRX3087684.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:09:26: #4 Write summits bed file... SRX3087684.20_summits.bed INFO @ Sun, 18 Mar 2018 11:09:26: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (9702 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:09:27: #4 Write output xls file... SRX3087684.10_peaks.xls INFO @ Sun, 18 Mar 2018 11:09:27: #4 Write peak in narrowPeak format file... SRX3087684.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:09:27: #4 Write summits bed file... SRX3087684.10_summits.bed INFO @ Sun, 18 Mar 2018 11:09:27: Done! pass1 - making usageList (106 chroms): 5 millis pass2 - checking and writing primary data (22074 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。