Job ID = 10487602 sra ファイルのダウンロード中... Completed: 1284201K bytes transferred in 28 seconds (365915K 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 46685875 spots for /home/okishinya/chipatlas/results/rn6/SRX3087682/SRR5927318.sra Written 46685875 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: 00:00:00 Multiseed full-index search: 00:58:59 46685875 reads; of these: 46685875 (100.00%) were unpaired; of these: 1435208 (3.07%) aligned 0 times 38162508 (81.74%) aligned exactly 1 time 7088159 (15.18%) aligned >1 times 96.93% overall alignment rate Time searching: 00:59:01 Overall time: 00:59:01 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] 3921897 / 45250667 = 0.0867 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 11:02:12: # Command line: callpeak -t SRX3087682.bam -f BAM -g 2.15e9 -n SRX3087682.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087682.20 # format = BAM # ChIP-seq file = ['SRX3087682.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 11:02:12: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:02:12: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:02:12: # Command line: callpeak -t SRX3087682.bam -f BAM -g 2.15e9 -n SRX3087682.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087682.10 # format = BAM # ChIP-seq file = ['SRX3087682.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 11:02:12: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:02:12: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:02:12: # Command line: callpeak -t SRX3087682.bam -f BAM -g 2.15e9 -n SRX3087682.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087682.05 # format = BAM # ChIP-seq file = ['SRX3087682.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 11:02:12: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:02:12: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:02:19: 1000000 INFO @ Sun, 18 Mar 2018 11:02:19: 1000000 INFO @ Sun, 18 Mar 2018 11:02:20: 1000000 INFO @ Sun, 18 Mar 2018 11:02:26: 2000000 INFO @ Sun, 18 Mar 2018 11:02:27: 2000000 INFO @ Sun, 18 Mar 2018 11:02:27: 2000000 INFO @ Sun, 18 Mar 2018 11:02:33: 3000000 INFO @ Sun, 18 Mar 2018 11:02:35: 3000000 INFO @ Sun, 18 Mar 2018 11:02:35: 3000000 INFO @ Sun, 18 Mar 2018 11:02:40: 4000000 INFO @ Sun, 18 Mar 2018 11:02:42: 4000000 INFO @ Sun, 18 Mar 2018 11:02:42: 4000000 INFO @ Sun, 18 Mar 2018 11:02:46: 5000000 INFO @ Sun, 18 Mar 2018 11:02:50: 5000000 INFO @ Sun, 18 Mar 2018 11:02:50: 5000000 INFO @ Sun, 18 Mar 2018 11:02:53: 6000000 INFO @ Sun, 18 Mar 2018 11:02:58: 6000000 INFO @ Sun, 18 Mar 2018 11:02:58: 6000000 INFO @ Sun, 18 Mar 2018 11:03:00: 7000000 INFO @ Sun, 18 Mar 2018 11:03:05: 7000000 INFO @ Sun, 18 Mar 2018 11:03:05: 7000000 INFO @ Sun, 18 Mar 2018 11:03:07: 8000000 INFO @ Sun, 18 Mar 2018 11:03:13: 8000000 INFO @ Sun, 18 Mar 2018 11:03:13: 8000000 INFO @ Sun, 18 Mar 2018 11:03:14: 9000000 INFO @ Sun, 18 Mar 2018 11:03:21: 10000000 INFO @ Sun, 18 Mar 2018 11:03:21: 9000000 INFO @ Sun, 18 Mar 2018 11:03:21: 9000000 INFO @ Sun, 18 Mar 2018 11:03:28: 11000000 INFO @ Sun, 18 Mar 2018 11:03:28: 10000000 INFO @ Sun, 18 Mar 2018 11:03:28: 10000000 INFO @ Sun, 18 Mar 2018 11:03:36: 12000000 INFO @ Sun, 18 Mar 2018 11:03:36: 11000000 INFO @ Sun, 18 Mar 2018 11:03:36: 11000000 INFO @ Sun, 18 Mar 2018 11:03:43: 13000000 INFO @ Sun, 18 Mar 2018 11:03:44: 12000000 INFO @ Sun, 18 Mar 2018 11:03:44: 12000000 INFO @ Sun, 18 Mar 2018 11:03:50: 14000000 INFO @ Sun, 18 Mar 2018 11:03:51: 13000000 INFO @ Sun, 18 Mar 2018 11:03:51: 13000000 INFO @ Sun, 18 Mar 2018 11:03:56: 15000000 INFO @ Sun, 18 Mar 2018 11:03:59: 14000000 INFO @ Sun, 18 Mar 2018 11:03:59: 14000000 INFO @ Sun, 18 Mar 2018 11:04:03: 16000000 INFO @ Sun, 18 Mar 2018 11:04:07: 15000000 INFO @ Sun, 18 Mar 2018 11:04:07: 15000000 INFO @ Sun, 18 Mar 2018 11:04:10: 17000000 INFO @ Sun, 18 Mar 2018 11:04:15: 16000000 INFO @ Sun, 18 Mar 2018 11:04:15: 16000000 INFO @ Sun, 18 Mar 2018 11:04:17: 18000000 INFO @ Sun, 18 Mar 2018 11:04:22: 17000000 INFO @ Sun, 18 Mar 2018 11:04:22: 17000000 INFO @ Sun, 18 Mar 2018 11:04:25: 19000000 INFO @ Sun, 18 Mar 2018 11:04:30: 18000000 INFO @ Sun, 18 Mar 2018 11:04:30: 18000000 INFO @ Sun, 18 Mar 2018 11:04:32: 20000000 INFO @ Sun, 18 Mar 2018 11:04:37: 19000000 INFO @ Sun, 18 Mar 2018 11:04:37: 19000000 INFO @ Sun, 18 Mar 2018 11:04:39: 21000000 INFO @ Sun, 18 Mar 2018 11:04:45: 20000000 INFO @ Sun, 18 Mar 2018 11:04:45: 20000000 INFO @ Sun, 18 Mar 2018 11:04:47: 22000000 INFO @ Sun, 18 Mar 2018 11:04:52: 21000000 INFO @ Sun, 18 Mar 2018 11:04:52: 21000000 INFO @ Sun, 18 Mar 2018 11:04:54: 23000000 INFO @ Sun, 18 Mar 2018 11:05:00: 22000000 INFO @ Sun, 18 Mar 2018 11:05:00: 22000000 INFO @ Sun, 18 Mar 2018 11:05:01: 24000000 INFO @ Sun, 18 Mar 2018 11:05:07: 23000000 INFO @ Sun, 18 Mar 2018 11:05:07: 23000000 INFO @ Sun, 18 Mar 2018 11:05:08: 25000000 INFO @ Sun, 18 Mar 2018 11:05:15: 24000000 INFO @ Sun, 18 Mar 2018 11:05:15: 24000000 INFO @ Sun, 18 Mar 2018 11:05:16: 26000000 INFO @ Sun, 18 Mar 2018 11:05:22: 25000000 INFO @ Sun, 18 Mar 2018 11:05:22: 25000000 INFO @ Sun, 18 Mar 2018 11:05:22: 27000000 INFO @ Sun, 18 Mar 2018 11:05:29: 28000000 INFO @ Sun, 18 Mar 2018 11:05:30: 26000000 INFO @ Sun, 18 Mar 2018 11:05:30: 26000000 INFO @ Sun, 18 Mar 2018 11:05:37: 29000000 INFO @ Sun, 18 Mar 2018 11:05:37: 27000000 INFO @ Sun, 18 Mar 2018 11:05:37: 27000000 INFO @ Sun, 18 Mar 2018 11:05:45: 28000000 INFO @ Sun, 18 Mar 2018 11:05:45: 30000000 INFO @ Sun, 18 Mar 2018 11:05:46: 28000000 INFO @ Sun, 18 Mar 2018 11:05:52: 31000000 INFO @ Sun, 18 Mar 2018 11:05:53: 29000000 INFO @ Sun, 18 Mar 2018 11:05:54: 29000000 INFO @ Sun, 18 Mar 2018 11:05:58: 32000000 INFO @ Sun, 18 Mar 2018 11:06:01: 30000000 INFO @ Sun, 18 Mar 2018 11:06:02: 30000000 INFO @ Sun, 18 Mar 2018 11:06:05: 33000000 INFO @ Sun, 18 Mar 2018 11:06:09: 31000000 INFO @ Sun, 18 Mar 2018 11:06:10: 31000000 INFO @ Sun, 18 Mar 2018 11:06:13: 34000000 INFO @ Sun, 18 Mar 2018 11:06:17: 32000000 INFO @ Sun, 18 Mar 2018 11:06:17: 32000000 INFO @ Sun, 18 Mar 2018 11:06:20: 35000000 INFO @ Sun, 18 Mar 2018 11:06:25: 33000000 INFO @ Sun, 18 Mar 2018 11:06:25: 33000000 INFO @ Sun, 18 Mar 2018 11:06:27: 36000000 INFO @ Sun, 18 Mar 2018 11:06:33: 34000000 INFO @ Sun, 18 Mar 2018 11:06:33: 34000000 INFO @ Sun, 18 Mar 2018 11:06:33: 37000000 INFO @ Sun, 18 Mar 2018 11:06:40: 35000000 INFO @ Sun, 18 Mar 2018 11:06:40: 35000000 INFO @ Sun, 18 Mar 2018 11:06:41: 38000000 INFO @ Sun, 18 Mar 2018 11:06:48: 36000000 INFO @ Sun, 18 Mar 2018 11:06:48: 36000000 INFO @ Sun, 18 Mar 2018 11:06:48: 39000000 INFO @ Sun, 18 Mar 2018 11:06:55: 40000000 INFO @ Sun, 18 Mar 2018 11:06:56: 37000000 INFO @ Sun, 18 Mar 2018 11:06:56: 37000000 INFO @ Sun, 18 Mar 2018 11:07:03: 41000000 INFO @ Sun, 18 Mar 2018 11:07:03: 38000000 INFO @ Sun, 18 Mar 2018 11:07:03: 38000000 INFO @ Sun, 18 Mar 2018 11:07:05: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:07:05: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:07:05: #1 total tags in treatment: 41328770 INFO @ Sun, 18 Mar 2018 11:07:05: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:07:05: #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 11:07:06: #1 tags after filtering in treatment: 41328635 INFO @ Sun, 18 Mar 2018 11:07:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:07:06: #1 finished! INFO @ Sun, 18 Mar 2018 11:07:06: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:07:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:07:11: 39000000 INFO @ Sun, 18 Mar 2018 11:07:11: 39000000 INFO @ Sun, 18 Mar 2018 11:07:12: #2 number of paired peaks: 55416 INFO @ Sun, 18 Mar 2018 11:07:12: start model_add_line... INFO @ Sun, 18 Mar 2018 11:07:13: start X-correlation... INFO @ Sun, 18 Mar 2018 11:07:13: end of X-cor INFO @ Sun, 18 Mar 2018 11:07:13: #2 finished! INFO @ Sun, 18 Mar 2018 11:07:13: #2 predicted fragment length is 268 bps INFO @ Sun, 18 Mar 2018 11:07:13: #2 alternative fragment length(s) may be 268 bps INFO @ Sun, 18 Mar 2018 11:07:13: #2.2 Generate R script for model : SRX3087682.05_model.r INFO @ Sun, 18 Mar 2018 11:07:13: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:07:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:07:18: 40000000 INFO @ Sun, 18 Mar 2018 11:07:18: 40000000 INFO @ Sun, 18 Mar 2018 11:07:26: 41000000 INFO @ Sun, 18 Mar 2018 11:07:26: 41000000 INFO @ Sun, 18 Mar 2018 11:07:29: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:07:29: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:07:29: #1 total tags in treatment: 41328770 INFO @ Sun, 18 Mar 2018 11:07:29: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:07:29: #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 11:07:29: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:07:29: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:07:29: #1 total tags in treatment: 41328770 INFO @ Sun, 18 Mar 2018 11:07:29: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:07:29: #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 11:07:30: #1 tags after filtering in treatment: 41328635 INFO @ Sun, 18 Mar 2018 11:07:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:07:30: #1 finished! INFO @ Sun, 18 Mar 2018 11:07:30: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:07:30: #1 tags after filtering in treatment: 41328635 INFO @ Sun, 18 Mar 2018 11:07:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:07:30: #1 finished! INFO @ Sun, 18 Mar 2018 11:07:30: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:07:36: #2 number of paired peaks: 55416 INFO @ Sun, 18 Mar 2018 11:07:36: start model_add_line... INFO @ Sun, 18 Mar 2018 11:07:36: #2 number of paired peaks: 55416 INFO @ Sun, 18 Mar 2018 11:07:36: start model_add_line... INFO @ Sun, 18 Mar 2018 11:07:37: start X-correlation... INFO @ Sun, 18 Mar 2018 11:07:37: start X-correlation... INFO @ Sun, 18 Mar 2018 11:07:37: end of X-cor INFO @ Sun, 18 Mar 2018 11:07:37: #2 finished! INFO @ Sun, 18 Mar 2018 11:07:37: #2 predicted fragment length is 268 bps INFO @ Sun, 18 Mar 2018 11:07:37: #2 alternative fragment length(s) may be 268 bps INFO @ Sun, 18 Mar 2018 11:07:37: #2.2 Generate R script for model : SRX3087682.10_model.r INFO @ Sun, 18 Mar 2018 11:07:37: end of X-cor INFO @ Sun, 18 Mar 2018 11:07:37: #2 finished! INFO @ Sun, 18 Mar 2018 11:07:37: #2 predicted fragment length is 268 bps INFO @ Sun, 18 Mar 2018 11:07:37: #2 alternative fragment length(s) may be 268 bps INFO @ Sun, 18 Mar 2018 11:07:37: #2.2 Generate R script for model : SRX3087682.20_model.r INFO @ Sun, 18 Mar 2018 11:07:37: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:07:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:07:37: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:07:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:09:00: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:09:18: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:09:21: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:10:08: #4 Write output xls file... SRX3087682.05_peaks.xls INFO @ Sun, 18 Mar 2018 11:10:08: #4 Write peak in narrowPeak format file... SRX3087682.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:10:09: #4 Write summits bed file... SRX3087682.05_summits.bed INFO @ Sun, 18 Mar 2018 11:10:09: Done! pass1 - making usageList (93 chroms): 5 millis pass2 - checking and writing primary data (18625 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:10:22: #4 Write output xls file... SRX3087682.20_peaks.xls INFO @ Sun, 18 Mar 2018 11:10:22: #4 Write peak in narrowPeak format file... SRX3087682.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:10:22: #4 Write summits bed file... SRX3087682.20_summits.bed INFO @ Sun, 18 Mar 2018 11:10:22: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (1606 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:10:25: #4 Write output xls file... SRX3087682.10_peaks.xls INFO @ Sun, 18 Mar 2018 11:10:25: #4 Write peak in narrowPeak format file... SRX3087682.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:10:25: #4 Write summits bed file... SRX3087682.10_summits.bed INFO @ Sun, 18 Mar 2018 11:10:25: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (8161 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。