Job ID = 10453664 sra ファイルのダウンロード中... Completed: 621031K bytes transferred in 22 seconds (227981K 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 35714368 spots for /home/okishinya/chipatlas/results/rn6/SRX3478269/SRR6384648.sra Written 35714368 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: 00:00:02 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:24:05 35714368 reads; of these: 35714368 (100.00%) were unpaired; of these: 3064151 (8.58%) aligned 0 times 23716804 (66.41%) aligned exactly 1 time 8933413 (25.01%) aligned >1 times 91.42% overall alignment rate Time searching: 00:24:12 Overall time: 00:24:12 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 16 files... [bam_rmdupse_core] 8868297 / 32650217 = 0.2716 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 @ Thu, 08 Feb 2018 17:22:51: # Command line: callpeak -t SRX3478269.bam -f BAM -g 2.15e9 -n SRX3478269.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3478269.05 # format = BAM # ChIP-seq file = ['SRX3478269.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 @ Thu, 08 Feb 2018 17:22:51: # Command line: callpeak -t SRX3478269.bam -f BAM -g 2.15e9 -n SRX3478269.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3478269.20 # format = BAM # ChIP-seq file = ['SRX3478269.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 @ Thu, 08 Feb 2018 17:22:51: # Command line: callpeak -t SRX3478269.bam -f BAM -g 2.15e9 -n SRX3478269.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3478269.10 # format = BAM # ChIP-seq file = ['SRX3478269.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 @ Thu, 08 Feb 2018 17:22:51: #1 read tag files... INFO @ Thu, 08 Feb 2018 17:22:51: #1 read tag files... INFO @ Thu, 08 Feb 2018 17:22:51: #1 read tag files... INFO @ Thu, 08 Feb 2018 17:22:51: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 17:22:51: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 17:22:51: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 17:22:58: 1000000 INFO @ Thu, 08 Feb 2018 17:22:58: 1000000 INFO @ Thu, 08 Feb 2018 17:22:58: 1000000 INFO @ Thu, 08 Feb 2018 17:23:06: 2000000 INFO @ Thu, 08 Feb 2018 17:23:06: 2000000 INFO @ Thu, 08 Feb 2018 17:23:06: 2000000 INFO @ Thu, 08 Feb 2018 17:23:14: 3000000 INFO @ Thu, 08 Feb 2018 17:23:14: 3000000 INFO @ Thu, 08 Feb 2018 17:23:14: 3000000 INFO @ Thu, 08 Feb 2018 17:23:21: 4000000 INFO @ Thu, 08 Feb 2018 17:23:21: 4000000 INFO @ Thu, 08 Feb 2018 17:23:21: 4000000 INFO @ Thu, 08 Feb 2018 17:23:29: 5000000 INFO @ Thu, 08 Feb 2018 17:23:29: 5000000 INFO @ Thu, 08 Feb 2018 17:23:29: 5000000 INFO @ Thu, 08 Feb 2018 17:23:37: 6000000 INFO @ Thu, 08 Feb 2018 17:23:37: 6000000 INFO @ Thu, 08 Feb 2018 17:23:37: 6000000 INFO @ Thu, 08 Feb 2018 17:23:44: 7000000 INFO @ Thu, 08 Feb 2018 17:23:44: 7000000 INFO @ Thu, 08 Feb 2018 17:23:44: 7000000 INFO @ Thu, 08 Feb 2018 17:23:52: 8000000 INFO @ Thu, 08 Feb 2018 17:23:52: 8000000 INFO @ Thu, 08 Feb 2018 17:23:52: 8000000 INFO @ Thu, 08 Feb 2018 17:24:00: 9000000 INFO @ Thu, 08 Feb 2018 17:24:00: 9000000 INFO @ Thu, 08 Feb 2018 17:24:00: 9000000 INFO @ Thu, 08 Feb 2018 17:24:06: 10000000 INFO @ Thu, 08 Feb 2018 17:24:07: 10000000 INFO @ Thu, 08 Feb 2018 17:24:07: 10000000 INFO @ Thu, 08 Feb 2018 17:24:13: 11000000 INFO @ Thu, 08 Feb 2018 17:24:14: 11000000 INFO @ Thu, 08 Feb 2018 17:24:14: 11000000 INFO @ Thu, 08 Feb 2018 17:24:19: 12000000 INFO @ Thu, 08 Feb 2018 17:24:21: 12000000 INFO @ Thu, 08 Feb 2018 17:24:21: 12000000 INFO @ Thu, 08 Feb 2018 17:24:26: 13000000 INFO @ Thu, 08 Feb 2018 17:24:28: 13000000 INFO @ Thu, 08 Feb 2018 17:24:29: 13000000 INFO @ Thu, 08 Feb 2018 17:24:33: 14000000 INFO @ Thu, 08 Feb 2018 17:24:35: 14000000 INFO @ Thu, 08 Feb 2018 17:24:36: 14000000 INFO @ Thu, 08 Feb 2018 17:24:39: 15000000 INFO @ Thu, 08 Feb 2018 17:24:43: 15000000 INFO @ Thu, 08 Feb 2018 17:24:44: 15000000 INFO @ Thu, 08 Feb 2018 17:24:46: 16000000 INFO @ Thu, 08 Feb 2018 17:24:50: 16000000 INFO @ Thu, 08 Feb 2018 17:24:52: 16000000 INFO @ Thu, 08 Feb 2018 17:24:53: 17000000 INFO @ Thu, 08 Feb 2018 17:24:58: 17000000 INFO @ Thu, 08 Feb 2018 17:24:59: 18000000 INFO @ Thu, 08 Feb 2018 17:25:00: 17000000 INFO @ Thu, 08 Feb 2018 17:25:05: 18000000 INFO @ Thu, 08 Feb 2018 17:25:06: 19000000 INFO @ Thu, 08 Feb 2018 17:25:07: 18000000 INFO @ Thu, 08 Feb 2018 17:25:12: 19000000 INFO @ Thu, 08 Feb 2018 17:25:12: 20000000 INFO @ Thu, 08 Feb 2018 17:25:15: 19000000 INFO @ Thu, 08 Feb 2018 17:25:19: 21000000 INFO @ Thu, 08 Feb 2018 17:25:20: 20000000 INFO @ Thu, 08 Feb 2018 17:25:23: 20000000 INFO @ Thu, 08 Feb 2018 17:25:26: 22000000 INFO @ Thu, 08 Feb 2018 17:25:27: 21000000 INFO @ Thu, 08 Feb 2018 17:25:30: 21000000 INFO @ Thu, 08 Feb 2018 17:25:33: 23000000 INFO @ Thu, 08 Feb 2018 17:25:34: 22000000 INFO @ Thu, 08 Feb 2018 17:25:38: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 17:25:38: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 17:25:38: #1 total tags in treatment: 23781920 INFO @ Thu, 08 Feb 2018 17:25:38: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 17:25:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 17:25:38: 22000000 INFO @ Thu, 08 Feb 2018 17:25:39: #1 tags after filtering in treatment: 23781789 INFO @ Thu, 08 Feb 2018 17:25:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 17:25:39: #1 finished! INFO @ Thu, 08 Feb 2018 17:25:39: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 17:25:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 17:25:42: 23000000 INFO @ Thu, 08 Feb 2018 17:25:42: #2 number of paired peaks: 36603 INFO @ Thu, 08 Feb 2018 17:25:42: start model_add_line... INFO @ Thu, 08 Feb 2018 17:25:42: start X-correlation... INFO @ Thu, 08 Feb 2018 17:25:42: end of X-cor INFO @ Thu, 08 Feb 2018 17:25:42: #2 finished! INFO @ Thu, 08 Feb 2018 17:25:42: #2 predicted fragment length is 104 bps INFO @ Thu, 08 Feb 2018 17:25:42: #2 alternative fragment length(s) may be 4,104 bps INFO @ Thu, 08 Feb 2018 17:25:42: #2.2 Generate R script for model : SRX3478269.20_model.r INFO @ Thu, 08 Feb 2018 17:25:42: #3 Call peaks... INFO @ Thu, 08 Feb 2018 17:25:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 17:25:46: 23000000 INFO @ Thu, 08 Feb 2018 17:25:48: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 17:25:48: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 17:25:48: #1 total tags in treatment: 23781920 INFO @ Thu, 08 Feb 2018 17:25:48: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 17:25:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 17:25:49: #1 tags after filtering in treatment: 23781789 INFO @ Thu, 08 Feb 2018 17:25:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 17:25:49: #1 finished! INFO @ Thu, 08 Feb 2018 17:25:49: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 17:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 17:25:51: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 17:25:51: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 17:25:51: #1 total tags in treatment: 23781920 INFO @ Thu, 08 Feb 2018 17:25:51: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 17:25:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 17:25:52: #1 tags after filtering in treatment: 23781789 INFO @ Thu, 08 Feb 2018 17:25:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 17:25:52: #1 finished! INFO @ Thu, 08 Feb 2018 17:25:52: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 17:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 17:25:52: #2 number of paired peaks: 36603 INFO @ Thu, 08 Feb 2018 17:25:52: start model_add_line... INFO @ Thu, 08 Feb 2018 17:25:53: start X-correlation... INFO @ Thu, 08 Feb 2018 17:25:53: end of X-cor INFO @ Thu, 08 Feb 2018 17:25:53: #2 finished! INFO @ Thu, 08 Feb 2018 17:25:53: #2 predicted fragment length is 104 bps INFO @ Thu, 08 Feb 2018 17:25:53: #2 alternative fragment length(s) may be 4,104 bps INFO @ Thu, 08 Feb 2018 17:25:53: #2.2 Generate R script for model : SRX3478269.05_model.r INFO @ Thu, 08 Feb 2018 17:25:53: #3 Call peaks... INFO @ Thu, 08 Feb 2018 17:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 17:25:56: #2 number of paired peaks: 36603 INFO @ Thu, 08 Feb 2018 17:25:56: start model_add_line... INFO @ Thu, 08 Feb 2018 17:25:56: start X-correlation... INFO @ Thu, 08 Feb 2018 17:25:56: end of X-cor INFO @ Thu, 08 Feb 2018 17:25:56: #2 finished! INFO @ Thu, 08 Feb 2018 17:25:56: #2 predicted fragment length is 104 bps INFO @ Thu, 08 Feb 2018 17:25:56: #2 alternative fragment length(s) may be 4,104 bps INFO @ Thu, 08 Feb 2018 17:25:56: #2.2 Generate R script for model : SRX3478269.10_model.r INFO @ Thu, 08 Feb 2018 17:25:56: #3 Call peaks... INFO @ Thu, 08 Feb 2018 17:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 17:26:44: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 17:26:50: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 17:26:50: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 17:27:18: #4 Write output xls file... SRX3478269.20_peaks.xls INFO @ Thu, 08 Feb 2018 17:27:18: #4 Write peak in narrowPeak format file... SRX3478269.20_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 17:27:18: #4 Write summits bed file... SRX3478269.20_summits.bed INFO @ Thu, 08 Feb 2018 17:27:18: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (298 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 17:27:22: #4 Write output xls file... SRX3478269.05_peaks.xls INFO @ Thu, 08 Feb 2018 17:27:22: #4 Write peak in narrowPeak format file... SRX3478269.05_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 17:27:22: #4 Write summits bed file... SRX3478269.05_summits.bed INFO @ Thu, 08 Feb 2018 17:27:22: Done! pass1 - making usageList (65 chroms): 1 millis pass2 - checking and writing primary data (2429 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 17:27:24: #4 Write output xls file... SRX3478269.10_peaks.xls INFO @ Thu, 08 Feb 2018 17:27:24: #4 Write peak in narrowPeak format file... SRX3478269.10_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 17:27:24: #4 Write summits bed file... SRX3478269.10_summits.bed INFO @ Thu, 08 Feb 2018 17:27:24: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (747 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。