Job ID = 11192594 sra ファイルのダウンロード中... Completed: 322188K bytes transferred in 29 seconds (88698K 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... Read 30631129 spots for /home/okishinya/chipatlas/results/rn6/SRX4014814/SRR7085063.sra Written 30631129 spots for /home/okishinya/chipatlas/results/rn6/SRX4014814/SRR7085063.sra 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: 00:31:58 30631129 reads; of these: 30631129 (100.00%) were unpaired; of these: 909356 (2.97%) aligned 0 times 26350720 (86.03%) aligned exactly 1 time 3371053 (11.01%) aligned >1 times 97.03% overall alignment rate Time searching: 00:32:00 Overall time: 00:32:00 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] 2628597 / 29721773 = 0.0884 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 @ Sat, 15 Sep 2018 11:31:22: # Command line: callpeak -t SRX4014814.bam -f BAM -g 2.15e9 -n SRX4014814.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014814.10 # format = BAM # ChIP-seq file = ['SRX4014814.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 @ Sat, 15 Sep 2018 11:31:22: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:31:22: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:31:22: # Command line: callpeak -t SRX4014814.bam -f BAM -g 2.15e9 -n SRX4014814.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014814.20 # format = BAM # ChIP-seq file = ['SRX4014814.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 @ Sat, 15 Sep 2018 11:31:22: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:31:22: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:31:22: # Command line: callpeak -t SRX4014814.bam -f BAM -g 2.15e9 -n SRX4014814.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014814.05 # format = BAM # ChIP-seq file = ['SRX4014814.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 @ Sat, 15 Sep 2018 11:31:22: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:31:22: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:31:29: 1000000 INFO @ Sat, 15 Sep 2018 11:31:30: 1000000 INFO @ Sat, 15 Sep 2018 11:31:30: 1000000 INFO @ Sat, 15 Sep 2018 11:31:36: 2000000 INFO @ Sat, 15 Sep 2018 11:31:37: 2000000 INFO @ Sat, 15 Sep 2018 11:31:37: 2000000 INFO @ Sat, 15 Sep 2018 11:31:43: 3000000 INFO @ Sat, 15 Sep 2018 11:31:45: 3000000 INFO @ Sat, 15 Sep 2018 11:31:45: 3000000 INFO @ Sat, 15 Sep 2018 11:31:50: 4000000 INFO @ Sat, 15 Sep 2018 11:31:52: 4000000 INFO @ Sat, 15 Sep 2018 11:31:53: 4000000 INFO @ Sat, 15 Sep 2018 11:31:58: 5000000 INFO @ Sat, 15 Sep 2018 11:31:59: 5000000 INFO @ Sat, 15 Sep 2018 11:32:00: 5000000 INFO @ Sat, 15 Sep 2018 11:32:05: 6000000 INFO @ Sat, 15 Sep 2018 11:32:06: 6000000 INFO @ Sat, 15 Sep 2018 11:32:08: 6000000 INFO @ Sat, 15 Sep 2018 11:32:13: 7000000 INFO @ Sat, 15 Sep 2018 11:32:13: 7000000 INFO @ Sat, 15 Sep 2018 11:32:16: 7000000 INFO @ Sat, 15 Sep 2018 11:32:20: 8000000 INFO @ Sat, 15 Sep 2018 11:32:20: 8000000 INFO @ Sat, 15 Sep 2018 11:32:23: 8000000 INFO @ Sat, 15 Sep 2018 11:32:27: 9000000 INFO @ Sat, 15 Sep 2018 11:32:28: 9000000 INFO @ Sat, 15 Sep 2018 11:32:31: 9000000 INFO @ Sat, 15 Sep 2018 11:32:35: 10000000 INFO @ Sat, 15 Sep 2018 11:32:35: 10000000 INFO @ Sat, 15 Sep 2018 11:32:39: 10000000 INFO @ Sat, 15 Sep 2018 11:32:42: 11000000 INFO @ Sat, 15 Sep 2018 11:32:42: 11000000 INFO @ Sat, 15 Sep 2018 11:32:46: 11000000 INFO @ Sat, 15 Sep 2018 11:32:49: 12000000 INFO @ Sat, 15 Sep 2018 11:32:50: 12000000 INFO @ Sat, 15 Sep 2018 11:32:54: 12000000 INFO @ Sat, 15 Sep 2018 11:32:57: 13000000 INFO @ Sat, 15 Sep 2018 11:32:57: 13000000 INFO @ Sat, 15 Sep 2018 11:33:01: 13000000 INFO @ Sat, 15 Sep 2018 11:33:04: 14000000 INFO @ Sat, 15 Sep 2018 11:33:04: 14000000 INFO @ Sat, 15 Sep 2018 11:33:08: 14000000 INFO @ Sat, 15 Sep 2018 11:33:11: 15000000 INFO @ Sat, 15 Sep 2018 11:33:11: 15000000 INFO @ Sat, 15 Sep 2018 11:33:15: 15000000 INFO @ Sat, 15 Sep 2018 11:33:18: 16000000 INFO @ Sat, 15 Sep 2018 11:33:19: 16000000 INFO @ Sat, 15 Sep 2018 11:33:22: 16000000 INFO @ Sat, 15 Sep 2018 11:33:26: 17000000 INFO @ Sat, 15 Sep 2018 11:33:27: 17000000 INFO @ Sat, 15 Sep 2018 11:33:29: 17000000 INFO @ Sat, 15 Sep 2018 11:33:33: 18000000 INFO @ Sat, 15 Sep 2018 11:33:34: 18000000 INFO @ Sat, 15 Sep 2018 11:33:36: 18000000 INFO @ Sat, 15 Sep 2018 11:33:41: 19000000 INFO @ Sat, 15 Sep 2018 11:33:42: 19000000 INFO @ Sat, 15 Sep 2018 11:33:43: 19000000 INFO @ Sat, 15 Sep 2018 11:33:48: 20000000 INFO @ Sat, 15 Sep 2018 11:33:50: 20000000 INFO @ Sat, 15 Sep 2018 11:33:51: 20000000 INFO @ Sat, 15 Sep 2018 11:33:55: 21000000 INFO @ Sat, 15 Sep 2018 11:33:57: 21000000 INFO @ Sat, 15 Sep 2018 11:33:58: 21000000 INFO @ Sat, 15 Sep 2018 11:34:03: 22000000 INFO @ Sat, 15 Sep 2018 11:34:05: 22000000 INFO @ Sat, 15 Sep 2018 11:34:05: 22000000 INFO @ Sat, 15 Sep 2018 11:34:10: 23000000 INFO @ Sat, 15 Sep 2018 11:34:12: 23000000 INFO @ Sat, 15 Sep 2018 11:34:13: 23000000 INFO @ Sat, 15 Sep 2018 11:34:17: 24000000 INFO @ Sat, 15 Sep 2018 11:34:19: 24000000 INFO @ Sat, 15 Sep 2018 11:34:20: 24000000 INFO @ Sat, 15 Sep 2018 11:34:25: 25000000 INFO @ Sat, 15 Sep 2018 11:34:26: 25000000 INFO @ Sat, 15 Sep 2018 11:34:28: 25000000 INFO @ Sat, 15 Sep 2018 11:34:32: 26000000 INFO @ Sat, 15 Sep 2018 11:34:34: 26000000 INFO @ Sat, 15 Sep 2018 11:34:36: 26000000 INFO @ Sat, 15 Sep 2018 11:34:40: 27000000 INFO @ Sat, 15 Sep 2018 11:34:41: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:34:41: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:34:41: #1 total tags in treatment: 27093176 INFO @ Sat, 15 Sep 2018 11:34:41: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:34:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:34:41: 27000000 INFO @ Sat, 15 Sep 2018 11:34:42: #1 tags after filtering in treatment: 27092967 INFO @ Sat, 15 Sep 2018 11:34:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:34:42: #1 finished! INFO @ Sat, 15 Sep 2018 11:34:42: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:34:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:34:42: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:34:42: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:34:42: #1 total tags in treatment: 27093176 INFO @ Sat, 15 Sep 2018 11:34:42: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:34:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:34:43: #1 tags after filtering in treatment: 27092967 INFO @ Sat, 15 Sep 2018 11:34:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:34:43: #1 finished! INFO @ Sat, 15 Sep 2018 11:34:43: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:34:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:34:44: 27000000 INFO @ Sat, 15 Sep 2018 11:34:45: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:34:45: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:34:45: #1 total tags in treatment: 27093176 INFO @ Sat, 15 Sep 2018 11:34:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:34:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:34:45: #1 tags after filtering in treatment: 27092967 INFO @ Sat, 15 Sep 2018 11:34:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:34:45: #1 finished! INFO @ Sat, 15 Sep 2018 11:34:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:34:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:34:50: #2 number of paired peaks: 155935 INFO @ Sat, 15 Sep 2018 11:34:50: start model_add_line... INFO @ Sat, 15 Sep 2018 11:34:51: #2 number of paired peaks: 155935 INFO @ Sat, 15 Sep 2018 11:34:51: start model_add_line... INFO @ Sat, 15 Sep 2018 11:34:51: start X-correlation... INFO @ Sat, 15 Sep 2018 11:34:51: end of X-cor INFO @ Sat, 15 Sep 2018 11:34:51: #2 finished! INFO @ Sat, 15 Sep 2018 11:34:51: #2 predicted fragment length is 244 bps INFO @ Sat, 15 Sep 2018 11:34:51: #2 alternative fragment length(s) may be 4,244 bps INFO @ Sat, 15 Sep 2018 11:34:51: #2.2 Generate R script for model : SRX4014814.05_model.r INFO @ Sat, 15 Sep 2018 11:34:51: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:34:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:34:51: start X-correlation... INFO @ Sat, 15 Sep 2018 11:34:51: end of X-cor INFO @ Sat, 15 Sep 2018 11:34:51: #2 finished! INFO @ Sat, 15 Sep 2018 11:34:51: #2 predicted fragment length is 244 bps INFO @ Sat, 15 Sep 2018 11:34:51: #2 alternative fragment length(s) may be 4,244 bps INFO @ Sat, 15 Sep 2018 11:34:51: #2.2 Generate R script for model : SRX4014814.20_model.r INFO @ Sat, 15 Sep 2018 11:34:51: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:34:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:34:54: #2 number of paired peaks: 155935 INFO @ Sat, 15 Sep 2018 11:34:54: start model_add_line... INFO @ Sat, 15 Sep 2018 11:34:54: start X-correlation... INFO @ Sat, 15 Sep 2018 11:34:54: end of X-cor INFO @ Sat, 15 Sep 2018 11:34:54: #2 finished! INFO @ Sat, 15 Sep 2018 11:34:54: #2 predicted fragment length is 244 bps INFO @ Sat, 15 Sep 2018 11:34:54: #2 alternative fragment length(s) may be 4,244 bps INFO @ Sat, 15 Sep 2018 11:34:54: #2.2 Generate R script for model : SRX4014814.10_model.r INFO @ Sat, 15 Sep 2018 11:34:54: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:34:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:36:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:36:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:36:11: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:36:45: #4 Write output xls file... SRX4014814.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:36:45: #4 Write peak in narrowPeak format file... SRX4014814.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:36:45: #4 Write summits bed file... SRX4014814.20_summits.bed INFO @ Sat, 15 Sep 2018 11:36:45: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (1024 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:36:47: #4 Write output xls file... SRX4014814.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:36:47: #4 Write peak in narrowPeak format file... SRX4014814.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:36:47: #4 Write summits bed file... SRX4014814.05_summits.bed INFO @ Sat, 15 Sep 2018 11:36:47: Done! pass1 - making usageList (119 chroms): 4 millis pass2 - checking and writing primary data (19275 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:36:51: #4 Write output xls file... SRX4014814.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:36:51: #4 Write peak in narrowPeak format file... SRX4014814.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:36:51: #4 Write summits bed file... SRX4014814.10_summits.bed INFO @ Sat, 15 Sep 2018 11:36:51: Done! pass1 - making usageList (70 chroms): 2 millis pass2 - checking and writing primary data (5576 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。