Job ID = 11192588 sra ファイルのダウンロード中... Completed: 346135K bytes transferred in 38 seconds (73565K 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 33154137 spots for /home/okishinya/chipatlas/results/rn6/SRX4014808/SRR7085057.sra Written 33154137 spots for /home/okishinya/chipatlas/results/rn6/SRX4014808/SRR7085057.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: 00:00:01 Multiseed full-index search: 00:34:19 33154137 reads; of these: 33154137 (100.00%) were unpaired; of these: 1038658 (3.13%) aligned 0 times 28236511 (85.17%) aligned exactly 1 time 3878968 (11.70%) aligned >1 times 96.87% overall alignment rate Time searching: 00:34:23 Overall time: 00:34:23 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] 2777589 / 32115479 = 0.0865 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 11:35:21: # Command line: callpeak -t SRX4014808.bam -f BAM -g 2.15e9 -n SRX4014808.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014808.20 # format = BAM # ChIP-seq file = ['SRX4014808.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 11:35:21: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:35:21: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:35:21: # Command line: callpeak -t SRX4014808.bam -f BAM -g 2.15e9 -n SRX4014808.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014808.05 # format = BAM # ChIP-seq file = ['SRX4014808.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 11:35:21: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:35:21: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:35:21: # Command line: callpeak -t SRX4014808.bam -f BAM -g 2.15e9 -n SRX4014808.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014808.10 # format = BAM # ChIP-seq file = ['SRX4014808.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 11:35:21: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:35:21: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:35:27: 1000000 INFO @ Sat, 15 Sep 2018 11:35:28: 1000000 INFO @ Sat, 15 Sep 2018 11:35:28: 1000000 INFO @ Sat, 15 Sep 2018 11:35:34: 2000000 INFO @ Sat, 15 Sep 2018 11:35:34: 2000000 INFO @ Sat, 15 Sep 2018 11:35:34: 2000000 INFO @ Sat, 15 Sep 2018 11:35:40: 3000000 INFO @ Sat, 15 Sep 2018 11:35:40: 3000000 INFO @ Sat, 15 Sep 2018 11:35:41: 3000000 INFO @ Sat, 15 Sep 2018 11:35:46: 4000000 INFO @ Sat, 15 Sep 2018 11:35:47: 4000000 INFO @ Sat, 15 Sep 2018 11:35:47: 4000000 INFO @ Sat, 15 Sep 2018 11:35:53: 5000000 INFO @ Sat, 15 Sep 2018 11:35:54: 5000000 INFO @ Sat, 15 Sep 2018 11:35:54: 5000000 INFO @ Sat, 15 Sep 2018 11:35:59: 6000000 INFO @ Sat, 15 Sep 2018 11:36:00: 6000000 INFO @ Sat, 15 Sep 2018 11:36:00: 6000000 INFO @ Sat, 15 Sep 2018 11:36:06: 7000000 INFO @ Sat, 15 Sep 2018 11:36:07: 7000000 INFO @ Sat, 15 Sep 2018 11:36:07: 7000000 INFO @ Sat, 15 Sep 2018 11:36:12: 8000000 INFO @ Sat, 15 Sep 2018 11:36:13: 8000000 INFO @ Sat, 15 Sep 2018 11:36:14: 8000000 INFO @ Sat, 15 Sep 2018 11:36:18: 9000000 INFO @ Sat, 15 Sep 2018 11:36:20: 9000000 INFO @ Sat, 15 Sep 2018 11:36:20: 9000000 INFO @ Sat, 15 Sep 2018 11:36:25: 10000000 INFO @ Sat, 15 Sep 2018 11:36:26: 10000000 INFO @ Sat, 15 Sep 2018 11:36:27: 10000000 INFO @ Sat, 15 Sep 2018 11:36:31: 11000000 INFO @ Sat, 15 Sep 2018 11:36:33: 11000000 INFO @ Sat, 15 Sep 2018 11:36:34: 11000000 INFO @ Sat, 15 Sep 2018 11:36:38: 12000000 INFO @ Sat, 15 Sep 2018 11:36:39: 12000000 INFO @ Sat, 15 Sep 2018 11:36:40: 12000000 INFO @ Sat, 15 Sep 2018 11:36:44: 13000000 INFO @ Sat, 15 Sep 2018 11:36:46: 13000000 INFO @ Sat, 15 Sep 2018 11:36:47: 13000000 INFO @ Sat, 15 Sep 2018 11:36:51: 14000000 INFO @ Sat, 15 Sep 2018 11:36:52: 14000000 INFO @ Sat, 15 Sep 2018 11:36:54: 14000000 INFO @ Sat, 15 Sep 2018 11:36:57: 15000000 INFO @ Sat, 15 Sep 2018 11:36:59: 15000000 INFO @ Sat, 15 Sep 2018 11:37:00: 15000000 INFO @ Sat, 15 Sep 2018 11:37:04: 16000000 INFO @ Sat, 15 Sep 2018 11:37:05: 16000000 INFO @ Sat, 15 Sep 2018 11:37:07: 16000000 INFO @ Sat, 15 Sep 2018 11:37:10: 17000000 INFO @ Sat, 15 Sep 2018 11:37:12: 17000000 INFO @ Sat, 15 Sep 2018 11:37:14: 17000000 INFO @ Sat, 15 Sep 2018 11:37:17: 18000000 INFO @ Sat, 15 Sep 2018 11:37:18: 18000000 INFO @ Sat, 15 Sep 2018 11:37:21: 18000000 INFO @ Sat, 15 Sep 2018 11:37:23: 19000000 INFO @ Sat, 15 Sep 2018 11:37:25: 19000000 INFO @ Sat, 15 Sep 2018 11:37:27: 19000000 INFO @ Sat, 15 Sep 2018 11:37:30: 20000000 INFO @ Sat, 15 Sep 2018 11:37:31: 20000000 INFO @ Sat, 15 Sep 2018 11:37:34: 20000000 INFO @ Sat, 15 Sep 2018 11:37:36: 21000000 INFO @ Sat, 15 Sep 2018 11:37:38: 21000000 INFO @ Sat, 15 Sep 2018 11:37:41: 21000000 INFO @ Sat, 15 Sep 2018 11:37:43: 22000000 INFO @ Sat, 15 Sep 2018 11:37:44: 22000000 INFO @ Sat, 15 Sep 2018 11:37:47: 22000000 INFO @ Sat, 15 Sep 2018 11:37:49: 23000000 INFO @ Sat, 15 Sep 2018 11:37:51: 23000000 INFO @ Sat, 15 Sep 2018 11:37:54: 23000000 INFO @ Sat, 15 Sep 2018 11:37:56: 24000000 INFO @ Sat, 15 Sep 2018 11:37:57: 24000000 INFO @ Sat, 15 Sep 2018 11:38:01: 24000000 INFO @ Sat, 15 Sep 2018 11:38:02: 25000000 INFO @ Sat, 15 Sep 2018 11:38:04: 25000000 INFO @ Sat, 15 Sep 2018 11:38:08: 25000000 INFO @ Sat, 15 Sep 2018 11:38:09: 26000000 INFO @ Sat, 15 Sep 2018 11:38:10: 26000000 INFO @ Sat, 15 Sep 2018 11:38:14: 26000000 INFO @ Sat, 15 Sep 2018 11:38:15: 27000000 INFO @ Sat, 15 Sep 2018 11:38:17: 27000000 INFO @ Sat, 15 Sep 2018 11:38:21: 27000000 INFO @ Sat, 15 Sep 2018 11:38:22: 28000000 INFO @ Sat, 15 Sep 2018 11:38:23: 28000000 INFO @ Sat, 15 Sep 2018 11:38:28: 28000000 INFO @ Sat, 15 Sep 2018 11:38:28: 29000000 INFO @ Sat, 15 Sep 2018 11:38:30: 29000000 INFO @ Sat, 15 Sep 2018 11:38:31: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:38:31: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:38:31: #1 total tags in treatment: 29337890 INFO @ Sat, 15 Sep 2018 11:38:31: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:38:31: #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 11:38:32: #1 tags after filtering in treatment: 29337693 INFO @ Sat, 15 Sep 2018 11:38:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:38:32: #1 finished! INFO @ Sat, 15 Sep 2018 11:38:32: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:38:32: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:38:32: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:38:32: #1 total tags in treatment: 29337890 INFO @ Sat, 15 Sep 2018 11:38:32: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:38:32: #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 11:38:33: #1 tags after filtering in treatment: 29337693 INFO @ Sat, 15 Sep 2018 11:38:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:38:33: #1 finished! INFO @ Sat, 15 Sep 2018 11:38:33: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:38:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:38:34: 29000000 INFO @ Sat, 15 Sep 2018 11:38:37: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:38:37: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:38:37: #1 total tags in treatment: 29337890 INFO @ Sat, 15 Sep 2018 11:38:37: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:38:37: #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 11:38:38: #1 tags after filtering in treatment: 29337693 INFO @ Sat, 15 Sep 2018 11:38:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:38:38: #1 finished! INFO @ Sat, 15 Sep 2018 11:38:38: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:38:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:38:40: #2 number of paired peaks: 161884 INFO @ Sat, 15 Sep 2018 11:38:40: start model_add_line... INFO @ Sat, 15 Sep 2018 11:38:41: start X-correlation... INFO @ Sat, 15 Sep 2018 11:38:41: end of X-cor INFO @ Sat, 15 Sep 2018 11:38:41: #2 finished! INFO @ Sat, 15 Sep 2018 11:38:41: #2 predicted fragment length is 244 bps INFO @ Sat, 15 Sep 2018 11:38:41: #2 alternative fragment length(s) may be 4,244 bps INFO @ Sat, 15 Sep 2018 11:38:41: #2.2 Generate R script for model : SRX4014808.20_model.r INFO @ Sat, 15 Sep 2018 11:38:41: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:38:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:38:42: #2 number of paired peaks: 161884 INFO @ Sat, 15 Sep 2018 11:38:42: start model_add_line... INFO @ Sat, 15 Sep 2018 11:38:42: start X-correlation... INFO @ Sat, 15 Sep 2018 11:38:42: end of X-cor INFO @ Sat, 15 Sep 2018 11:38:42: #2 finished! INFO @ Sat, 15 Sep 2018 11:38:42: #2 predicted fragment length is 244 bps INFO @ Sat, 15 Sep 2018 11:38:42: #2 alternative fragment length(s) may be 4,244 bps INFO @ Sat, 15 Sep 2018 11:38:42: #2.2 Generate R script for model : SRX4014808.10_model.r INFO @ Sat, 15 Sep 2018 11:38:42: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:38:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:38:46: #2 number of paired peaks: 161884 INFO @ Sat, 15 Sep 2018 11:38:46: start model_add_line... INFO @ Sat, 15 Sep 2018 11:38:47: start X-correlation... INFO @ Sat, 15 Sep 2018 11:38:47: end of X-cor INFO @ Sat, 15 Sep 2018 11:38:47: #2 finished! INFO @ Sat, 15 Sep 2018 11:38:47: #2 predicted fragment length is 244 bps INFO @ Sat, 15 Sep 2018 11:38:47: #2 alternative fragment length(s) may be 4,244 bps INFO @ Sat, 15 Sep 2018 11:38:47: #2.2 Generate R script for model : SRX4014808.05_model.r INFO @ Sat, 15 Sep 2018 11:38:47: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:38:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:40:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:40:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:40:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:40:47: #4 Write output xls file... SRX4014808.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:40:47: #4 Write peak in narrowPeak format file... SRX4014808.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:40:47: #4 Write summits bed file... SRX4014808.05_summits.bed INFO @ Sat, 15 Sep 2018 11:40:47: Done! pass1 - making usageList (133 chroms): 5 millis pass2 - checking and writing primary data (22107 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:40:48: #4 Write output xls file... SRX4014808.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:40:48: #4 Write peak in narrowPeak format file... SRX4014808.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:40:48: #4 Write summits bed file... SRX4014808.20_summits.bed INFO @ Sat, 15 Sep 2018 11:40:48: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (994 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:40:51: #4 Write output xls file... SRX4014808.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:40:51: #4 Write peak in narrowPeak format file... SRX4014808.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:40:51: #4 Write summits bed file... SRX4014808.10_summits.bed INFO @ Sat, 15 Sep 2018 11:40:51: Done! pass1 - making usageList (85 chroms): 2 millis pass2 - checking and writing primary data (6340 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。