Job ID = 10714404 sra ファイルのダウンロード中... Completed: 1124620K bytes transferred in 22 seconds (408130K 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 32928597 spots for /home/okishinya/chipatlas/results/ce10/SRX4082364/SRR7164182.sra Written 32928597 spots for /home/okishinya/chipatlas/results/ce10/SRX4082364/SRR7164182.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:24 32928597 reads; of these: 32928597 (100.00%) were unpaired; of these: 843571 (2.56%) aligned 0 times 29024256 (88.14%) aligned exactly 1 time 3060770 (9.30%) aligned >1 times 97.44% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 10908668 / 32085026 = 0.3400 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, 03 Jun 2018 12:46:36: # Command line: callpeak -t SRX4082364.bam -f BAM -g ce -n SRX4082364.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082364.20 # format = BAM # ChIP-seq file = ['SRX4082364.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 03 Jun 2018 12:46:36: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:46:36: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:46:36: # Command line: callpeak -t SRX4082364.bam -f BAM -g ce -n SRX4082364.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082364.10 # format = BAM # ChIP-seq file = ['SRX4082364.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 03 Jun 2018 12:46:36: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:46:36: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:46:36: # Command line: callpeak -t SRX4082364.bam -f BAM -g ce -n SRX4082364.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082364.05 # format = BAM # ChIP-seq file = ['SRX4082364.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 03 Jun 2018 12:46:36: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:46:36: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:46:42: 1000000 INFO @ Sun, 03 Jun 2018 12:46:43: 1000000 INFO @ Sun, 03 Jun 2018 12:46:43: 1000000 INFO @ Sun, 03 Jun 2018 12:46:49: 2000000 INFO @ Sun, 03 Jun 2018 12:46:49: 2000000 INFO @ Sun, 03 Jun 2018 12:46:49: 2000000 INFO @ Sun, 03 Jun 2018 12:46:55: 3000000 INFO @ Sun, 03 Jun 2018 12:46:55: 3000000 INFO @ Sun, 03 Jun 2018 12:46:55: 3000000 INFO @ Sun, 03 Jun 2018 12:47:01: 4000000 INFO @ Sun, 03 Jun 2018 12:47:01: 4000000 INFO @ Sun, 03 Jun 2018 12:47:02: 4000000 INFO @ Sun, 03 Jun 2018 12:47:07: 5000000 INFO @ Sun, 03 Jun 2018 12:47:07: 5000000 INFO @ Sun, 03 Jun 2018 12:47:08: 5000000 INFO @ Sun, 03 Jun 2018 12:47:13: 6000000 INFO @ Sun, 03 Jun 2018 12:47:14: 6000000 INFO @ Sun, 03 Jun 2018 12:47:15: 6000000 INFO @ Sun, 03 Jun 2018 12:47:19: 7000000 INFO @ Sun, 03 Jun 2018 12:47:20: 7000000 INFO @ Sun, 03 Jun 2018 12:47:22: 7000000 INFO @ Sun, 03 Jun 2018 12:47:25: 8000000 INFO @ Sun, 03 Jun 2018 12:47:27: 8000000 INFO @ Sun, 03 Jun 2018 12:47:28: 8000000 INFO @ Sun, 03 Jun 2018 12:47:31: 9000000 INFO @ Sun, 03 Jun 2018 12:47:33: 9000000 INFO @ Sun, 03 Jun 2018 12:47:35: 9000000 INFO @ Sun, 03 Jun 2018 12:47:37: 10000000 INFO @ Sun, 03 Jun 2018 12:47:40: 10000000 INFO @ Sun, 03 Jun 2018 12:47:41: 10000000 INFO @ Sun, 03 Jun 2018 12:47:43: 11000000 INFO @ Sun, 03 Jun 2018 12:47:46: 11000000 INFO @ Sun, 03 Jun 2018 12:47:48: 11000000 INFO @ Sun, 03 Jun 2018 12:47:49: 12000000 INFO @ Sun, 03 Jun 2018 12:47:52: 12000000 INFO @ Sun, 03 Jun 2018 12:47:55: 12000000 INFO @ Sun, 03 Jun 2018 12:47:56: 13000000 INFO @ Sun, 03 Jun 2018 12:47:59: 13000000 INFO @ Sun, 03 Jun 2018 12:48:01: 13000000 INFO @ Sun, 03 Jun 2018 12:48:02: 14000000 INFO @ Sun, 03 Jun 2018 12:48:05: 14000000 INFO @ Sun, 03 Jun 2018 12:48:08: 15000000 INFO @ Sun, 03 Jun 2018 12:48:08: 14000000 INFO @ Sun, 03 Jun 2018 12:48:12: 15000000 INFO @ Sun, 03 Jun 2018 12:48:14: 16000000 INFO @ Sun, 03 Jun 2018 12:48:15: 15000000 INFO @ Sun, 03 Jun 2018 12:48:18: 16000000 INFO @ Sun, 03 Jun 2018 12:48:20: 17000000 INFO @ Sun, 03 Jun 2018 12:48:21: 16000000 INFO @ Sun, 03 Jun 2018 12:48:25: 17000000 INFO @ Sun, 03 Jun 2018 12:48:26: 18000000 INFO @ Sun, 03 Jun 2018 12:48:28: 17000000 INFO @ Sun, 03 Jun 2018 12:48:31: 18000000 INFO @ Sun, 03 Jun 2018 12:48:32: 19000000 INFO @ Sun, 03 Jun 2018 12:48:34: 18000000 INFO @ Sun, 03 Jun 2018 12:48:37: 19000000 INFO @ Sun, 03 Jun 2018 12:48:38: 20000000 INFO @ Sun, 03 Jun 2018 12:48:41: 19000000 INFO @ Sun, 03 Jun 2018 12:48:44: 20000000 INFO @ Sun, 03 Jun 2018 12:48:44: 21000000 INFO @ Sun, 03 Jun 2018 12:48:46: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:48:46: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:48:46: #1 total tags in treatment: 21176358 INFO @ Sun, 03 Jun 2018 12:48:46: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:48:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:48:46: #1 tags after filtering in treatment: 21176358 INFO @ Sun, 03 Jun 2018 12:48:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:48:46: #1 finished! INFO @ Sun, 03 Jun 2018 12:48:46: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:48:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:48:48: 20000000 INFO @ Sun, 03 Jun 2018 12:48:48: #2 number of paired peaks: 1780 INFO @ Sun, 03 Jun 2018 12:48:48: start model_add_line... INFO @ Sun, 03 Jun 2018 12:48:48: start X-correlation... INFO @ Sun, 03 Jun 2018 12:48:48: end of X-cor INFO @ Sun, 03 Jun 2018 12:48:48: #2 finished! INFO @ Sun, 03 Jun 2018 12:48:48: #2 predicted fragment length is 105 bps INFO @ Sun, 03 Jun 2018 12:48:48: #2 alternative fragment length(s) may be 2,84,105,119 bps INFO @ Sun, 03 Jun 2018 12:48:48: #2.2 Generate R script for model : SRX4082364.05_model.r INFO @ Sun, 03 Jun 2018 12:48:48: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:48:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:48:50: 21000000 INFO @ Sun, 03 Jun 2018 12:48:52: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:48:52: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:48:52: #1 total tags in treatment: 21176358 INFO @ Sun, 03 Jun 2018 12:48:52: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:48:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:48:52: #1 tags after filtering in treatment: 21176358 INFO @ Sun, 03 Jun 2018 12:48:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:48:52: #1 finished! INFO @ Sun, 03 Jun 2018 12:48:52: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:48:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:48:54: #2 number of paired peaks: 1780 INFO @ Sun, 03 Jun 2018 12:48:54: start model_add_line... INFO @ Sun, 03 Jun 2018 12:48:54: 21000000 INFO @ Sun, 03 Jun 2018 12:48:54: start X-correlation... INFO @ Sun, 03 Jun 2018 12:48:54: end of X-cor INFO @ Sun, 03 Jun 2018 12:48:54: #2 finished! INFO @ Sun, 03 Jun 2018 12:48:54: #2 predicted fragment length is 105 bps INFO @ Sun, 03 Jun 2018 12:48:54: #2 alternative fragment length(s) may be 2,84,105,119 bps INFO @ Sun, 03 Jun 2018 12:48:54: #2.2 Generate R script for model : SRX4082364.10_model.r INFO @ Sun, 03 Jun 2018 12:48:54: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:48:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:48:55: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:48:55: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:48:55: #1 total tags in treatment: 21176358 INFO @ Sun, 03 Jun 2018 12:48:55: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:48:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:48:56: #1 tags after filtering in treatment: 21176358 INFO @ Sun, 03 Jun 2018 12:48:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:48:56: #1 finished! INFO @ Sun, 03 Jun 2018 12:48:56: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:48:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:48:57: #2 number of paired peaks: 1780 INFO @ Sun, 03 Jun 2018 12:48:57: start model_add_line... INFO @ Sun, 03 Jun 2018 12:48:58: start X-correlation... INFO @ Sun, 03 Jun 2018 12:48:58: end of X-cor INFO @ Sun, 03 Jun 2018 12:48:58: #2 finished! INFO @ Sun, 03 Jun 2018 12:48:58: #2 predicted fragment length is 105 bps INFO @ Sun, 03 Jun 2018 12:48:58: #2 alternative fragment length(s) may be 2,84,105,119 bps INFO @ Sun, 03 Jun 2018 12:48:58: #2.2 Generate R script for model : SRX4082364.20_model.r INFO @ Sun, 03 Jun 2018 12:48:58: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:48:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:49:35: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:49:39: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:49:43: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:49:55: #4 Write output xls file... SRX4082364.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:49:55: #4 Write peak in narrowPeak format file... SRX4082364.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:49:56: #4 Write summits bed file... SRX4082364.05_summits.bed INFO @ Sun, 03 Jun 2018 12:49:56: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (13428 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:50:00: #4 Write output xls file... SRX4082364.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:50:01: #4 Write peak in narrowPeak format file... SRX4082364.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:50:01: #4 Write summits bed file... SRX4082364.10_summits.bed INFO @ Sun, 03 Jun 2018 12:50:01: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (8363 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:50:04: #4 Write output xls file... SRX4082364.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:50:04: #4 Write peak in narrowPeak format file... SRX4082364.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:50:04: #4 Write summits bed file... SRX4082364.20_summits.bed INFO @ Sun, 03 Jun 2018 12:50:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2834 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。