Job ID = 11171277 sra ファイルのダウンロード中... Completed: 102818K bytes transferred in 7 seconds (114763K bits/sec), in 1 file. Completed: 101585K bytes transferred in 5 seconds (161789K bits/sec), in 1 file. Completed: 101770K bytes transferred in 5 seconds (150353K bits/sec), in 1 file. Completed: 101075K bytes transferred in 16 seconds (49204K 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 5322573 spots for /home/okishinya/chipatlas/results/dm3/SRX3020543/SRR5850435.sra Written 5322573 spots for /home/okishinya/chipatlas/results/dm3/SRX3020543/SRR5850435.sra Read 5363639 spots for /home/okishinya/chipatlas/results/dm3/SRX3020543/SRR5850433.sra Written 5363639 spots for /home/okishinya/chipatlas/results/dm3/SRX3020543/SRR5850433.sra Read 5365682 spots for /home/okishinya/chipatlas/results/dm3/SRX3020543/SRR5850434.sra Written 5365682 spots for /home/okishinya/chipatlas/results/dm3/SRX3020543/SRR5850434.sra Read 5420745 spots for /home/okishinya/chipatlas/results/dm3/SRX3020543/SRR5850432.sra Written 5420745 spots for /home/okishinya/chipatlas/results/dm3/SRX3020543/SRR5850432.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 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: 00:07:46 21472639 reads; of these: 21472639 (100.00%) were unpaired; of these: 589315 (2.74%) aligned 0 times 15999562 (74.51%) aligned exactly 1 time 4883762 (22.74%) aligned >1 times 97.26% overall alignment rate Time searching: 00:07:46 Overall time: 00:07:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3370320 / 20883324 = 0.1614 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, 08 Sep 2018 13:38:21: # Command line: callpeak -t SRX3020543.bam -f BAM -g dm -n SRX3020543.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020543.10 # format = BAM # ChIP-seq file = ['SRX3020543.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:38:21: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:38:21: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:38:21: # Command line: callpeak -t SRX3020543.bam -f BAM -g dm -n SRX3020543.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020543.05 # format = BAM # ChIP-seq file = ['SRX3020543.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:38:21: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:38:21: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:38:21: # Command line: callpeak -t SRX3020543.bam -f BAM -g dm -n SRX3020543.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020543.20 # format = BAM # ChIP-seq file = ['SRX3020543.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:38:21: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:38:21: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:38:28: 1000000 INFO @ Sat, 08 Sep 2018 13:38:29: 1000000 INFO @ Sat, 08 Sep 2018 13:38:29: 1000000 INFO @ Sat, 08 Sep 2018 13:38:34: 2000000 INFO @ Sat, 08 Sep 2018 13:38:38: 2000000 INFO @ Sat, 08 Sep 2018 13:38:38: 2000000 INFO @ Sat, 08 Sep 2018 13:38:41: 3000000 INFO @ Sat, 08 Sep 2018 13:38:46: 3000000 INFO @ Sat, 08 Sep 2018 13:38:46: 3000000 INFO @ Sat, 08 Sep 2018 13:38:48: 4000000 INFO @ Sat, 08 Sep 2018 13:38:53: 4000000 INFO @ Sat, 08 Sep 2018 13:38:53: 4000000 INFO @ Sat, 08 Sep 2018 13:38:54: 5000000 INFO @ Sat, 08 Sep 2018 13:39:00: 5000000 INFO @ Sat, 08 Sep 2018 13:39:00: 5000000 INFO @ Sat, 08 Sep 2018 13:39:01: 6000000 INFO @ Sat, 08 Sep 2018 13:39:08: 7000000 INFO @ Sat, 08 Sep 2018 13:39:08: 6000000 INFO @ Sat, 08 Sep 2018 13:39:08: 6000000 INFO @ Sat, 08 Sep 2018 13:39:15: 8000000 INFO @ Sat, 08 Sep 2018 13:39:16: 7000000 INFO @ Sat, 08 Sep 2018 13:39:16: 7000000 INFO @ Sat, 08 Sep 2018 13:39:21: 9000000 INFO @ Sat, 08 Sep 2018 13:39:23: 8000000 INFO @ Sat, 08 Sep 2018 13:39:23: 8000000 INFO @ Sat, 08 Sep 2018 13:39:28: 10000000 INFO @ Sat, 08 Sep 2018 13:39:31: 9000000 INFO @ Sat, 08 Sep 2018 13:39:31: 9000000 INFO @ Sat, 08 Sep 2018 13:39:35: 11000000 INFO @ Sat, 08 Sep 2018 13:39:39: 10000000 INFO @ Sat, 08 Sep 2018 13:39:39: 10000000 INFO @ Sat, 08 Sep 2018 13:39:41: 12000000 INFO @ Sat, 08 Sep 2018 13:39:47: 11000000 INFO @ Sat, 08 Sep 2018 13:39:47: 11000000 INFO @ Sat, 08 Sep 2018 13:39:48: 13000000 INFO @ Sat, 08 Sep 2018 13:39:55: 14000000 INFO @ Sat, 08 Sep 2018 13:39:56: 12000000 INFO @ Sat, 08 Sep 2018 13:39:56: 12000000 INFO @ Sat, 08 Sep 2018 13:40:02: 15000000 INFO @ Sat, 08 Sep 2018 13:40:05: 13000000 INFO @ Sat, 08 Sep 2018 13:40:05: 13000000 INFO @ Sat, 08 Sep 2018 13:40:08: 16000000 INFO @ Sat, 08 Sep 2018 13:40:13: 14000000 INFO @ Sat, 08 Sep 2018 13:40:13: 14000000 INFO @ Sat, 08 Sep 2018 13:40:15: 17000000 INFO @ Sat, 08 Sep 2018 13:40:18: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:40:18: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:40:18: #1 total tags in treatment: 17513004 INFO @ Sat, 08 Sep 2018 13:40:18: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:40:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:40:19: #1 tags after filtering in treatment: 17513004 INFO @ Sat, 08 Sep 2018 13:40:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:40:19: #1 finished! INFO @ Sat, 08 Sep 2018 13:40:19: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:40:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:40:20: #2 number of paired peaks: 1495 INFO @ Sat, 08 Sep 2018 13:40:20: start model_add_line... INFO @ Sat, 08 Sep 2018 13:40:20: start X-correlation... INFO @ Sat, 08 Sep 2018 13:40:20: end of X-cor INFO @ Sat, 08 Sep 2018 13:40:20: #2 finished! INFO @ Sat, 08 Sep 2018 13:40:20: #2 predicted fragment length is 114 bps INFO @ Sat, 08 Sep 2018 13:40:20: #2 alternative fragment length(s) may be 3,114 bps INFO @ Sat, 08 Sep 2018 13:40:20: #2.2 Generate R script for model : SRX3020543.10_model.r INFO @ Sat, 08 Sep 2018 13:40:20: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:40:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:40:22: 15000000 INFO @ Sat, 08 Sep 2018 13:40:22: 15000000 INFO @ Sat, 08 Sep 2018 13:40:31: 16000000 INFO @ Sat, 08 Sep 2018 13:40:31: 16000000 INFO @ Sat, 08 Sep 2018 13:40:38: 17000000 INFO @ Sat, 08 Sep 2018 13:40:38: 17000000 INFO @ Sat, 08 Sep 2018 13:40:42: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:40:42: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:40:42: #1 total tags in treatment: 17513004 INFO @ Sat, 08 Sep 2018 13:40:42: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:40:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:40:42: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:40:42: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:40:42: #1 total tags in treatment: 17513004 INFO @ Sat, 08 Sep 2018 13:40:42: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:40:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:40:42: #1 tags after filtering in treatment: 17513004 INFO @ Sat, 08 Sep 2018 13:40:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:40:42: #1 finished! INFO @ Sat, 08 Sep 2018 13:40:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:40:42: #1 tags after filtering in treatment: 17513004 INFO @ Sat, 08 Sep 2018 13:40:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:40:42: #1 finished! INFO @ Sat, 08 Sep 2018 13:40:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:40:43: #2 number of paired peaks: 1495 INFO @ Sat, 08 Sep 2018 13:40:43: start model_add_line... INFO @ Sat, 08 Sep 2018 13:40:43: #2 number of paired peaks: 1495 INFO @ Sat, 08 Sep 2018 13:40:43: start model_add_line... INFO @ Sat, 08 Sep 2018 13:40:44: start X-correlation... INFO @ Sat, 08 Sep 2018 13:40:44: end of X-cor INFO @ Sat, 08 Sep 2018 13:40:44: #2 finished! INFO @ Sat, 08 Sep 2018 13:40:44: #2 predicted fragment length is 114 bps INFO @ Sat, 08 Sep 2018 13:40:44: #2 alternative fragment length(s) may be 3,114 bps INFO @ Sat, 08 Sep 2018 13:40:44: #2.2 Generate R script for model : SRX3020543.05_model.r INFO @ Sat, 08 Sep 2018 13:40:44: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:40:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:40:44: start X-correlation... INFO @ Sat, 08 Sep 2018 13:40:44: end of X-cor INFO @ Sat, 08 Sep 2018 13:40:44: #2 finished! INFO @ Sat, 08 Sep 2018 13:40:44: #2 predicted fragment length is 114 bps INFO @ Sat, 08 Sep 2018 13:40:44: #2 alternative fragment length(s) may be 3,114 bps INFO @ Sat, 08 Sep 2018 13:40:44: #2.2 Generate R script for model : SRX3020543.20_model.r INFO @ Sat, 08 Sep 2018 13:40:44: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:40:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:41:03: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:41:24: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:41:25: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:41:26: #4 Write output xls file... SRX3020543.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:41:26: #4 Write peak in narrowPeak format file... SRX3020543.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:41:26: #4 Write summits bed file... SRX3020543.10_summits.bed INFO @ Sat, 08 Sep 2018 13:41:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3750 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:41:48: #4 Write output xls file... SRX3020543.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:41:48: #4 Write peak in narrowPeak format file... SRX3020543.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:41:48: #4 Write summits bed file... SRX3020543.20_summits.bed INFO @ Sat, 08 Sep 2018 13:41:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1027 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:41:49: #4 Write output xls file... SRX3020543.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:41:49: #4 Write peak in narrowPeak format file... SRX3020543.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:41:49: #4 Write summits bed file... SRX3020543.05_summits.bed INFO @ Sat, 08 Sep 2018 13:41:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9379 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。