Job ID = 9157958 sra ファイルのダウンロード中... Completed: 539682K bytes transferred in 14 seconds (302839K bits/sec), in 1 file, 2 directories. 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 31529433 spots for /home/okishinya/chipatlas/results/dm3/SRX2734365/SRR5445342.sra Written 31529433 spots total 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: 00:08:00 31529433 reads; of these: 31529433 (100.00%) were unpaired; of these: 4763785 (15.11%) aligned 0 times 23065268 (73.15%) aligned exactly 1 time 3700380 (11.74%) aligned >1 times 84.89% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9663927 / 26765648 = 0.3611 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 @ Tue, 27 Jun 2017 14:27:22: # Command line: callpeak -t SRX2734365.bam -f BAM -g dm -n SRX2734365.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2734365.20 # format = BAM # ChIP-seq file = ['SRX2734365.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 @ Tue, 27 Jun 2017 14:27:22: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:27:22: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:27:22: # Command line: callpeak -t SRX2734365.bam -f BAM -g dm -n SRX2734365.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2734365.10 # format = BAM # ChIP-seq file = ['SRX2734365.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 @ Tue, 27 Jun 2017 14:27:22: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:27:22: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:27:22: # Command line: callpeak -t SRX2734365.bam -f BAM -g dm -n SRX2734365.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2734365.05 # format = BAM # ChIP-seq file = ['SRX2734365.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 @ Tue, 27 Jun 2017 14:27:22: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:27:22: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:27:28: 1000000 INFO @ Tue, 27 Jun 2017 14:27:28: 1000000 INFO @ Tue, 27 Jun 2017 14:27:29: 1000000 INFO @ Tue, 27 Jun 2017 14:27:35: 2000000 INFO @ Tue, 27 Jun 2017 14:27:35: 2000000 INFO @ Tue, 27 Jun 2017 14:27:35: 2000000 INFO @ Tue, 27 Jun 2017 14:27:41: 3000000 INFO @ Tue, 27 Jun 2017 14:27:41: 3000000 INFO @ Tue, 27 Jun 2017 14:27:42: 3000000 INFO @ Tue, 27 Jun 2017 14:27:48: 4000000 INFO @ Tue, 27 Jun 2017 14:27:48: 4000000 INFO @ Tue, 27 Jun 2017 14:27:49: 4000000 INFO @ Tue, 27 Jun 2017 14:27:55: 5000000 INFO @ Tue, 27 Jun 2017 14:27:55: 5000000 INFO @ Tue, 27 Jun 2017 14:27:56: 5000000 INFO @ Tue, 27 Jun 2017 14:28:02: 6000000 INFO @ Tue, 27 Jun 2017 14:28:02: 6000000 INFO @ Tue, 27 Jun 2017 14:28:04: 6000000 INFO @ Tue, 27 Jun 2017 14:28:09: 7000000 INFO @ Tue, 27 Jun 2017 14:28:09: 7000000 INFO @ Tue, 27 Jun 2017 14:28:11: 7000000 INFO @ Tue, 27 Jun 2017 14:28:15: 8000000 INFO @ Tue, 27 Jun 2017 14:28:15: 8000000 INFO @ Tue, 27 Jun 2017 14:28:18: 8000000 INFO @ Tue, 27 Jun 2017 14:28:22: 9000000 INFO @ Tue, 27 Jun 2017 14:28:22: 9000000 INFO @ Tue, 27 Jun 2017 14:28:25: 9000000 INFO @ Tue, 27 Jun 2017 14:28:28: 10000000 INFO @ Tue, 27 Jun 2017 14:28:29: 10000000 INFO @ Tue, 27 Jun 2017 14:28:32: 10000000 INFO @ Tue, 27 Jun 2017 14:28:35: 11000000 INFO @ Tue, 27 Jun 2017 14:28:35: 11000000 INFO @ Tue, 27 Jun 2017 14:28:39: 11000000 INFO @ Tue, 27 Jun 2017 14:28:42: 12000000 INFO @ Tue, 27 Jun 2017 14:28:42: 12000000 INFO @ Tue, 27 Jun 2017 14:28:46: 12000000 INFO @ Tue, 27 Jun 2017 14:28:49: 13000000 INFO @ Tue, 27 Jun 2017 14:28:49: 13000000 INFO @ Tue, 27 Jun 2017 14:28:54: 13000000 INFO @ Tue, 27 Jun 2017 14:28:56: 14000000 INFO @ Tue, 27 Jun 2017 14:28:56: 14000000 INFO @ Tue, 27 Jun 2017 14:29:01: 14000000 INFO @ Tue, 27 Jun 2017 14:29:03: 15000000 INFO @ Tue, 27 Jun 2017 14:29:03: 15000000 INFO @ Tue, 27 Jun 2017 14:29:08: 15000000 INFO @ Tue, 27 Jun 2017 14:29:09: 16000000 INFO @ Tue, 27 Jun 2017 14:29:10: 16000000 INFO @ Tue, 27 Jun 2017 14:29:15: 16000000 INFO @ Tue, 27 Jun 2017 14:29:16: 17000000 INFO @ Tue, 27 Jun 2017 14:29:17: 17000000 INFO @ Tue, 27 Jun 2017 14:29:17: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:29:17: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:29:17: #1 total tags in treatment: 17101721 INFO @ Tue, 27 Jun 2017 14:29:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:29:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:29:17: #1 tags after filtering in treatment: 17101721 INFO @ Tue, 27 Jun 2017 14:29:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:29:17: #1 finished! INFO @ Tue, 27 Jun 2017 14:29:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:29:17: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:29:17: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:29:17: #1 total tags in treatment: 17101721 INFO @ Tue, 27 Jun 2017 14:29:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:29:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:29:18: #1 tags after filtering in treatment: 17101721 INFO @ Tue, 27 Jun 2017 14:29:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:29:18: #1 finished! INFO @ Tue, 27 Jun 2017 14:29:18: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:29:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:29:19: #2 number of paired peaks: 2977 INFO @ Tue, 27 Jun 2017 14:29:19: start model_add_line... INFO @ Tue, 27 Jun 2017 14:29:19: start X-correlation... INFO @ Tue, 27 Jun 2017 14:29:19: end of X-cor INFO @ Tue, 27 Jun 2017 14:29:19: #2 finished! INFO @ Tue, 27 Jun 2017 14:29:19: #2 predicted fragment length is 201 bps INFO @ Tue, 27 Jun 2017 14:29:19: #2 alternative fragment length(s) may be 201 bps INFO @ Tue, 27 Jun 2017 14:29:19: #2.2 Generate R script for model : SRX2734365.10_model.r INFO @ Tue, 27 Jun 2017 14:29:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:29:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:29:19: #2 number of paired peaks: 2977 INFO @ Tue, 27 Jun 2017 14:29:19: start model_add_line... INFO @ Tue, 27 Jun 2017 14:29:20: start X-correlation... INFO @ Tue, 27 Jun 2017 14:29:20: end of X-cor INFO @ Tue, 27 Jun 2017 14:29:20: #2 finished! INFO @ Tue, 27 Jun 2017 14:29:20: #2 predicted fragment length is 201 bps INFO @ Tue, 27 Jun 2017 14:29:20: #2 alternative fragment length(s) may be 201 bps INFO @ Tue, 27 Jun 2017 14:29:20: #2.2 Generate R script for model : SRX2734365.05_model.r INFO @ Tue, 27 Jun 2017 14:29:20: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:29:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:29:22: 17000000 INFO @ Tue, 27 Jun 2017 14:29:22: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:29:22: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:29:22: #1 total tags in treatment: 17101721 INFO @ Tue, 27 Jun 2017 14:29:22: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:29:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:29:23: #1 tags after filtering in treatment: 17101721 INFO @ Tue, 27 Jun 2017 14:29:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:29:23: #1 finished! INFO @ Tue, 27 Jun 2017 14:29:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:29:24: #2 number of paired peaks: 2977 INFO @ Tue, 27 Jun 2017 14:29:24: start model_add_line... INFO @ Tue, 27 Jun 2017 14:29:24: start X-correlation... INFO @ Tue, 27 Jun 2017 14:29:24: end of X-cor INFO @ Tue, 27 Jun 2017 14:29:24: #2 finished! INFO @ Tue, 27 Jun 2017 14:29:24: #2 predicted fragment length is 201 bps INFO @ Tue, 27 Jun 2017 14:29:24: #2 alternative fragment length(s) may be 201 bps INFO @ Tue, 27 Jun 2017 14:29:24: #2.2 Generate R script for model : SRX2734365.20_model.r INFO @ Tue, 27 Jun 2017 14:29:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:30:12: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:30:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:30:16: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:30:36: #4 Write output xls file... SRX2734365.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:30:36: #4 Write peak in narrowPeak format file... SRX2734365.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:30:36: #4 Write summits bed file... SRX2734365.10_summits.bed INFO @ Tue, 27 Jun 2017 14:30:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5561 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:30:37: #4 Write output xls file... SRX2734365.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:30:37: #4 Write peak in narrowPeak format file... SRX2734365.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:30:37: #4 Write summits bed file... SRX2734365.05_summits.bed INFO @ Tue, 27 Jun 2017 14:30:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6622 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:30:39: #4 Write output xls file... SRX2734365.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:30:39: #4 Write peak in narrowPeak format file... SRX2734365.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:30:39: #4 Write summits bed file... SRX2734365.20_summits.bed INFO @ Tue, 27 Jun 2017 14:30:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4262 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。