Job ID = 9157959 sra ファイルのダウンロード中... Completed: 490263K bytes transferred in 15 seconds (253196K 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 28687818 spots for /home/okishinya/chipatlas/results/dm3/SRX2734366/SRR5445343.sra Written 28687818 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: 00:09:04 28687818 reads; of these: 28687818 (100.00%) were unpaired; of these: 2916281 (10.17%) aligned 0 times 22014751 (76.74%) aligned exactly 1 time 3756786 (13.10%) aligned >1 times 89.83% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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] 6490353 / 25771537 = 0.2518 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 14:29:00: # Command line: callpeak -t SRX2734366.bam -f BAM -g dm -n SRX2734366.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2734366.05 # format = BAM # ChIP-seq file = ['SRX2734366.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 14:29:00: # Command line: callpeak -t SRX2734366.bam -f BAM -g dm -n SRX2734366.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2734366.10 # format = BAM # ChIP-seq file = ['SRX2734366.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 14:29:00: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:29:00: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:29:00: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:29:00: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:29:00: # Command line: callpeak -t SRX2734366.bam -f BAM -g dm -n SRX2734366.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2734366.20 # format = BAM # ChIP-seq file = ['SRX2734366.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 14:29:00: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:29:00: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:29:07: 1000000 INFO @ Tue, 27 Jun 2017 14:29:07: 1000000 INFO @ Tue, 27 Jun 2017 14:29:07: 1000000 INFO @ Tue, 27 Jun 2017 14:29:14: 2000000 INFO @ Tue, 27 Jun 2017 14:29:15: 2000000 INFO @ Tue, 27 Jun 2017 14:29:15: 2000000 INFO @ Tue, 27 Jun 2017 14:29:21: 3000000 INFO @ Tue, 27 Jun 2017 14:29:22: 3000000 INFO @ Tue, 27 Jun 2017 14:29:22: 3000000 INFO @ Tue, 27 Jun 2017 14:29:28: 4000000 INFO @ Tue, 27 Jun 2017 14:29:29: 4000000 INFO @ Tue, 27 Jun 2017 14:29:29: 4000000 INFO @ Tue, 27 Jun 2017 14:29:37: 5000000 INFO @ Tue, 27 Jun 2017 14:29:37: 5000000 INFO @ Tue, 27 Jun 2017 14:29:37: 5000000 INFO @ Tue, 27 Jun 2017 14:29:44: 6000000 INFO @ Tue, 27 Jun 2017 14:29:44: 6000000 INFO @ Tue, 27 Jun 2017 14:29:44: 6000000 INFO @ Tue, 27 Jun 2017 14:29:50: 7000000 INFO @ Tue, 27 Jun 2017 14:29:52: 7000000 INFO @ Tue, 27 Jun 2017 14:29:52: 7000000 INFO @ Tue, 27 Jun 2017 14:29:57: 8000000 INFO @ Tue, 27 Jun 2017 14:29:59: 8000000 INFO @ Tue, 27 Jun 2017 14:29:59: 8000000 INFO @ Tue, 27 Jun 2017 14:30:04: 9000000 INFO @ Tue, 27 Jun 2017 14:30:06: 9000000 INFO @ Tue, 27 Jun 2017 14:30:06: 9000000 INFO @ Tue, 27 Jun 2017 14:30:11: 10000000 INFO @ Tue, 27 Jun 2017 14:30:14: 10000000 INFO @ Tue, 27 Jun 2017 14:30:14: 10000000 INFO @ Tue, 27 Jun 2017 14:30:20: 11000000 INFO @ Tue, 27 Jun 2017 14:30:21: 11000000 INFO @ Tue, 27 Jun 2017 14:30:22: 11000000 INFO @ Tue, 27 Jun 2017 14:30:27: 12000000 INFO @ Tue, 27 Jun 2017 14:30:29: 12000000 INFO @ Tue, 27 Jun 2017 14:30:29: 12000000 INFO @ Tue, 27 Jun 2017 14:30:34: 13000000 INFO @ Tue, 27 Jun 2017 14:30:36: 13000000 INFO @ Tue, 27 Jun 2017 14:30:36: 13000000 INFO @ Tue, 27 Jun 2017 14:30:40: 14000000 INFO @ Tue, 27 Jun 2017 14:30:43: 14000000 INFO @ Tue, 27 Jun 2017 14:30:44: 14000000 INFO @ Tue, 27 Jun 2017 14:30:47: 15000000 INFO @ Tue, 27 Jun 2017 14:30:51: 15000000 INFO @ Tue, 27 Jun 2017 14:30:51: 15000000 INFO @ Tue, 27 Jun 2017 14:30:55: 16000000 INFO @ Tue, 27 Jun 2017 14:30:58: 16000000 INFO @ Tue, 27 Jun 2017 14:30:58: 16000000 INFO @ Tue, 27 Jun 2017 14:31:02: 17000000 INFO @ Tue, 27 Jun 2017 14:31:06: 17000000 INFO @ Tue, 27 Jun 2017 14:31:06: 17000000 INFO @ Tue, 27 Jun 2017 14:31:09: 18000000 INFO @ Tue, 27 Jun 2017 14:31:13: 18000000 INFO @ Tue, 27 Jun 2017 14:31:13: 18000000 INFO @ Tue, 27 Jun 2017 14:31:16: 19000000 INFO @ Tue, 27 Jun 2017 14:31:18: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:31:18: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:31:18: #1 total tags in treatment: 19281184 INFO @ Tue, 27 Jun 2017 14:31:18: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:31:18: #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 14:31:18: #1 tags after filtering in treatment: 19281184 INFO @ Tue, 27 Jun 2017 14:31:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:31:18: #1 finished! INFO @ Tue, 27 Jun 2017 14:31:18: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:31:19: #2 number of paired peaks: 1646 INFO @ Tue, 27 Jun 2017 14:31:19: start model_add_line... INFO @ Tue, 27 Jun 2017 14:31:20: start X-correlation... INFO @ Tue, 27 Jun 2017 14:31:20: end of X-cor INFO @ Tue, 27 Jun 2017 14:31:20: #2 finished! INFO @ Tue, 27 Jun 2017 14:31:20: #2 predicted fragment length is 195 bps INFO @ Tue, 27 Jun 2017 14:31:20: #2 alternative fragment length(s) may be 195 bps INFO @ Tue, 27 Jun 2017 14:31:20: #2.2 Generate R script for model : SRX2734366.05_model.r INFO @ Tue, 27 Jun 2017 14:31:20: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:31:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:31:20: 19000000 INFO @ Tue, 27 Jun 2017 14:31:20: 19000000 INFO @ Tue, 27 Jun 2017 14:31:22: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:31:22: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:31:22: #1 total tags in treatment: 19281184 INFO @ Tue, 27 Jun 2017 14:31:22: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:31:22: #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 14:31:22: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:31:22: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:31:22: #1 total tags in treatment: 19281184 INFO @ Tue, 27 Jun 2017 14:31:22: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:31:22: #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 14:31:23: #1 tags after filtering in treatment: 19281184 INFO @ Tue, 27 Jun 2017 14:31:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:31:23: #1 finished! INFO @ Tue, 27 Jun 2017 14:31:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:31:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:31:23: #1 tags after filtering in treatment: 19281184 INFO @ Tue, 27 Jun 2017 14:31:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:31:23: #1 finished! INFO @ Tue, 27 Jun 2017 14:31:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:31:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:31:24: #2 number of paired peaks: 1646 INFO @ Tue, 27 Jun 2017 14:31:24: start model_add_line... INFO @ Tue, 27 Jun 2017 14:31:24: start X-correlation... INFO @ Tue, 27 Jun 2017 14:31:24: end of X-cor INFO @ Tue, 27 Jun 2017 14:31:24: #2 finished! INFO @ Tue, 27 Jun 2017 14:31:24: #2 predicted fragment length is 195 bps INFO @ Tue, 27 Jun 2017 14:31:24: #2 alternative fragment length(s) may be 195 bps INFO @ Tue, 27 Jun 2017 14:31:24: #2.2 Generate R script for model : SRX2734366.20_model.r INFO @ Tue, 27 Jun 2017 14:31:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:31:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:31:24: #2 number of paired peaks: 1646 INFO @ Tue, 27 Jun 2017 14:31:24: start model_add_line... INFO @ Tue, 27 Jun 2017 14:31:25: start X-correlation... INFO @ Tue, 27 Jun 2017 14:31:25: end of X-cor INFO @ Tue, 27 Jun 2017 14:31:25: #2 finished! INFO @ Tue, 27 Jun 2017 14:31:25: #2 predicted fragment length is 195 bps INFO @ Tue, 27 Jun 2017 14:31:25: #2 alternative fragment length(s) may be 195 bps INFO @ Tue, 27 Jun 2017 14:31:25: #2.2 Generate R script for model : SRX2734366.10_model.r INFO @ Tue, 27 Jun 2017 14:31:25: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:31:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:32:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:32:16: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:32:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:32:37: #4 Write output xls file... SRX2734366.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:32:38: #4 Write peak in narrowPeak format file... SRX2734366.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:32:38: #4 Write summits bed file... SRX2734366.05_summits.bed INFO @ Tue, 27 Jun 2017 14:32:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6973 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:32:40: #4 Write output xls file... SRX2734366.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:32:40: #4 Write peak in narrowPeak format file... SRX2734366.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:32:40: #4 Write summits bed file... SRX2734366.20_summits.bed INFO @ Tue, 27 Jun 2017 14:32:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4033 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:32:43: #4 Write output xls file... SRX2734366.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:32:43: #4 Write peak in narrowPeak format file... SRX2734366.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:32:43: #4 Write summits bed file... SRX2734366.10_summits.bed INFO @ Tue, 27 Jun 2017 14:32:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5516 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。