Job ID = 1294992 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,315,235 reads read : 17,315,235 reads written : 17,315,235 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory 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: 00:04:58 17315235 reads; of these: 17315235 (100.00%) were unpaired; of these: 853782 (4.93%) aligned 0 times 14025574 (81.00%) aligned exactly 1 time 2435879 (14.07%) aligned >1 times 95.07% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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 8 files... [bam_rmdupse_core] 2377769 / 16461453 = 0.1444 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 @ Mon, 03 Jun 2019 11:23:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.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 @ Mon, 03 Jun 2019 11:23:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:23:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:23:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.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 @ Mon, 03 Jun 2019 11:23:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:23:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:23:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.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 @ Mon, 03 Jun 2019 11:23:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:23:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:23:44: 1000000 INFO @ Mon, 03 Jun 2019 11:23:45: 1000000 INFO @ Mon, 03 Jun 2019 11:23:46: 1000000 INFO @ Mon, 03 Jun 2019 11:23:52: 2000000 INFO @ Mon, 03 Jun 2019 11:23:53: 2000000 INFO @ Mon, 03 Jun 2019 11:23:54: 2000000 INFO @ Mon, 03 Jun 2019 11:23:59: 3000000 INFO @ Mon, 03 Jun 2019 11:24:01: 3000000 INFO @ Mon, 03 Jun 2019 11:24:03: 3000000 INFO @ Mon, 03 Jun 2019 11:24:06: 4000000 INFO @ Mon, 03 Jun 2019 11:24:09: 4000000 INFO @ Mon, 03 Jun 2019 11:24:11: 4000000 INFO @ Mon, 03 Jun 2019 11:24:13: 5000000 INFO @ Mon, 03 Jun 2019 11:24:17: 5000000 INFO @ Mon, 03 Jun 2019 11:24:19: 5000000 INFO @ Mon, 03 Jun 2019 11:24:20: 6000000 INFO @ Mon, 03 Jun 2019 11:24:24: 6000000 INFO @ Mon, 03 Jun 2019 11:24:27: 6000000 INFO @ Mon, 03 Jun 2019 11:24:28: 7000000 INFO @ Mon, 03 Jun 2019 11:24:32: 7000000 INFO @ Mon, 03 Jun 2019 11:24:34: 7000000 INFO @ Mon, 03 Jun 2019 11:24:35: 8000000 INFO @ Mon, 03 Jun 2019 11:24:40: 8000000 INFO @ Mon, 03 Jun 2019 11:24:42: 9000000 INFO @ Mon, 03 Jun 2019 11:24:43: 8000000 INFO @ Mon, 03 Jun 2019 11:24:49: 9000000 INFO @ Mon, 03 Jun 2019 11:24:49: 10000000 INFO @ Mon, 03 Jun 2019 11:24:51: 9000000 INFO @ Mon, 03 Jun 2019 11:24:56: 11000000 INFO @ Mon, 03 Jun 2019 11:24:57: 10000000 INFO @ Mon, 03 Jun 2019 11:24:59: 10000000 INFO @ Mon, 03 Jun 2019 11:25:03: 12000000 INFO @ Mon, 03 Jun 2019 11:25:05: 11000000 INFO @ Mon, 03 Jun 2019 11:25:07: 11000000 INFO @ Mon, 03 Jun 2019 11:25:11: 13000000 INFO @ Mon, 03 Jun 2019 11:25:13: 12000000 INFO @ Mon, 03 Jun 2019 11:25:15: 12000000 INFO @ Mon, 03 Jun 2019 11:25:18: 14000000 INFO @ Mon, 03 Jun 2019 11:25:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:25:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:25:19: #1 total tags in treatment: 14083684 INFO @ Mon, 03 Jun 2019 11:25:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:25:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:25:19: #1 tags after filtering in treatment: 14083684 INFO @ Mon, 03 Jun 2019 11:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:25:19: #1 finished! INFO @ Mon, 03 Jun 2019 11:25:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:25:20: 13000000 INFO @ Mon, 03 Jun 2019 11:25:21: #2 number of paired peaks: 3492 INFO @ Mon, 03 Jun 2019 11:25:21: start model_add_line... INFO @ Mon, 03 Jun 2019 11:25:21: start X-correlation... INFO @ Mon, 03 Jun 2019 11:25:21: end of X-cor INFO @ Mon, 03 Jun 2019 11:25:21: #2 finished! INFO @ Mon, 03 Jun 2019 11:25:21: #2 predicted fragment length is 226 bps INFO @ Mon, 03 Jun 2019 11:25:21: #2 alternative fragment length(s) may be 2,210,226 bps INFO @ Mon, 03 Jun 2019 11:25:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.05_model.r INFO @ Mon, 03 Jun 2019 11:25:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:25:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:25:23: 13000000 INFO @ Mon, 03 Jun 2019 11:25:28: 14000000 INFO @ Mon, 03 Jun 2019 11:25:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:25:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:25:29: #1 total tags in treatment: 14083684 INFO @ Mon, 03 Jun 2019 11:25:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:25:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:25:29: #1 tags after filtering in treatment: 14083684 INFO @ Mon, 03 Jun 2019 11:25:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:25:29: #1 finished! INFO @ Mon, 03 Jun 2019 11:25:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:25:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:25:30: 14000000 INFO @ Mon, 03 Jun 2019 11:25:31: #2 number of paired peaks: 3492 INFO @ Mon, 03 Jun 2019 11:25:31: start model_add_line... INFO @ Mon, 03 Jun 2019 11:25:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:25:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:25:31: #1 total tags in treatment: 14083684 INFO @ Mon, 03 Jun 2019 11:25:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:25:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:25:31: start X-correlation... INFO @ Mon, 03 Jun 2019 11:25:31: end of X-cor INFO @ Mon, 03 Jun 2019 11:25:31: #2 finished! INFO @ Mon, 03 Jun 2019 11:25:31: #2 predicted fragment length is 226 bps INFO @ Mon, 03 Jun 2019 11:25:31: #2 alternative fragment length(s) may be 2,210,226 bps INFO @ Mon, 03 Jun 2019 11:25:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.20_model.r INFO @ Mon, 03 Jun 2019 11:25:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:25:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:25:31: #1 tags after filtering in treatment: 14083684 INFO @ Mon, 03 Jun 2019 11:25:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:25:31: #1 finished! INFO @ Mon, 03 Jun 2019 11:25:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:25:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:25:33: #2 number of paired peaks: 3492 INFO @ Mon, 03 Jun 2019 11:25:33: start model_add_line... INFO @ Mon, 03 Jun 2019 11:25:33: start X-correlation... INFO @ Mon, 03 Jun 2019 11:25:33: end of X-cor INFO @ Mon, 03 Jun 2019 11:25:33: #2 finished! INFO @ Mon, 03 Jun 2019 11:25:33: #2 predicted fragment length is 226 bps INFO @ Mon, 03 Jun 2019 11:25:33: #2 alternative fragment length(s) may be 2,210,226 bps INFO @ Mon, 03 Jun 2019 11:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.10_model.r INFO @ Mon, 03 Jun 2019 11:25:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:26:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:26:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:26:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.05_summits.bed INFO @ Mon, 03 Jun 2019 11:26:29: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (9228 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:26:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:26:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:26:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.20_summits.bed INFO @ Mon, 03 Jun 2019 11:26:39: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1702 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:26:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:26:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:26:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288046/SRX288046.10_summits.bed INFO @ Mon, 03 Jun 2019 11:26:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5201 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。