Job ID = 2590289 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,799,743 reads read : 14,799,743 reads written : 14,799,743 rm: cannot remove ‘[DSE]RR*’: 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: 00:04:53 14799743 reads; of these: 14799743 (100.00%) were unpaired; of these: 751687 (5.08%) aligned 0 times 11897108 (80.39%) aligned exactly 1 time 2150948 (14.53%) aligned >1 times 94.92% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 2134614 / 14048056 = 0.1520 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, 12 Aug 2019 20:45:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.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, 12 Aug 2019 20:45:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:45:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:45:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.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, 12 Aug 2019 20:45:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:45:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:45:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.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, 12 Aug 2019 20:45:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:45:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:45:57: 1000000 INFO @ Mon, 12 Aug 2019 20:45:59: 1000000 INFO @ Mon, 12 Aug 2019 20:46:01: 1000000 INFO @ Mon, 12 Aug 2019 20:46:03: 2000000 INFO @ Mon, 12 Aug 2019 20:46:08: 2000000 INFO @ Mon, 12 Aug 2019 20:46:09: 3000000 INFO @ Mon, 12 Aug 2019 20:46:10: 2000000 INFO @ Mon, 12 Aug 2019 20:46:16: 4000000 INFO @ Mon, 12 Aug 2019 20:46:16: 3000000 INFO @ Mon, 12 Aug 2019 20:46:18: 3000000 INFO @ Mon, 12 Aug 2019 20:46:23: 5000000 INFO @ Mon, 12 Aug 2019 20:46:24: 4000000 INFO @ Mon, 12 Aug 2019 20:46:26: 4000000 INFO @ Mon, 12 Aug 2019 20:46:30: 6000000 INFO @ Mon, 12 Aug 2019 20:46:32: 5000000 INFO @ Mon, 12 Aug 2019 20:46:34: 5000000 INFO @ Mon, 12 Aug 2019 20:46:37: 7000000 INFO @ Mon, 12 Aug 2019 20:46:39: 6000000 INFO @ Mon, 12 Aug 2019 20:46:41: 6000000 INFO @ Mon, 12 Aug 2019 20:46:44: 8000000 INFO @ Mon, 12 Aug 2019 20:46:46: 7000000 INFO @ Mon, 12 Aug 2019 20:46:48: 7000000 INFO @ Mon, 12 Aug 2019 20:46:51: 9000000 INFO @ Mon, 12 Aug 2019 20:46:53: 8000000 INFO @ Mon, 12 Aug 2019 20:46:55: 8000000 INFO @ Mon, 12 Aug 2019 20:46:58: 10000000 INFO @ Mon, 12 Aug 2019 20:47:00: 9000000 INFO @ Mon, 12 Aug 2019 20:47:02: 9000000 INFO @ Mon, 12 Aug 2019 20:47:04: 11000000 INFO @ Mon, 12 Aug 2019 20:47:07: 10000000 INFO @ Mon, 12 Aug 2019 20:47:09: 10000000 INFO @ Mon, 12 Aug 2019 20:47:11: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:47:11: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:47:11: #1 total tags in treatment: 11913442 INFO @ Mon, 12 Aug 2019 20:47:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:47:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:47:11: #1 tags after filtering in treatment: 11913442 INFO @ Mon, 12 Aug 2019 20:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:47:11: #1 finished! INFO @ Mon, 12 Aug 2019 20:47:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:47:12: #2 number of paired peaks: 2917 INFO @ Mon, 12 Aug 2019 20:47:12: start model_add_line... INFO @ Mon, 12 Aug 2019 20:47:13: start X-correlation... INFO @ Mon, 12 Aug 2019 20:47:13: end of X-cor INFO @ Mon, 12 Aug 2019 20:47:13: #2 finished! INFO @ Mon, 12 Aug 2019 20:47:13: #2 predicted fragment length is 212 bps INFO @ Mon, 12 Aug 2019 20:47:13: #2 alternative fragment length(s) may be 3,212,224 bps INFO @ Mon, 12 Aug 2019 20:47:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.10_model.r INFO @ Mon, 12 Aug 2019 20:47:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:47:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:47:14: 11000000 INFO @ Mon, 12 Aug 2019 20:47:16: 11000000 INFO @ Mon, 12 Aug 2019 20:47:21: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:47:21: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:47:21: #1 total tags in treatment: 11913442 INFO @ Mon, 12 Aug 2019 20:47:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:47:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:47:21: #1 tags after filtering in treatment: 11913442 INFO @ Mon, 12 Aug 2019 20:47:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:47:21: #1 finished! INFO @ Mon, 12 Aug 2019 20:47:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:47:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:47:22: #2 number of paired peaks: 2917 INFO @ Mon, 12 Aug 2019 20:47:22: start model_add_line... INFO @ Mon, 12 Aug 2019 20:47:22: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:47:22: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:47:22: #1 total tags in treatment: 11913442 INFO @ Mon, 12 Aug 2019 20:47:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:47:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:47:23: start X-correlation... INFO @ Mon, 12 Aug 2019 20:47:23: end of X-cor INFO @ Mon, 12 Aug 2019 20:47:23: #2 finished! INFO @ Mon, 12 Aug 2019 20:47:23: #2 predicted fragment length is 212 bps INFO @ Mon, 12 Aug 2019 20:47:23: #2 alternative fragment length(s) may be 3,212,224 bps INFO @ Mon, 12 Aug 2019 20:47:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.05_model.r INFO @ Mon, 12 Aug 2019 20:47:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:47:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:47:23: #1 tags after filtering in treatment: 11913442 INFO @ Mon, 12 Aug 2019 20:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:47:23: #1 finished! INFO @ Mon, 12 Aug 2019 20:47:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:47:24: #2 number of paired peaks: 2917 INFO @ Mon, 12 Aug 2019 20:47:24: start model_add_line... INFO @ Mon, 12 Aug 2019 20:47:24: start X-correlation... INFO @ Mon, 12 Aug 2019 20:47:24: end of X-cor INFO @ Mon, 12 Aug 2019 20:47:24: #2 finished! INFO @ Mon, 12 Aug 2019 20:47:24: #2 predicted fragment length is 212 bps INFO @ Mon, 12 Aug 2019 20:47:24: #2 alternative fragment length(s) may be 3,212,224 bps INFO @ Mon, 12 Aug 2019 20:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.20_model.r INFO @ Mon, 12 Aug 2019 20:47:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:47:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:47:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:48:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:48:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:48:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:48:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.10_summits.bed INFO @ Mon, 12 Aug 2019 20:48:06: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4198 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:48:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:48:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:48:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.05_summits.bed INFO @ Mon, 12 Aug 2019 20:48:17: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7619 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:48:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:48:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:48:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288042/SRX288042.20_summits.bed INFO @ Mon, 12 Aug 2019 20:48:18: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1227 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。