Job ID = 1295837 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,070,576 reads read : 24,141,152 reads written : 24,141,152 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:28:06 12070576 reads; of these: 12070576 (100.00%) were paired; of these: 2104640 (17.44%) aligned concordantly 0 times 7318735 (60.63%) aligned concordantly exactly 1 time 2647201 (21.93%) aligned concordantly >1 times ---- 2104640 pairs aligned concordantly 0 times; of these: 289495 (13.76%) aligned discordantly 1 time ---- 1815145 pairs aligned 0 times concordantly or discordantly; of these: 3630290 mates make up the pairs; of these: 2933243 (80.80%) aligned 0 times 377362 (10.39%) aligned exactly 1 time 319685 (8.81%) aligned >1 times 87.85% overall alignment rate Time searching: 00:28:07 Overall time: 00:28:07 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1141049 / 10233346 = 0.1115 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 16:24:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.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 16:24:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:24:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:24:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.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 16:24:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:24:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:24:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.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 16:24:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:24:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:24:45: 1000000 INFO @ Mon, 03 Jun 2019 16:24:45: 1000000 INFO @ Mon, 03 Jun 2019 16:24:46: 1000000 INFO @ Mon, 03 Jun 2019 16:24:54: 2000000 INFO @ Mon, 03 Jun 2019 16:24:55: 2000000 INFO @ Mon, 03 Jun 2019 16:24:56: 2000000 INFO @ Mon, 03 Jun 2019 16:25:03: 3000000 INFO @ Mon, 03 Jun 2019 16:25:04: 3000000 INFO @ Mon, 03 Jun 2019 16:25:06: 3000000 INFO @ Mon, 03 Jun 2019 16:25:11: 4000000 INFO @ Mon, 03 Jun 2019 16:25:12: 4000000 INFO @ Mon, 03 Jun 2019 16:25:15: 4000000 INFO @ Mon, 03 Jun 2019 16:25:19: 5000000 INFO @ Mon, 03 Jun 2019 16:25:21: 5000000 INFO @ Mon, 03 Jun 2019 16:25:24: 5000000 INFO @ Mon, 03 Jun 2019 16:25:27: 6000000 INFO @ Mon, 03 Jun 2019 16:25:29: 6000000 INFO @ Mon, 03 Jun 2019 16:25:33: 6000000 INFO @ Mon, 03 Jun 2019 16:25:35: 7000000 INFO @ Mon, 03 Jun 2019 16:25:38: 7000000 INFO @ Mon, 03 Jun 2019 16:25:42: 7000000 INFO @ Mon, 03 Jun 2019 16:25:43: 8000000 INFO @ Mon, 03 Jun 2019 16:25:46: 8000000 INFO @ Mon, 03 Jun 2019 16:25:51: 8000000 INFO @ Mon, 03 Jun 2019 16:25:52: 9000000 INFO @ Mon, 03 Jun 2019 16:25:55: 9000000 INFO @ Mon, 03 Jun 2019 16:26:00: 9000000 INFO @ Mon, 03 Jun 2019 16:26:00: 10000000 INFO @ Mon, 03 Jun 2019 16:26:04: 10000000 INFO @ Mon, 03 Jun 2019 16:26:08: 11000000 INFO @ Mon, 03 Jun 2019 16:26:08: 10000000 INFO @ Mon, 03 Jun 2019 16:26:12: 11000000 INFO @ Mon, 03 Jun 2019 16:26:17: 12000000 INFO @ Mon, 03 Jun 2019 16:26:18: 11000000 INFO @ Mon, 03 Jun 2019 16:26:22: 12000000 INFO @ Mon, 03 Jun 2019 16:26:25: 13000000 INFO @ Mon, 03 Jun 2019 16:26:28: 12000000 INFO @ Mon, 03 Jun 2019 16:26:31: 13000000 INFO @ Mon, 03 Jun 2019 16:26:33: 14000000 INFO @ Mon, 03 Jun 2019 16:26:37: 13000000 INFO @ Mon, 03 Jun 2019 16:26:39: 14000000 INFO @ Mon, 03 Jun 2019 16:26:41: 15000000 INFO @ Mon, 03 Jun 2019 16:26:46: 14000000 INFO @ Mon, 03 Jun 2019 16:26:48: 15000000 INFO @ Mon, 03 Jun 2019 16:26:49: 16000000 INFO @ Mon, 03 Jun 2019 16:26:55: 15000000 INFO @ Mon, 03 Jun 2019 16:26:56: 16000000 INFO @ Mon, 03 Jun 2019 16:26:57: 17000000 INFO @ Mon, 03 Jun 2019 16:27:04: 16000000 INFO @ Mon, 03 Jun 2019 16:27:05: 17000000 INFO @ Mon, 03 Jun 2019 16:27:05: 18000000 INFO @ Mon, 03 Jun 2019 16:27:13: 17000000 INFO @ Mon, 03 Jun 2019 16:27:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:27:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:27:13: #1 total tags in treatment: 8838737 INFO @ Mon, 03 Jun 2019 16:27:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:27:13: #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 16:27:13: #1 tags after filtering in treatment: 7485551 INFO @ Mon, 03 Jun 2019 16:27:13: #1 Redundant rate of treatment: 0.15 INFO @ Mon, 03 Jun 2019 16:27:13: #1 finished! INFO @ Mon, 03 Jun 2019 16:27:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:27:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:27:14: 18000000 INFO @ Mon, 03 Jun 2019 16:27:14: #2 number of paired peaks: 5029 INFO @ Mon, 03 Jun 2019 16:27:14: start model_add_line... INFO @ Mon, 03 Jun 2019 16:27:15: start X-correlation... INFO @ Mon, 03 Jun 2019 16:27:15: end of X-cor INFO @ Mon, 03 Jun 2019 16:27:15: #2 finished! INFO @ Mon, 03 Jun 2019 16:27:15: #2 predicted fragment length is 182 bps INFO @ Mon, 03 Jun 2019 16:27:15: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 03 Jun 2019 16:27:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.10_model.r INFO @ Mon, 03 Jun 2019 16:27:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:27:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:27:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:27:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:27:21: #1 total tags in treatment: 8838737 INFO @ Mon, 03 Jun 2019 16:27:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:27:21: #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 16:27:21: #1 tags after filtering in treatment: 7485551 INFO @ Mon, 03 Jun 2019 16:27:21: #1 Redundant rate of treatment: 0.15 INFO @ Mon, 03 Jun 2019 16:27:21: #1 finished! INFO @ Mon, 03 Jun 2019 16:27:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:27:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:27:22: 18000000 INFO @ Mon, 03 Jun 2019 16:27:23: #2 number of paired peaks: 5029 INFO @ Mon, 03 Jun 2019 16:27:23: start model_add_line... INFO @ Mon, 03 Jun 2019 16:27:23: start X-correlation... INFO @ Mon, 03 Jun 2019 16:27:23: end of X-cor INFO @ Mon, 03 Jun 2019 16:27:23: #2 finished! INFO @ Mon, 03 Jun 2019 16:27:23: #2 predicted fragment length is 182 bps INFO @ Mon, 03 Jun 2019 16:27:23: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 03 Jun 2019 16:27:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.05_model.r INFO @ Mon, 03 Jun 2019 16:27:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:27:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:27:30: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:27:30: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:27:30: #1 total tags in treatment: 8838737 INFO @ Mon, 03 Jun 2019 16:27:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:27:30: #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 16:27:31: #1 tags after filtering in treatment: 7485551 INFO @ Mon, 03 Jun 2019 16:27:31: #1 Redundant rate of treatment: 0.15 INFO @ Mon, 03 Jun 2019 16:27:31: #1 finished! INFO @ Mon, 03 Jun 2019 16:27:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:27:32: #2 number of paired peaks: 5029 INFO @ Mon, 03 Jun 2019 16:27:32: start model_add_line... INFO @ Mon, 03 Jun 2019 16:27:32: start X-correlation... INFO @ Mon, 03 Jun 2019 16:27:32: end of X-cor INFO @ Mon, 03 Jun 2019 16:27:32: #2 finished! INFO @ Mon, 03 Jun 2019 16:27:32: #2 predicted fragment length is 182 bps INFO @ Mon, 03 Jun 2019 16:27:32: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 03 Jun 2019 16:27:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.20_model.r INFO @ Mon, 03 Jun 2019 16:27:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:27:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:27:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:27:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:27:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:27:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.10_summits.bed INFO @ Mon, 03 Jun 2019 16:27:54: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6117 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:27:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.05_summits.bed INFO @ Mon, 03 Jun 2019 16:28:02: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7778 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:28:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:28:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:28:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577936/SRX4577936.20_summits.bed INFO @ Mon, 03 Jun 2019 16:28:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4224 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。