Job ID = 1300235 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,180,850 reads read : 11,180,850 reads written : 11,180,850 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: 00:05:32 11180850 reads; of these: 11180850 (100.00%) were unpaired; of these: 372291 (3.33%) aligned 0 times 7593020 (67.91%) aligned exactly 1 time 3215539 (28.76%) aligned >1 times 96.67% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 2214246 / 10808559 = 0.2049 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 19:13:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.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 19:13:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:13:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:13:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.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 19:13:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:13:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:13:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.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 19:13:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:13:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:13:52: 1000000 INFO @ Mon, 03 Jun 2019 19:13:56: 1000000 INFO @ Mon, 03 Jun 2019 19:13:56: 1000000 INFO @ Mon, 03 Jun 2019 19:14:00: 2000000 INFO @ Mon, 03 Jun 2019 19:14:07: 2000000 INFO @ Mon, 03 Jun 2019 19:14:08: 2000000 INFO @ Mon, 03 Jun 2019 19:14:08: 3000000 INFO @ Mon, 03 Jun 2019 19:14:17: 4000000 INFO @ Mon, 03 Jun 2019 19:14:18: 3000000 INFO @ Mon, 03 Jun 2019 19:14:20: 3000000 INFO @ Mon, 03 Jun 2019 19:14:25: 5000000 INFO @ Mon, 03 Jun 2019 19:14:29: 4000000 INFO @ Mon, 03 Jun 2019 19:14:32: 4000000 INFO @ Mon, 03 Jun 2019 19:14:33: 6000000 INFO @ Mon, 03 Jun 2019 19:14:40: 5000000 INFO @ Mon, 03 Jun 2019 19:14:41: 7000000 INFO @ Mon, 03 Jun 2019 19:14:45: 5000000 INFO @ Mon, 03 Jun 2019 19:14:50: 8000000 INFO @ Mon, 03 Jun 2019 19:14:51: 6000000 INFO @ Mon, 03 Jun 2019 19:14:54: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:14:54: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:14:54: #1 total tags in treatment: 8594313 INFO @ Mon, 03 Jun 2019 19:14:54: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:14:54: #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 19:14:55: #1 tags after filtering in treatment: 8594313 INFO @ Mon, 03 Jun 2019 19:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:14:55: #1 finished! INFO @ Mon, 03 Jun 2019 19:14:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:14:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:14:56: #2 number of paired peaks: 4678 INFO @ Mon, 03 Jun 2019 19:14:56: start model_add_line... INFO @ Mon, 03 Jun 2019 19:14:56: start X-correlation... INFO @ Mon, 03 Jun 2019 19:14:56: end of X-cor INFO @ Mon, 03 Jun 2019 19:14:56: #2 finished! INFO @ Mon, 03 Jun 2019 19:14:56: #2 predicted fragment length is 156 bps INFO @ Mon, 03 Jun 2019 19:14:56: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 03 Jun 2019 19:14:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.10_model.r INFO @ Mon, 03 Jun 2019 19:14:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:14:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:14:57: 6000000 INFO @ Mon, 03 Jun 2019 19:15:02: 7000000 INFO @ Mon, 03 Jun 2019 19:15:08: 7000000 INFO @ Mon, 03 Jun 2019 19:15:13: 8000000 INFO @ Mon, 03 Jun 2019 19:15:18: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:15:18: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:15:18: #1 total tags in treatment: 8594313 INFO @ Mon, 03 Jun 2019 19:15:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:15:18: #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 19:15:19: #1 tags after filtering in treatment: 8594313 INFO @ Mon, 03 Jun 2019 19:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:15:19: #1 finished! INFO @ Mon, 03 Jun 2019 19:15:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:15:20: #2 number of paired peaks: 4678 INFO @ Mon, 03 Jun 2019 19:15:20: start model_add_line... INFO @ Mon, 03 Jun 2019 19:15:20: start X-correlation... INFO @ Mon, 03 Jun 2019 19:15:20: end of X-cor INFO @ Mon, 03 Jun 2019 19:15:20: #2 finished! INFO @ Mon, 03 Jun 2019 19:15:20: #2 predicted fragment length is 156 bps INFO @ Mon, 03 Jun 2019 19:15:20: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 03 Jun 2019 19:15:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.20_model.r INFO @ Mon, 03 Jun 2019 19:15:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:15:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:15:20: 8000000 INFO @ Mon, 03 Jun 2019 19:15:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:15:27: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:15:27: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:15:27: #1 total tags in treatment: 8594313 INFO @ Mon, 03 Jun 2019 19:15:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:15:27: #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 19:15:27: #1 tags after filtering in treatment: 8594313 INFO @ Mon, 03 Jun 2019 19:15:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:15:27: #1 finished! INFO @ Mon, 03 Jun 2019 19:15:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:15:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:15:29: #2 number of paired peaks: 4678 INFO @ Mon, 03 Jun 2019 19:15:29: start model_add_line... INFO @ Mon, 03 Jun 2019 19:15:29: start X-correlation... INFO @ Mon, 03 Jun 2019 19:15:29: end of X-cor INFO @ Mon, 03 Jun 2019 19:15:29: #2 finished! INFO @ Mon, 03 Jun 2019 19:15:29: #2 predicted fragment length is 156 bps INFO @ Mon, 03 Jun 2019 19:15:29: #2 alternative fragment length(s) may be 156 bps INFO @ Mon, 03 Jun 2019 19:15:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.05_model.r INFO @ Mon, 03 Jun 2019 19:15:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:15:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:15:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:15:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.10_summits.bed INFO @ Mon, 03 Jun 2019 19:15:38: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7316 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:15:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:15:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:16:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:16:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:16:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.20_summits.bed INFO @ Mon, 03 Jun 2019 19:16:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5493 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:16:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:16:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:16:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801816/SRX4801816.05_summits.bed INFO @ Mon, 03 Jun 2019 19:16:13: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8840 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。