Job ID = 1294426 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,238,699 reads read : 17,238,699 reads written : 17,238,699 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: 00:06:15 17238699 reads; of these: 17238699 (100.00%) were unpaired; of these: 1094259 (6.35%) aligned 0 times 13298206 (77.14%) aligned exactly 1 time 2846234 (16.51%) aligned >1 times 93.65% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 6721977 / 16144440 = 0.4164 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 07:54:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.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 07:54:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:54:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:54:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.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 07:54:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:54:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:54:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.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 07:54:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:54:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:54:45: 1000000 INFO @ Mon, 03 Jun 2019 07:54:45: 1000000 INFO @ Mon, 03 Jun 2019 07:54:48: 1000000 INFO @ Mon, 03 Jun 2019 07:54:52: 2000000 INFO @ Mon, 03 Jun 2019 07:54:53: 2000000 INFO @ Mon, 03 Jun 2019 07:54:57: 2000000 INFO @ Mon, 03 Jun 2019 07:55:00: 3000000 INFO @ Mon, 03 Jun 2019 07:55:00: 3000000 INFO @ Mon, 03 Jun 2019 07:55:06: 3000000 INFO @ Mon, 03 Jun 2019 07:55:07: 4000000 INFO @ Mon, 03 Jun 2019 07:55:08: 4000000 INFO @ Mon, 03 Jun 2019 07:55:14: 4000000 INFO @ Mon, 03 Jun 2019 07:55:14: 5000000 INFO @ Mon, 03 Jun 2019 07:55:15: 5000000 INFO @ Mon, 03 Jun 2019 07:55:22: 6000000 INFO @ Mon, 03 Jun 2019 07:55:23: 6000000 INFO @ Mon, 03 Jun 2019 07:55:23: 5000000 INFO @ Mon, 03 Jun 2019 07:55:29: 7000000 INFO @ Mon, 03 Jun 2019 07:55:30: 7000000 INFO @ Mon, 03 Jun 2019 07:55:32: 6000000 INFO @ Mon, 03 Jun 2019 07:55:36: 8000000 INFO @ Mon, 03 Jun 2019 07:55:38: 8000000 INFO @ Mon, 03 Jun 2019 07:55:41: 7000000 INFO @ Mon, 03 Jun 2019 07:55:44: 9000000 INFO @ Mon, 03 Jun 2019 07:55:45: 9000000 INFO @ Mon, 03 Jun 2019 07:55:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:55:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:55:47: #1 total tags in treatment: 9422463 INFO @ Mon, 03 Jun 2019 07:55:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:55:47: #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 07:55:47: #1 tags after filtering in treatment: 9422463 INFO @ Mon, 03 Jun 2019 07:55:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:55:47: #1 finished! INFO @ Mon, 03 Jun 2019 07:55:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:55:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:55:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:55:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:55:48: #1 total tags in treatment: 9422463 INFO @ Mon, 03 Jun 2019 07:55:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:55:48: #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 07:55:48: #1 tags after filtering in treatment: 9422463 INFO @ Mon, 03 Jun 2019 07:55:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:55:48: #1 finished! INFO @ Mon, 03 Jun 2019 07:55:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:55:48: #2 number of paired peaks: 5617 INFO @ Mon, 03 Jun 2019 07:55:48: start model_add_line... INFO @ Mon, 03 Jun 2019 07:55:49: start X-correlation... INFO @ Mon, 03 Jun 2019 07:55:49: end of X-cor INFO @ Mon, 03 Jun 2019 07:55:49: #2 finished! INFO @ Mon, 03 Jun 2019 07:55:49: #2 predicted fragment length is 193 bps INFO @ Mon, 03 Jun 2019 07:55:49: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 03 Jun 2019 07:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.10_model.r INFO @ Mon, 03 Jun 2019 07:55:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:55:50: #2 number of paired peaks: 5617 INFO @ Mon, 03 Jun 2019 07:55:50: start model_add_line... INFO @ Mon, 03 Jun 2019 07:55:50: 8000000 INFO @ Mon, 03 Jun 2019 07:55:50: start X-correlation... INFO @ Mon, 03 Jun 2019 07:55:50: end of X-cor INFO @ Mon, 03 Jun 2019 07:55:50: #2 finished! INFO @ Mon, 03 Jun 2019 07:55:50: #2 predicted fragment length is 193 bps INFO @ Mon, 03 Jun 2019 07:55:50: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 03 Jun 2019 07:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.05_model.r INFO @ Mon, 03 Jun 2019 07:55:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:55:59: 9000000 INFO @ Mon, 03 Jun 2019 07:56:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:56:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:56:03: #1 total tags in treatment: 9422463 INFO @ Mon, 03 Jun 2019 07:56:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:56:03: #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 07:56:03: #1 tags after filtering in treatment: 9422463 INFO @ Mon, 03 Jun 2019 07:56:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:56:03: #1 finished! INFO @ Mon, 03 Jun 2019 07:56:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:56:04: #2 number of paired peaks: 5617 INFO @ Mon, 03 Jun 2019 07:56:04: start model_add_line... INFO @ Mon, 03 Jun 2019 07:56:04: start X-correlation... INFO @ Mon, 03 Jun 2019 07:56:04: end of X-cor INFO @ Mon, 03 Jun 2019 07:56:04: #2 finished! INFO @ Mon, 03 Jun 2019 07:56:04: #2 predicted fragment length is 193 bps INFO @ Mon, 03 Jun 2019 07:56:04: #2 alternative fragment length(s) may be 193 bps INFO @ Mon, 03 Jun 2019 07:56:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.20_model.r INFO @ Mon, 03 Jun 2019 07:56:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:56:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:56:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:56:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:56:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:56:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.10_summits.bed INFO @ Mon, 03 Jun 2019 07:56:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8608 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:56:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:56:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.05_summits.bed INFO @ Mon, 03 Jun 2019 07:56:38: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10552 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:56:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:56:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:56:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:56:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287596/SRX287596.20_summits.bed INFO @ Mon, 03 Jun 2019 07:56:53: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6653 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。