Job ID = 1294925 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,761,386 reads read : 18,761,386 reads written : 18,761,386 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: 00:07:33 18761386 reads; of these: 18761386 (100.00%) were unpaired; of these: 1163321 (6.20%) aligned 0 times 12868691 (68.59%) aligned exactly 1 time 4729374 (25.21%) aligned >1 times 93.80% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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] 2161086 / 17598065 = 0.1228 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 11:05:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.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 11:05:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:05:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:05:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.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 11:05:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:05:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:05:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.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 11:05:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:05:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:05:21: 1000000 INFO @ Mon, 03 Jun 2019 11:05:23: 1000000 INFO @ Mon, 03 Jun 2019 11:05:23: 1000000 INFO @ Mon, 03 Jun 2019 11:05:29: 2000000 INFO @ Mon, 03 Jun 2019 11:05:31: 2000000 INFO @ Mon, 03 Jun 2019 11:05:33: 2000000 INFO @ Mon, 03 Jun 2019 11:05:36: 3000000 INFO @ Mon, 03 Jun 2019 11:05:39: 3000000 INFO @ Mon, 03 Jun 2019 11:05:42: 3000000 INFO @ Mon, 03 Jun 2019 11:05:44: 4000000 INFO @ Mon, 03 Jun 2019 11:05:47: 4000000 INFO @ Mon, 03 Jun 2019 11:05:52: 4000000 INFO @ Mon, 03 Jun 2019 11:05:53: 5000000 INFO @ Mon, 03 Jun 2019 11:05:55: 5000000 INFO @ Mon, 03 Jun 2019 11:06:01: 6000000 INFO @ Mon, 03 Jun 2019 11:06:02: 5000000 INFO @ Mon, 03 Jun 2019 11:06:04: 6000000 INFO @ Mon, 03 Jun 2019 11:06:08: 7000000 INFO @ Mon, 03 Jun 2019 11:06:11: 7000000 INFO @ Mon, 03 Jun 2019 11:06:12: 6000000 INFO @ Mon, 03 Jun 2019 11:06:16: 8000000 INFO @ Mon, 03 Jun 2019 11:06:19: 8000000 INFO @ Mon, 03 Jun 2019 11:06:21: 7000000 INFO @ Mon, 03 Jun 2019 11:06:23: 9000000 INFO @ Mon, 03 Jun 2019 11:06:28: 9000000 INFO @ Mon, 03 Jun 2019 11:06:31: 8000000 INFO @ Mon, 03 Jun 2019 11:06:31: 10000000 INFO @ Mon, 03 Jun 2019 11:06:36: 10000000 INFO @ Mon, 03 Jun 2019 11:06:39: 11000000 INFO @ Mon, 03 Jun 2019 11:06:40: 9000000 INFO @ Mon, 03 Jun 2019 11:06:44: 11000000 INFO @ Mon, 03 Jun 2019 11:06:46: 12000000 INFO @ Mon, 03 Jun 2019 11:06:50: 10000000 INFO @ Mon, 03 Jun 2019 11:06:52: 12000000 INFO @ Mon, 03 Jun 2019 11:06:53: 13000000 INFO @ Mon, 03 Jun 2019 11:06:58: 11000000 INFO @ Mon, 03 Jun 2019 11:07:00: 13000000 INFO @ Mon, 03 Jun 2019 11:07:01: 14000000 INFO @ Mon, 03 Jun 2019 11:07:06: 12000000 INFO @ Mon, 03 Jun 2019 11:07:08: 14000000 INFO @ Mon, 03 Jun 2019 11:07:08: 15000000 INFO @ Mon, 03 Jun 2019 11:07:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:07:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:07:12: #1 total tags in treatment: 15436979 INFO @ Mon, 03 Jun 2019 11:07:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:07:12: #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 11:07:12: #1 tags after filtering in treatment: 15436979 INFO @ Mon, 03 Jun 2019 11:07:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:07:12: #1 finished! INFO @ Mon, 03 Jun 2019 11:07:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:07:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:07:14: #2 number of paired peaks: 246 WARNING @ Mon, 03 Jun 2019 11:07:14: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 03 Jun 2019 11:07:14: start model_add_line... INFO @ Mon, 03 Jun 2019 11:07:14: start X-correlation... INFO @ Mon, 03 Jun 2019 11:07:14: end of X-cor INFO @ Mon, 03 Jun 2019 11:07:14: #2 finished! INFO @ Mon, 03 Jun 2019 11:07:14: #2 predicted fragment length is 177 bps INFO @ Mon, 03 Jun 2019 11:07:14: #2 alternative fragment length(s) may be 177 bps INFO @ Mon, 03 Jun 2019 11:07:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.20_model.r INFO @ Mon, 03 Jun 2019 11:07:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:07:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:07:15: 15000000 INFO @ Mon, 03 Jun 2019 11:07:16: 13000000 INFO @ Mon, 03 Jun 2019 11:07:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:07:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:07:18: #1 total tags in treatment: 15436979 INFO @ Mon, 03 Jun 2019 11:07:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:07:18: #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 11:07:19: #1 tags after filtering in treatment: 15436979 INFO @ Mon, 03 Jun 2019 11:07:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:07:19: #1 finished! INFO @ Mon, 03 Jun 2019 11:07:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:07:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:07:20: #2 number of paired peaks: 246 WARNING @ Mon, 03 Jun 2019 11:07:20: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 03 Jun 2019 11:07:20: start model_add_line... INFO @ Mon, 03 Jun 2019 11:07:20: start X-correlation... INFO @ Mon, 03 Jun 2019 11:07:20: end of X-cor INFO @ Mon, 03 Jun 2019 11:07:20: #2 finished! INFO @ Mon, 03 Jun 2019 11:07:20: #2 predicted fragment length is 177 bps INFO @ Mon, 03 Jun 2019 11:07:20: #2 alternative fragment length(s) may be 177 bps INFO @ Mon, 03 Jun 2019 11:07:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.10_model.r INFO @ Mon, 03 Jun 2019 11:07:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:07:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:07:25: 14000000 INFO @ Mon, 03 Jun 2019 11:07:35: 15000000 INFO @ Mon, 03 Jun 2019 11:07:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:07:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:07:39: #1 total tags in treatment: 15436979 INFO @ Mon, 03 Jun 2019 11:07:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:07:39: #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 11:07:39: #1 tags after filtering in treatment: 15436979 INFO @ Mon, 03 Jun 2019 11:07:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:07:39: #1 finished! INFO @ Mon, 03 Jun 2019 11:07:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:07:41: #2 number of paired peaks: 246 WARNING @ Mon, 03 Jun 2019 11:07:41: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 03 Jun 2019 11:07:41: start model_add_line... INFO @ Mon, 03 Jun 2019 11:07:41: start X-correlation... INFO @ Mon, 03 Jun 2019 11:07:41: end of X-cor INFO @ Mon, 03 Jun 2019 11:07:41: #2 finished! INFO @ Mon, 03 Jun 2019 11:07:41: #2 predicted fragment length is 177 bps INFO @ Mon, 03 Jun 2019 11:07:41: #2 alternative fragment length(s) may be 177 bps INFO @ Mon, 03 Jun 2019 11:07:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.05_model.r INFO @ Mon, 03 Jun 2019 11:07:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:07:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:08:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:08:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:08:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:08:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.20_summits.bed INFO @ Mon, 03 Jun 2019 11:08:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1891 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:08:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.10_summits.bed INFO @ Mon, 03 Jun 2019 11:08:24: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3035 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:08:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:08:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:08:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287993/SRX287993.05_summits.bed INFO @ Mon, 03 Jun 2019 11:08:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4427 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。