Job ID = 1294600 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,877,622 reads read : 13,877,622 reads written : 13,877,622 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: 00:03:24 13877622 reads; of these: 13877622 (100.00%) were unpaired; of these: 2558245 (18.43%) aligned 0 times 10173525 (73.31%) aligned exactly 1 time 1145852 (8.26%) aligned >1 times 81.57% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 897027 / 11319377 = 0.0792 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 09:24:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.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 09:24:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:24:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:24:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.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 09:24:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:24:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:24:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.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 09:24:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:24:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:24:13: 1000000 INFO @ Mon, 03 Jun 2019 09:24:14: 1000000 INFO @ Mon, 03 Jun 2019 09:24:15: 1000000 INFO @ Mon, 03 Jun 2019 09:24:20: 2000000 INFO @ Mon, 03 Jun 2019 09:24:22: 2000000 INFO @ Mon, 03 Jun 2019 09:24:24: 2000000 INFO @ Mon, 03 Jun 2019 09:24:27: 3000000 INFO @ Mon, 03 Jun 2019 09:24:29: 3000000 INFO @ Mon, 03 Jun 2019 09:24:33: 3000000 INFO @ Mon, 03 Jun 2019 09:24:34: 4000000 INFO @ Mon, 03 Jun 2019 09:24:37: 4000000 INFO @ Mon, 03 Jun 2019 09:24:41: 5000000 INFO @ Mon, 03 Jun 2019 09:24:42: 4000000 INFO @ Mon, 03 Jun 2019 09:24:45: 5000000 INFO @ Mon, 03 Jun 2019 09:24:48: 6000000 INFO @ Mon, 03 Jun 2019 09:24:51: 5000000 INFO @ Mon, 03 Jun 2019 09:24:52: 6000000 INFO @ Mon, 03 Jun 2019 09:24:55: 7000000 INFO @ Mon, 03 Jun 2019 09:24:59: 6000000 INFO @ Mon, 03 Jun 2019 09:25:00: 7000000 INFO @ Mon, 03 Jun 2019 09:25:02: 8000000 INFO @ Mon, 03 Jun 2019 09:25:08: 8000000 INFO @ Mon, 03 Jun 2019 09:25:08: 7000000 INFO @ Mon, 03 Jun 2019 09:25:09: 9000000 INFO @ Mon, 03 Jun 2019 09:25:15: 9000000 INFO @ Mon, 03 Jun 2019 09:25:16: 10000000 INFO @ Mon, 03 Jun 2019 09:25:17: 8000000 INFO @ Mon, 03 Jun 2019 09:25:19: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:25:19: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:25:19: #1 total tags in treatment: 10422350 INFO @ Mon, 03 Jun 2019 09:25:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:25:19: #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 09:25:19: #1 tags after filtering in treatment: 10422350 INFO @ Mon, 03 Jun 2019 09:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:25:19: #1 finished! INFO @ Mon, 03 Jun 2019 09:25:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:25:20: #2 number of paired peaks: 768 WARNING @ Mon, 03 Jun 2019 09:25:20: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Mon, 03 Jun 2019 09:25:20: start model_add_line... INFO @ Mon, 03 Jun 2019 09:25:20: start X-correlation... INFO @ Mon, 03 Jun 2019 09:25:20: end of X-cor INFO @ Mon, 03 Jun 2019 09:25:20: #2 finished! INFO @ Mon, 03 Jun 2019 09:25:20: #2 predicted fragment length is 179 bps INFO @ Mon, 03 Jun 2019 09:25:20: #2 alternative fragment length(s) may be 2,179,203,219,239 bps INFO @ Mon, 03 Jun 2019 09:25:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.10_model.r INFO @ Mon, 03 Jun 2019 09:25:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:25:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:25:23: 10000000 INFO @ Mon, 03 Jun 2019 09:25:26: 9000000 INFO @ Mon, 03 Jun 2019 09:25:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:25:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:25:26: #1 total tags in treatment: 10422350 INFO @ Mon, 03 Jun 2019 09:25:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:25:26: #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 09:25:26: #1 tags after filtering in treatment: 10422350 INFO @ Mon, 03 Jun 2019 09:25:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:25:26: #1 finished! INFO @ Mon, 03 Jun 2019 09:25:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:25:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:25:27: #2 number of paired peaks: 768 WARNING @ Mon, 03 Jun 2019 09:25:27: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Mon, 03 Jun 2019 09:25:27: start model_add_line... INFO @ Mon, 03 Jun 2019 09:25:27: start X-correlation... INFO @ Mon, 03 Jun 2019 09:25:27: end of X-cor INFO @ Mon, 03 Jun 2019 09:25:27: #2 finished! INFO @ Mon, 03 Jun 2019 09:25:27: #2 predicted fragment length is 179 bps INFO @ Mon, 03 Jun 2019 09:25:27: #2 alternative fragment length(s) may be 2,179,203,219,239 bps INFO @ Mon, 03 Jun 2019 09:25:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.20_model.r INFO @ Mon, 03 Jun 2019 09:25:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:25:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:25:35: 10000000 INFO @ Mon, 03 Jun 2019 09:25:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:25:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:25:38: #1 total tags in treatment: 10422350 INFO @ Mon, 03 Jun 2019 09:25:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:25:38: #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 09:25:38: #1 tags after filtering in treatment: 10422350 INFO @ Mon, 03 Jun 2019 09:25:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:25:38: #1 finished! INFO @ Mon, 03 Jun 2019 09:25:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:25:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:25:39: #2 number of paired peaks: 768 WARNING @ Mon, 03 Jun 2019 09:25:39: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Mon, 03 Jun 2019 09:25:39: start model_add_line... INFO @ Mon, 03 Jun 2019 09:25:39: start X-correlation... INFO @ Mon, 03 Jun 2019 09:25:39: end of X-cor INFO @ Mon, 03 Jun 2019 09:25:39: #2 finished! INFO @ Mon, 03 Jun 2019 09:25:39: #2 predicted fragment length is 179 bps INFO @ Mon, 03 Jun 2019 09:25:39: #2 alternative fragment length(s) may be 2,179,203,219,239 bps INFO @ Mon, 03 Jun 2019 09:25:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.05_model.r INFO @ Mon, 03 Jun 2019 09:25:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:25:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:25:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:25:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.10_summits.bed INFO @ Mon, 03 Jun 2019 09:26:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1220 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:26:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:26:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:26:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:26:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.20_summits.bed INFO @ Mon, 03 Jun 2019 09:26:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:26:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:26:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:26:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287771/SRX287771.05_summits.bed INFO @ Mon, 03 Jun 2019 09:26:25: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (3174 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。