Job ID = 1295118 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,956,734 reads read : 16,956,734 reads written : 16,956,734 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: 00:05:29 16956734 reads; of these: 16956734 (100.00%) were unpaired; of these: 1424315 (8.40%) aligned 0 times 12933147 (76.27%) aligned exactly 1 time 2599272 (15.33%) aligned >1 times 91.60% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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_rmdupse_core] 5230396 / 15532419 = 0.3367 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 12:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.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 12:13:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:13:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.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 12:13:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:13:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.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 12:13:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:13:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:13:44: 1000000 INFO @ Mon, 03 Jun 2019 12:13:45: 1000000 INFO @ Mon, 03 Jun 2019 12:13:45: 1000000 INFO @ Mon, 03 Jun 2019 12:13:52: 2000000 INFO @ Mon, 03 Jun 2019 12:13:53: 2000000 INFO @ Mon, 03 Jun 2019 12:13:53: 2000000 INFO @ Mon, 03 Jun 2019 12:14:00: 3000000 INFO @ Mon, 03 Jun 2019 12:14:01: 3000000 INFO @ Mon, 03 Jun 2019 12:14:02: 3000000 INFO @ Mon, 03 Jun 2019 12:14:08: 4000000 INFO @ Mon, 03 Jun 2019 12:14:10: 4000000 INFO @ Mon, 03 Jun 2019 12:14:10: 4000000 INFO @ Mon, 03 Jun 2019 12:14:16: 5000000 INFO @ Mon, 03 Jun 2019 12:14:18: 5000000 INFO @ Mon, 03 Jun 2019 12:14:19: 5000000 INFO @ Mon, 03 Jun 2019 12:14:24: 6000000 INFO @ Mon, 03 Jun 2019 12:14:26: 6000000 INFO @ Mon, 03 Jun 2019 12:14:27: 6000000 INFO @ Mon, 03 Jun 2019 12:14:32: 7000000 INFO @ Mon, 03 Jun 2019 12:14:34: 7000000 INFO @ Mon, 03 Jun 2019 12:14:35: 7000000 INFO @ Mon, 03 Jun 2019 12:14:40: 8000000 INFO @ Mon, 03 Jun 2019 12:14:43: 8000000 INFO @ Mon, 03 Jun 2019 12:14:43: 8000000 INFO @ Mon, 03 Jun 2019 12:14:48: 9000000 INFO @ Mon, 03 Jun 2019 12:14:51: 9000000 INFO @ Mon, 03 Jun 2019 12:14:52: 9000000 INFO @ Mon, 03 Jun 2019 12:14:56: 10000000 INFO @ Mon, 03 Jun 2019 12:14:58: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 12:14:58: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 12:14:58: #1 total tags in treatment: 10302023 INFO @ Mon, 03 Jun 2019 12:14:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:14:58: #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 12:14:59: #1 tags after filtering in treatment: 10302023 INFO @ Mon, 03 Jun 2019 12:14:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:14:59: #1 finished! INFO @ Mon, 03 Jun 2019 12:14:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:14:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:14:59: 10000000 INFO @ Mon, 03 Jun 2019 12:15:00: #2 number of paired peaks: 182 WARNING @ Mon, 03 Jun 2019 12:15:00: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Mon, 03 Jun 2019 12:15:00: start model_add_line... INFO @ Mon, 03 Jun 2019 12:15:00: start X-correlation... INFO @ Mon, 03 Jun 2019 12:15:00: 10000000 INFO @ Mon, 03 Jun 2019 12:15:00: end of X-cor INFO @ Mon, 03 Jun 2019 12:15:00: #2 finished! INFO @ Mon, 03 Jun 2019 12:15:00: #2 predicted fragment length is 234 bps INFO @ Mon, 03 Jun 2019 12:15:00: #2 alternative fragment length(s) may be 234 bps INFO @ Mon, 03 Jun 2019 12:15:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.05_model.r INFO @ Mon, 03 Jun 2019 12:15:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:15:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:15:02: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 12:15:02: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 12:15:02: #1 total tags in treatment: 10302023 INFO @ Mon, 03 Jun 2019 12:15:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:15:02: #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 12:15:02: #1 tags after filtering in treatment: 10302023 INFO @ Mon, 03 Jun 2019 12:15:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:15:02: #1 finished! INFO @ Mon, 03 Jun 2019 12:15:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:15:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:15:02: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 12:15:02: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 12:15:02: #1 total tags in treatment: 10302023 INFO @ Mon, 03 Jun 2019 12:15:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:15:02: #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 12:15:03: #1 tags after filtering in treatment: 10302023 INFO @ Mon, 03 Jun 2019 12:15:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:15:03: #1 finished! INFO @ Mon, 03 Jun 2019 12:15:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:15:03: #2 number of paired peaks: 182 WARNING @ Mon, 03 Jun 2019 12:15:03: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Mon, 03 Jun 2019 12:15:03: start model_add_line... INFO @ Mon, 03 Jun 2019 12:15:03: start X-correlation... INFO @ Mon, 03 Jun 2019 12:15:03: end of X-cor INFO @ Mon, 03 Jun 2019 12:15:03: #2 finished! INFO @ Mon, 03 Jun 2019 12:15:03: #2 predicted fragment length is 234 bps INFO @ Mon, 03 Jun 2019 12:15:03: #2 alternative fragment length(s) may be 234 bps INFO @ Mon, 03 Jun 2019 12:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.20_model.r INFO @ Mon, 03 Jun 2019 12:15:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:15:04: #2 number of paired peaks: 182 WARNING @ Mon, 03 Jun 2019 12:15:04: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Mon, 03 Jun 2019 12:15:04: start model_add_line... INFO @ Mon, 03 Jun 2019 12:15:04: start X-correlation... INFO @ Mon, 03 Jun 2019 12:15:04: end of X-cor INFO @ Mon, 03 Jun 2019 12:15:04: #2 finished! INFO @ Mon, 03 Jun 2019 12:15:04: #2 predicted fragment length is 234 bps INFO @ Mon, 03 Jun 2019 12:15:04: #2 alternative fragment length(s) may be 234 bps INFO @ Mon, 03 Jun 2019 12:15:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.10_model.r INFO @ Mon, 03 Jun 2019 12:15:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:15:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:15:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:15:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:15:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:15:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:15:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:15:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.05_summits.bed INFO @ Mon, 03 Jun 2019 12:15:52: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4977 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:15:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:15:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:15:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.20_summits.bed INFO @ Mon, 03 Jun 2019 12:15:53: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (998 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:15:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:15:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:15:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX320155/SRX320155.10_summits.bed INFO @ Mon, 03 Jun 2019 12:15:54: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (2661 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。