Job ID = 1294183 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,339,444 reads read : 20,339,444 reads written : 20,339,444 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: 00:06:07 20339444 reads; of these: 20339444 (100.00%) were unpaired; of these: 6382160 (31.38%) aligned 0 times 9857162 (48.46%) aligned exactly 1 time 4100122 (20.16%) aligned >1 times 68.62% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 4212097 / 13957284 = 0.3018 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 05:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.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 05:30:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:30:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.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 05:30:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:30:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.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 05:30:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:30:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:30:47: 1000000 INFO @ Mon, 03 Jun 2019 05:30:47: 1000000 INFO @ Mon, 03 Jun 2019 05:30:48: 1000000 INFO @ Mon, 03 Jun 2019 05:30:54: 2000000 INFO @ Mon, 03 Jun 2019 05:30:56: 2000000 INFO @ Mon, 03 Jun 2019 05:30:56: 2000000 INFO @ Mon, 03 Jun 2019 05:31:01: 3000000 INFO @ Mon, 03 Jun 2019 05:31:04: 3000000 INFO @ Mon, 03 Jun 2019 05:31:04: 3000000 INFO @ Mon, 03 Jun 2019 05:31:09: 4000000 INFO @ Mon, 03 Jun 2019 05:31:12: 4000000 INFO @ Mon, 03 Jun 2019 05:31:12: 4000000 INFO @ Mon, 03 Jun 2019 05:31:16: 5000000 INFO @ Mon, 03 Jun 2019 05:31:20: 5000000 INFO @ Mon, 03 Jun 2019 05:31:20: 5000000 INFO @ Mon, 03 Jun 2019 05:31:23: 6000000 INFO @ Mon, 03 Jun 2019 05:31:28: 6000000 INFO @ Mon, 03 Jun 2019 05:31:28: 6000000 INFO @ Mon, 03 Jun 2019 05:31:31: 7000000 INFO @ Mon, 03 Jun 2019 05:31:36: 7000000 INFO @ Mon, 03 Jun 2019 05:31:37: 7000000 INFO @ Mon, 03 Jun 2019 05:31:38: 8000000 INFO @ Mon, 03 Jun 2019 05:31:45: 8000000 INFO @ Mon, 03 Jun 2019 05:31:45: 8000000 INFO @ Mon, 03 Jun 2019 05:31:46: 9000000 INFO @ Mon, 03 Jun 2019 05:31:51: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:31:51: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:31:51: #1 total tags in treatment: 9745187 INFO @ Mon, 03 Jun 2019 05:31:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:31:51: #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 05:31:52: #1 tags after filtering in treatment: 9745187 INFO @ Mon, 03 Jun 2019 05:31:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:31:52: #1 finished! INFO @ Mon, 03 Jun 2019 05:31:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:31:53: #2 number of paired peaks: 358 WARNING @ Mon, 03 Jun 2019 05:31:53: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Mon, 03 Jun 2019 05:31:53: start model_add_line... INFO @ Mon, 03 Jun 2019 05:31:53: start X-correlation... INFO @ Mon, 03 Jun 2019 05:31:53: end of X-cor INFO @ Mon, 03 Jun 2019 05:31:53: #2 finished! INFO @ Mon, 03 Jun 2019 05:31:53: #2 predicted fragment length is 133 bps INFO @ Mon, 03 Jun 2019 05:31:53: #2 alternative fragment length(s) may be 133 bps INFO @ Mon, 03 Jun 2019 05:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.10_model.r INFO @ Mon, 03 Jun 2019 05:31:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:31:53: 9000000 INFO @ Mon, 03 Jun 2019 05:31:54: 9000000 INFO @ Mon, 03 Jun 2019 05:31:59: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:31:59: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:31:59: #1 total tags in treatment: 9745187 INFO @ Mon, 03 Jun 2019 05:31:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:31:59: #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 05:31:59: #1 tags after filtering in treatment: 9745187 INFO @ Mon, 03 Jun 2019 05:31:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:31:59: #1 finished! INFO @ Mon, 03 Jun 2019 05:31:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:31:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:32:00: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:32:00: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:32:00: #1 total tags in treatment: 9745187 INFO @ Mon, 03 Jun 2019 05:32:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:32:00: #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 05:32:00: #2 number of paired peaks: 358 WARNING @ Mon, 03 Jun 2019 05:32:00: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Mon, 03 Jun 2019 05:32:00: start model_add_line... INFO @ Mon, 03 Jun 2019 05:32:00: #1 tags after filtering in treatment: 9745187 INFO @ Mon, 03 Jun 2019 05:32:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:32:00: #1 finished! INFO @ Mon, 03 Jun 2019 05:32:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:32:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:32:00: start X-correlation... INFO @ Mon, 03 Jun 2019 05:32:00: end of X-cor INFO @ Mon, 03 Jun 2019 05:32:00: #2 finished! INFO @ Mon, 03 Jun 2019 05:32:00: #2 predicted fragment length is 133 bps INFO @ Mon, 03 Jun 2019 05:32:00: #2 alternative fragment length(s) may be 133 bps INFO @ Mon, 03 Jun 2019 05:32:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.20_model.r INFO @ Mon, 03 Jun 2019 05:32:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:32:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:32:01: #2 number of paired peaks: 358 WARNING @ Mon, 03 Jun 2019 05:32:01: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Mon, 03 Jun 2019 05:32:01: start model_add_line... INFO @ Mon, 03 Jun 2019 05:32:01: start X-correlation... INFO @ Mon, 03 Jun 2019 05:32:01: end of X-cor INFO @ Mon, 03 Jun 2019 05:32:01: #2 finished! INFO @ Mon, 03 Jun 2019 05:32:01: #2 predicted fragment length is 133 bps INFO @ Mon, 03 Jun 2019 05:32:01: #2 alternative fragment length(s) may be 133 bps INFO @ Mon, 03 Jun 2019 05:32:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.05_model.r INFO @ Mon, 03 Jun 2019 05:32:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:32:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:32:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:32:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:32:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:32:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:32:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:32:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.10_summits.bed INFO @ Mon, 03 Jun 2019 05:32:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1437 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:32:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:32:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:32:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.20_summits.bed INFO @ Mon, 03 Jun 2019 05:32:43: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (853 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:32:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:32:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:32:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197570/SRX197570.05_summits.bed INFO @ Mon, 03 Jun 2019 05:32:45: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2385 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。