Job ID = 1295116 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,900,825 reads read : 35,900,825 reads written : 35,900,825 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: 00:05:53 35900825 reads; of these: 35900825 (100.00%) were unpaired; of these: 15627007 (43.53%) aligned 0 times 18012860 (50.17%) aligned exactly 1 time 2260958 (6.30%) aligned >1 times 56.47% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 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] 10127407 / 20273818 = 0.4995 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 12:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.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 12:18:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:18:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.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 12:18:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:18:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.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 12:18:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:18:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:18:44: 1000000 INFO @ Mon, 03 Jun 2019 12:18:44: 1000000 INFO @ Mon, 03 Jun 2019 12:18:45: 1000000 INFO @ Mon, 03 Jun 2019 12:18:52: 2000000 INFO @ Mon, 03 Jun 2019 12:18:52: 2000000 INFO @ Mon, 03 Jun 2019 12:18:53: 2000000 INFO @ Mon, 03 Jun 2019 12:18:59: 3000000 INFO @ Mon, 03 Jun 2019 12:18:59: 3000000 INFO @ Mon, 03 Jun 2019 12:19:01: 3000000 INFO @ Mon, 03 Jun 2019 12:19:06: 4000000 INFO @ Mon, 03 Jun 2019 12:19:06: 4000000 INFO @ Mon, 03 Jun 2019 12:19:09: 4000000 INFO @ Mon, 03 Jun 2019 12:19:13: 5000000 INFO @ Mon, 03 Jun 2019 12:19:14: 5000000 INFO @ Mon, 03 Jun 2019 12:19:17: 5000000 INFO @ Mon, 03 Jun 2019 12:19:20: 6000000 INFO @ Mon, 03 Jun 2019 12:19:21: 6000000 INFO @ Mon, 03 Jun 2019 12:19:24: 6000000 INFO @ Mon, 03 Jun 2019 12:19:28: 7000000 INFO @ Mon, 03 Jun 2019 12:19:28: 7000000 INFO @ Mon, 03 Jun 2019 12:19:32: 7000000 INFO @ Mon, 03 Jun 2019 12:19:35: 8000000 INFO @ Mon, 03 Jun 2019 12:19:35: 8000000 INFO @ Mon, 03 Jun 2019 12:19:40: 8000000 INFO @ Mon, 03 Jun 2019 12:19:42: 9000000 INFO @ Mon, 03 Jun 2019 12:19:42: 9000000 INFO @ Mon, 03 Jun 2019 12:19:48: 9000000 INFO @ Mon, 03 Jun 2019 12:19:49: 10000000 INFO @ Mon, 03 Jun 2019 12:19:49: 10000000 INFO @ Mon, 03 Jun 2019 12:19:50: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 12:19:50: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 12:19:50: #1 total tags in treatment: 10146411 INFO @ Mon, 03 Jun 2019 12:19:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:19:50: #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 12:19:50: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 12:19:50: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 12:19:50: #1 total tags in treatment: 10146411 INFO @ Mon, 03 Jun 2019 12:19:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:19:50: #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 12:19:50: #1 tags after filtering in treatment: 10146411 INFO @ Mon, 03 Jun 2019 12:19:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:19:50: #1 finished! INFO @ Mon, 03 Jun 2019 12:19:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:19:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:19:50: #1 tags after filtering in treatment: 10146411 INFO @ Mon, 03 Jun 2019 12:19:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:19:50: #1 finished! INFO @ Mon, 03 Jun 2019 12:19:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:19:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:19:51: #2 number of paired peaks: 757 WARNING @ Mon, 03 Jun 2019 12:19:51: Fewer paired peaks (757) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 757 pairs to build model! INFO @ Mon, 03 Jun 2019 12:19:51: start model_add_line... INFO @ Mon, 03 Jun 2019 12:19:51: #2 number of paired peaks: 757 WARNING @ Mon, 03 Jun 2019 12:19:51: Fewer paired peaks (757) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 757 pairs to build model! INFO @ Mon, 03 Jun 2019 12:19:51: start model_add_line... INFO @ Mon, 03 Jun 2019 12:19:51: start X-correlation... INFO @ Mon, 03 Jun 2019 12:19:51: end of X-cor INFO @ Mon, 03 Jun 2019 12:19:51: #2 finished! INFO @ Mon, 03 Jun 2019 12:19:51: #2 predicted fragment length is 233 bps INFO @ Mon, 03 Jun 2019 12:19:51: #2 alternative fragment length(s) may be 233 bps INFO @ Mon, 03 Jun 2019 12:19:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.10_model.r INFO @ Mon, 03 Jun 2019 12:19:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:19:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:19:51: start X-correlation... INFO @ Mon, 03 Jun 2019 12:19:51: end of X-cor INFO @ Mon, 03 Jun 2019 12:19:51: #2 finished! INFO @ Mon, 03 Jun 2019 12:19:51: #2 predicted fragment length is 233 bps INFO @ Mon, 03 Jun 2019 12:19:51: #2 alternative fragment length(s) may be 233 bps INFO @ Mon, 03 Jun 2019 12:19:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.20_model.r INFO @ Mon, 03 Jun 2019 12:19:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:19:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:19:55: 10000000 INFO @ Mon, 03 Jun 2019 12:19:56: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 12:19:56: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 12:19:56: #1 total tags in treatment: 10146411 INFO @ Mon, 03 Jun 2019 12:19:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:19:56: #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 12:19:56: #1 tags after filtering in treatment: 10146411 INFO @ Mon, 03 Jun 2019 12:19:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:19:56: #1 finished! INFO @ Mon, 03 Jun 2019 12:19:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:19:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:19:57: #2 number of paired peaks: 757 WARNING @ Mon, 03 Jun 2019 12:19:57: Fewer paired peaks (757) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 757 pairs to build model! INFO @ Mon, 03 Jun 2019 12:19:57: start model_add_line... INFO @ Mon, 03 Jun 2019 12:19:58: start X-correlation... INFO @ Mon, 03 Jun 2019 12:19:58: end of X-cor INFO @ Mon, 03 Jun 2019 12:19:58: #2 finished! INFO @ Mon, 03 Jun 2019 12:19:58: #2 predicted fragment length is 233 bps INFO @ Mon, 03 Jun 2019 12:19:58: #2 alternative fragment length(s) may be 233 bps INFO @ Mon, 03 Jun 2019 12:19:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.05_model.r INFO @ Mon, 03 Jun 2019 12:19:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:19:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:20:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:20:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:20:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:20:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:20:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:20:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.20_summits.bed INFO @ Mon, 03 Jun 2019 12:20:37: Done! INFO @ Mon, 03 Jun 2019 12:20:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.10_peaks.xls pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2450 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:20:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:20:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.10_summits.bed INFO @ Mon, 03 Jun 2019 12:20:37: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6138 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX319058/SRX319058.05_summits.bed INFO @ Mon, 03 Jun 2019 12:20:44: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (12988 records, 4 fields): 158 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。