Job ID = 1292816 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,076,562 reads read : 19,076,562 reads written : 19,076,562 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: 00:03:46 19076562 reads; of these: 19076562 (100.00%) were unpaired; of these: 3278950 (17.19%) aligned 0 times 13416392 (70.33%) aligned exactly 1 time 2381220 (12.48%) aligned >1 times 82.81% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 5713890 / 15797612 = 0.3617 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 @ Sun, 02 Jun 2019 21:00:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 21:00:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:00:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:00:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 21:00:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:00:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:00:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 21:00:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:00:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:00:41: 1000000 INFO @ Sun, 02 Jun 2019 21:00:41: 1000000 INFO @ Sun, 02 Jun 2019 21:00:42: 1000000 INFO @ Sun, 02 Jun 2019 21:00:48: 2000000 INFO @ Sun, 02 Jun 2019 21:00:48: 2000000 INFO @ Sun, 02 Jun 2019 21:00:50: 2000000 INFO @ Sun, 02 Jun 2019 21:00:55: 3000000 INFO @ Sun, 02 Jun 2019 21:00:56: 3000000 INFO @ Sun, 02 Jun 2019 21:00:58: 3000000 INFO @ Sun, 02 Jun 2019 21:01:03: 4000000 INFO @ Sun, 02 Jun 2019 21:01:04: 4000000 INFO @ Sun, 02 Jun 2019 21:01:05: 4000000 INFO @ Sun, 02 Jun 2019 21:01:11: 5000000 INFO @ Sun, 02 Jun 2019 21:01:12: 5000000 INFO @ Sun, 02 Jun 2019 21:01:13: 5000000 INFO @ Sun, 02 Jun 2019 21:01:18: 6000000 INFO @ Sun, 02 Jun 2019 21:01:19: 6000000 INFO @ Sun, 02 Jun 2019 21:01:21: 6000000 INFO @ Sun, 02 Jun 2019 21:01:26: 7000000 INFO @ Sun, 02 Jun 2019 21:01:27: 7000000 INFO @ Sun, 02 Jun 2019 21:01:29: 7000000 INFO @ Sun, 02 Jun 2019 21:01:34: 8000000 INFO @ Sun, 02 Jun 2019 21:01:35: 8000000 INFO @ Sun, 02 Jun 2019 21:01:37: 8000000 INFO @ Sun, 02 Jun 2019 21:01:41: 9000000 INFO @ Sun, 02 Jun 2019 21:01:42: 9000000 INFO @ Sun, 02 Jun 2019 21:01:44: 9000000 INFO @ Sun, 02 Jun 2019 21:01:49: 10000000 INFO @ Sun, 02 Jun 2019 21:01:49: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:01:49: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:01:49: #1 total tags in treatment: 10083722 INFO @ Sun, 02 Jun 2019 21:01:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:01:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:01:50: #1 tags after filtering in treatment: 10083722 INFO @ Sun, 02 Jun 2019 21:01:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:01:50: #1 finished! INFO @ Sun, 02 Jun 2019 21:01:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:01:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:01:50: 10000000 INFO @ Sun, 02 Jun 2019 21:01:50: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:01:50: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:01:50: #1 total tags in treatment: 10083722 INFO @ Sun, 02 Jun 2019 21:01:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:01:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:01:51: #1 tags after filtering in treatment: 10083722 INFO @ Sun, 02 Jun 2019 21:01:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:01:51: #1 finished! INFO @ Sun, 02 Jun 2019 21:01:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:01:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:01:51: #2 number of paired peaks: 753 WARNING @ Sun, 02 Jun 2019 21:01:51: Fewer paired peaks (753) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 753 pairs to build model! INFO @ Sun, 02 Jun 2019 21:01:51: start model_add_line... INFO @ Sun, 02 Jun 2019 21:01:51: start X-correlation... INFO @ Sun, 02 Jun 2019 21:01:51: end of X-cor INFO @ Sun, 02 Jun 2019 21:01:51: #2 finished! INFO @ Sun, 02 Jun 2019 21:01:51: #2 predicted fragment length is 219 bps INFO @ Sun, 02 Jun 2019 21:01:51: #2 alternative fragment length(s) may be 219 bps INFO @ Sun, 02 Jun 2019 21:01:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.05_model.r INFO @ Sun, 02 Jun 2019 21:01:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:01:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:01:51: #2 number of paired peaks: 753 WARNING @ Sun, 02 Jun 2019 21:01:51: Fewer paired peaks (753) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 753 pairs to build model! INFO @ Sun, 02 Jun 2019 21:01:51: start model_add_line... INFO @ Sun, 02 Jun 2019 21:01:52: start X-correlation... INFO @ Sun, 02 Jun 2019 21:01:52: end of X-cor INFO @ Sun, 02 Jun 2019 21:01:52: #2 finished! INFO @ Sun, 02 Jun 2019 21:01:52: #2 predicted fragment length is 219 bps INFO @ Sun, 02 Jun 2019 21:01:52: #2 alternative fragment length(s) may be 219 bps INFO @ Sun, 02 Jun 2019 21:01:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.10_model.r INFO @ Sun, 02 Jun 2019 21:01:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:01:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:01:52: 10000000 INFO @ Sun, 02 Jun 2019 21:01:53: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:01:53: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:01:53: #1 total tags in treatment: 10083722 INFO @ Sun, 02 Jun 2019 21:01:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:01:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:01:53: #1 tags after filtering in treatment: 10083722 INFO @ Sun, 02 Jun 2019 21:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:01:53: #1 finished! INFO @ Sun, 02 Jun 2019 21:01:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:01:54: #2 number of paired peaks: 753 WARNING @ Sun, 02 Jun 2019 21:01:54: Fewer paired peaks (753) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 753 pairs to build model! INFO @ Sun, 02 Jun 2019 21:01:54: start model_add_line... INFO @ Sun, 02 Jun 2019 21:01:54: start X-correlation... INFO @ Sun, 02 Jun 2019 21:01:54: end of X-cor INFO @ Sun, 02 Jun 2019 21:01:54: #2 finished! INFO @ Sun, 02 Jun 2019 21:01:54: #2 predicted fragment length is 219 bps INFO @ Sun, 02 Jun 2019 21:01:54: #2 alternative fragment length(s) may be 219 bps INFO @ Sun, 02 Jun 2019 21:01:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.20_model.r INFO @ Sun, 02 Jun 2019 21:01:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:01:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:02:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:02:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:02:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:02:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:02:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:02:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.05_summits.bed INFO @ Sun, 02 Jun 2019 21:02:37: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2814 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:02:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:02:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:02:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.10_summits.bed INFO @ Sun, 02 Jun 2019 21:02:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1642 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:02:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:02:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:02:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495060/SRX495060.20_summits.bed INFO @ Sun, 02 Jun 2019 21:02:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (903 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。