Job ID = 1291817 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,982,884 reads read : 11,982,884 reads written : 11,982,884 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: 00:03:59 11982884 reads; of these: 11982884 (100.00%) were unpaired; of these: 1115212 (9.31%) aligned 0 times 9281182 (77.45%) aligned exactly 1 time 1586490 (13.24%) aligned >1 times 90.69% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1917980 / 10867672 = 0.1765 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 16:47:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.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 16:47:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:47:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:47:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.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 16:47:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:47:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:47:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.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 16:47:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:47:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:47:30: 1000000 INFO @ Sun, 02 Jun 2019 16:47:31: 1000000 INFO @ Sun, 02 Jun 2019 16:47:31: 1000000 INFO @ Sun, 02 Jun 2019 16:47:37: 2000000 INFO @ Sun, 02 Jun 2019 16:47:39: 2000000 INFO @ Sun, 02 Jun 2019 16:47:39: 2000000 INFO @ Sun, 02 Jun 2019 16:47:45: 3000000 INFO @ Sun, 02 Jun 2019 16:47:48: 3000000 INFO @ Sun, 02 Jun 2019 16:47:48: 3000000 INFO @ Sun, 02 Jun 2019 16:47:53: 4000000 INFO @ Sun, 02 Jun 2019 16:47:56: 4000000 INFO @ Sun, 02 Jun 2019 16:47:56: 4000000 INFO @ Sun, 02 Jun 2019 16:48:01: 5000000 INFO @ Sun, 02 Jun 2019 16:48:05: 5000000 INFO @ Sun, 02 Jun 2019 16:48:05: 5000000 INFO @ Sun, 02 Jun 2019 16:48:08: 6000000 INFO @ Sun, 02 Jun 2019 16:48:13: 6000000 INFO @ Sun, 02 Jun 2019 16:48:13: 6000000 INFO @ Sun, 02 Jun 2019 16:48:16: 7000000 INFO @ Sun, 02 Jun 2019 16:48:22: 7000000 INFO @ Sun, 02 Jun 2019 16:48:22: 7000000 INFO @ Sun, 02 Jun 2019 16:48:24: 8000000 INFO @ Sun, 02 Jun 2019 16:48:30: 8000000 INFO @ Sun, 02 Jun 2019 16:48:30: 8000000 INFO @ Sun, 02 Jun 2019 16:48:32: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 16:48:32: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 16:48:32: #1 total tags in treatment: 8949692 INFO @ Sun, 02 Jun 2019 16:48:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:32: #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 16:48:32: #1 tags after filtering in treatment: 8949692 INFO @ Sun, 02 Jun 2019 16:48:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:32: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:33: #2 number of paired peaks: 802 WARNING @ Sun, 02 Jun 2019 16:48:33: Fewer paired peaks (802) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 802 pairs to build model! INFO @ Sun, 02 Jun 2019 16:48:33: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:33: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:33: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:33: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:33: #2 predicted fragment length is 154 bps INFO @ Sun, 02 Jun 2019 16:48:33: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 02 Jun 2019 16:48:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.20_model.r INFO @ Sun, 02 Jun 2019 16:48:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:38: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 16:48:38: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 16:48:38: #1 total tags in treatment: 8949692 INFO @ Sun, 02 Jun 2019 16:48:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:38: #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 16:48:38: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 16:48:38: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 16:48:38: #1 total tags in treatment: 8949692 INFO @ Sun, 02 Jun 2019 16:48:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:48:38: #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 16:48:38: #1 tags after filtering in treatment: 8949692 INFO @ Sun, 02 Jun 2019 16:48:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:38: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:38: #1 tags after filtering in treatment: 8949692 INFO @ Sun, 02 Jun 2019 16:48:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:48:38: #1 finished! INFO @ Sun, 02 Jun 2019 16:48:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:48:39: #2 number of paired peaks: 802 WARNING @ Sun, 02 Jun 2019 16:48:39: Fewer paired peaks (802) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 802 pairs to build model! INFO @ Sun, 02 Jun 2019 16:48:39: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:39: #2 number of paired peaks: 802 WARNING @ Sun, 02 Jun 2019 16:48:39: Fewer paired peaks (802) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 802 pairs to build model! INFO @ Sun, 02 Jun 2019 16:48:39: start model_add_line... INFO @ Sun, 02 Jun 2019 16:48:39: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:39: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:39: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:39: #2 predicted fragment length is 154 bps INFO @ Sun, 02 Jun 2019 16:48:39: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 02 Jun 2019 16:48:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.10_model.r INFO @ Sun, 02 Jun 2019 16:48:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:39: start X-correlation... INFO @ Sun, 02 Jun 2019 16:48:39: end of X-cor INFO @ Sun, 02 Jun 2019 16:48:39: #2 finished! INFO @ Sun, 02 Jun 2019 16:48:39: #2 predicted fragment length is 154 bps INFO @ Sun, 02 Jun 2019 16:48:39: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 02 Jun 2019 16:48:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.05_model.r INFO @ Sun, 02 Jun 2019 16:48:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:48:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:49:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.20_summits.bed INFO @ Sun, 02 Jun 2019 16:49:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (766 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:49:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.10_summits.bed INFO @ Sun, 02 Jun 2019 16:49:19: Done! INFO @ Sun, 02 Jun 2019 16:49:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:49:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:49:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257658/SRX257658.05_summits.bed INFO @ Sun, 02 Jun 2019 16:49:20: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1207 records, 4 fields): 6 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1819 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。