Job ID = 1292339 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,468,938 reads read : 13,468,938 reads written : 13,468,938 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: 00:04:15 13468938 reads; of these: 13468938 (100.00%) were unpaired; of these: 573056 (4.25%) aligned 0 times 10416864 (77.34%) aligned exactly 1 time 2479018 (18.41%) aligned >1 times 95.75% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 2437148 / 12895882 = 0.1890 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 18:02:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.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 18:02:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:02:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:02:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.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 18:02:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:02:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:02:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.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 18:02:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:02:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:03:10: 1000000 INFO @ Sun, 02 Jun 2019 18:03:10: 1000000 INFO @ Sun, 02 Jun 2019 18:03:11: 1000000 INFO @ Sun, 02 Jun 2019 18:03:23: 2000000 INFO @ Sun, 02 Jun 2019 18:03:23: 2000000 INFO @ Sun, 02 Jun 2019 18:03:24: 2000000 INFO @ Sun, 02 Jun 2019 18:03:35: 3000000 INFO @ Sun, 02 Jun 2019 18:03:36: 3000000 INFO @ Sun, 02 Jun 2019 18:03:36: 3000000 INFO @ Sun, 02 Jun 2019 18:03:47: 4000000 INFO @ Sun, 02 Jun 2019 18:03:47: 4000000 INFO @ Sun, 02 Jun 2019 18:03:47: 4000000 INFO @ Sun, 02 Jun 2019 18:03:59: 5000000 INFO @ Sun, 02 Jun 2019 18:03:59: 5000000 INFO @ Sun, 02 Jun 2019 18:04:00: 5000000 INFO @ Sun, 02 Jun 2019 18:04:10: 6000000 INFO @ Sun, 02 Jun 2019 18:04:11: 6000000 INFO @ Sun, 02 Jun 2019 18:04:12: 6000000 INFO @ Sun, 02 Jun 2019 18:04:22: 7000000 INFO @ Sun, 02 Jun 2019 18:04:23: 7000000 INFO @ Sun, 02 Jun 2019 18:04:24: 7000000 INFO @ Sun, 02 Jun 2019 18:04:33: 8000000 INFO @ Sun, 02 Jun 2019 18:04:34: 8000000 INFO @ Sun, 02 Jun 2019 18:04:36: 8000000 INFO @ Sun, 02 Jun 2019 18:04:44: 9000000 INFO @ Sun, 02 Jun 2019 18:04:45: 9000000 INFO @ Sun, 02 Jun 2019 18:04:48: 9000000 INFO @ Sun, 02 Jun 2019 18:04:55: 10000000 INFO @ Sun, 02 Jun 2019 18:04:57: 10000000 INFO @ Sun, 02 Jun 2019 18:05:00: 10000000 INFO @ Sun, 02 Jun 2019 18:05:00: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:05:00: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:05:00: #1 total tags in treatment: 10458734 INFO @ Sun, 02 Jun 2019 18:05:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:05:00: #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 18:05:00: #1 tags after filtering in treatment: 10458734 INFO @ Sun, 02 Jun 2019 18:05:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:05:00: #1 finished! INFO @ Sun, 02 Jun 2019 18:05:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:05:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:05:01: #2 number of paired peaks: 584 WARNING @ Sun, 02 Jun 2019 18:05:01: Fewer paired peaks (584) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 584 pairs to build model! INFO @ Sun, 02 Jun 2019 18:05:01: start model_add_line... INFO @ Sun, 02 Jun 2019 18:05:02: start X-correlation... INFO @ Sun, 02 Jun 2019 18:05:02: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:05:02: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:05:02: end of X-cor INFO @ Sun, 02 Jun 2019 18:05:02: #1 total tags in treatment: 10458734 INFO @ Sun, 02 Jun 2019 18:05:02: #2 finished! INFO @ Sun, 02 Jun 2019 18:05:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:05:02: #2 predicted fragment length is 107 bps INFO @ Sun, 02 Jun 2019 18:05:02: #2 alternative fragment length(s) may be 4,107 bps INFO @ Sun, 02 Jun 2019 18:05:02: #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 18:05:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.10_model.r INFO @ Sun, 02 Jun 2019 18:05:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:05:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:05:02: #1 tags after filtering in treatment: 10458734 INFO @ Sun, 02 Jun 2019 18:05:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:05:02: #1 finished! INFO @ Sun, 02 Jun 2019 18:05:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:05:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:05:03: #2 number of paired peaks: 584 WARNING @ Sun, 02 Jun 2019 18:05:03: Fewer paired peaks (584) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 584 pairs to build model! INFO @ Sun, 02 Jun 2019 18:05:03: start model_add_line... INFO @ Sun, 02 Jun 2019 18:05:03: start X-correlation... INFO @ Sun, 02 Jun 2019 18:05:03: end of X-cor INFO @ Sun, 02 Jun 2019 18:05:03: #2 finished! INFO @ Sun, 02 Jun 2019 18:05:03: #2 predicted fragment length is 107 bps INFO @ Sun, 02 Jun 2019 18:05:03: #2 alternative fragment length(s) may be 4,107 bps INFO @ Sun, 02 Jun 2019 18:05:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.20_model.r INFO @ Sun, 02 Jun 2019 18:05:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:05:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:05:05: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:05:05: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:05:05: #1 total tags in treatment: 10458734 INFO @ Sun, 02 Jun 2019 18:05:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:05:05: #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 18:05:05: #1 tags after filtering in treatment: 10458734 INFO @ Sun, 02 Jun 2019 18:05:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:05:05: #1 finished! INFO @ Sun, 02 Jun 2019 18:05:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:05:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:05:07: #2 number of paired peaks: 584 WARNING @ Sun, 02 Jun 2019 18:05:07: Fewer paired peaks (584) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 584 pairs to build model! INFO @ Sun, 02 Jun 2019 18:05:07: start model_add_line... INFO @ Sun, 02 Jun 2019 18:05:07: start X-correlation... INFO @ Sun, 02 Jun 2019 18:05:07: end of X-cor INFO @ Sun, 02 Jun 2019 18:05:07: #2 finished! INFO @ Sun, 02 Jun 2019 18:05:07: #2 predicted fragment length is 107 bps INFO @ Sun, 02 Jun 2019 18:05:07: #2 alternative fragment length(s) may be 4,107 bps INFO @ Sun, 02 Jun 2019 18:05:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.05_model.r INFO @ Sun, 02 Jun 2019 18:05:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:05:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:05:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:05:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:05:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:06:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:06:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:06:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.10_summits.bed INFO @ Sun, 02 Jun 2019 18:06:06: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (1982 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:06:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:06:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:06:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.20_summits.bed INFO @ Sun, 02 Jun 2019 18:06:07: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (515 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:06:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:06:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:06:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331363/SRX331363.05_summits.bed INFO @ Sun, 02 Jun 2019 18:06:11: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6526 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。