Job ID = 1292310 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,236,336 reads read : 12,236,336 reads written : 12,236,336 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: 00:03:33 12236336 reads; of these: 12236336 (100.00%) were unpaired; of these: 1095262 (8.95%) aligned 0 times 7136091 (58.32%) aligned exactly 1 time 4004983 (32.73%) aligned >1 times 91.05% overall alignment rate Time searching: 00:03:33 Overall time: 00:03:33 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] 6816741 / 11141074 = 0.6119 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 18:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.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 18:06:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:06:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.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 18:06:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:06:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.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 18:06:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:06:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:06:29: 1000000 INFO @ Sun, 02 Jun 2019 18:06:30: 1000000 INFO @ Sun, 02 Jun 2019 18:06:31: 1000000 INFO @ Sun, 02 Jun 2019 18:06:39: 2000000 INFO @ Sun, 02 Jun 2019 18:06:41: 2000000 INFO @ Sun, 02 Jun 2019 18:06:43: 2000000 INFO @ Sun, 02 Jun 2019 18:06:49: 3000000 INFO @ Sun, 02 Jun 2019 18:06:51: 3000000 INFO @ Sun, 02 Jun 2019 18:06:54: 3000000 INFO @ Sun, 02 Jun 2019 18:06:59: 4000000 INFO @ Sun, 02 Jun 2019 18:07:01: 4000000 INFO @ Sun, 02 Jun 2019 18:07:02: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:07:02: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:07:02: #1 total tags in treatment: 4324333 INFO @ Sun, 02 Jun 2019 18:07:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:07:02: #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 18:07:02: #1 tags after filtering in treatment: 4324333 INFO @ Sun, 02 Jun 2019 18:07:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:07:02: #1 finished! INFO @ Sun, 02 Jun 2019 18:07:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:07:03: #2 number of paired peaks: 5765 INFO @ Sun, 02 Jun 2019 18:07:03: start model_add_line... INFO @ Sun, 02 Jun 2019 18:07:03: start X-correlation... INFO @ Sun, 02 Jun 2019 18:07:03: end of X-cor INFO @ Sun, 02 Jun 2019 18:07:03: #2 finished! INFO @ Sun, 02 Jun 2019 18:07:03: #2 predicted fragment length is 211 bps INFO @ Sun, 02 Jun 2019 18:07:03: #2 alternative fragment length(s) may be 2,211 bps INFO @ Sun, 02 Jun 2019 18:07:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.20_model.r INFO @ Sun, 02 Jun 2019 18:07:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:07:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:07:05: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:07:05: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:07:05: #1 total tags in treatment: 4324333 INFO @ Sun, 02 Jun 2019 18:07:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:07:05: #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 18:07:05: #1 tags after filtering in treatment: 4324333 INFO @ Sun, 02 Jun 2019 18:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:07:05: #1 finished! INFO @ Sun, 02 Jun 2019 18:07:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:07:06: #2 number of paired peaks: 5765 INFO @ Sun, 02 Jun 2019 18:07:06: start model_add_line... INFO @ Sun, 02 Jun 2019 18:07:06: start X-correlation... INFO @ Sun, 02 Jun 2019 18:07:06: end of X-cor INFO @ Sun, 02 Jun 2019 18:07:06: #2 finished! INFO @ Sun, 02 Jun 2019 18:07:06: #2 predicted fragment length is 211 bps INFO @ Sun, 02 Jun 2019 18:07:06: #2 alternative fragment length(s) may be 2,211 bps INFO @ Sun, 02 Jun 2019 18:07:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.10_model.r INFO @ Sun, 02 Jun 2019 18:07:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:07:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:07:06: 4000000 INFO @ Sun, 02 Jun 2019 18:07:10: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:07:10: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:07:10: #1 total tags in treatment: 4324333 INFO @ Sun, 02 Jun 2019 18:07:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:07:10: #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 18:07:10: #1 tags after filtering in treatment: 4324333 INFO @ Sun, 02 Jun 2019 18:07:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:07:10: #1 finished! INFO @ Sun, 02 Jun 2019 18:07:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:07:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:07:11: #2 number of paired peaks: 5765 INFO @ Sun, 02 Jun 2019 18:07:11: start model_add_line... INFO @ Sun, 02 Jun 2019 18:07:11: start X-correlation... INFO @ Sun, 02 Jun 2019 18:07:11: end of X-cor INFO @ Sun, 02 Jun 2019 18:07:11: #2 finished! INFO @ Sun, 02 Jun 2019 18:07:11: #2 predicted fragment length is 211 bps INFO @ Sun, 02 Jun 2019 18:07:11: #2 alternative fragment length(s) may be 2,211 bps INFO @ Sun, 02 Jun 2019 18:07:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.05_model.r INFO @ Sun, 02 Jun 2019 18:07:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:07:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:07:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:07:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:07:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:07:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:07:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:07:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.20_summits.bed INFO @ Sun, 02 Jun 2019 18:07:34: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (369 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:07:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:07:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:07:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.10_summits.bed INFO @ Sun, 02 Jun 2019 18:07:36: Done! BedGraph に変換しました。 pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (925 records, 4 fields): 5 millis BigWig に変換中... CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:07:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:07:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:07:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331335/SRX331335.05_summits.bed INFO @ Sun, 02 Jun 2019 18:07:40: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2006 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。