Job ID = 1292773 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,972,845 reads read : 6,972,845 reads written : 6,972,845 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: 00:01:29 6972845 reads; of these: 6972845 (100.00%) were unpaired; of these: 197145 (2.83%) aligned 0 times 5677413 (81.42%) aligned exactly 1 time 1098287 (15.75%) aligned >1 times 97.17% overall alignment rate Time searching: 00:01:29 Overall time: 00:01:29 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] 1899279 / 6775700 = 0.2803 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 20:24:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.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 20:24:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:24:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:24:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.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 20:24:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:24:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:24:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.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 20:24:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:24:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:25:00: 1000000 INFO @ Sun, 02 Jun 2019 20:25:02: 1000000 INFO @ Sun, 02 Jun 2019 20:25:03: 1000000 INFO @ Sun, 02 Jun 2019 20:25:07: 2000000 INFO @ Sun, 02 Jun 2019 20:25:11: 2000000 INFO @ Sun, 02 Jun 2019 20:25:13: 2000000 INFO @ Sun, 02 Jun 2019 20:25:14: 3000000 INFO @ Sun, 02 Jun 2019 20:25:19: 3000000 INFO @ Sun, 02 Jun 2019 20:25:21: 4000000 INFO @ Sun, 02 Jun 2019 20:25:24: 3000000 INFO @ Sun, 02 Jun 2019 20:25:27: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:25:27: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:25:27: #1 total tags in treatment: 4876421 INFO @ Sun, 02 Jun 2019 20:25:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:25:27: #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 20:25:27: #1 tags after filtering in treatment: 4876421 INFO @ Sun, 02 Jun 2019 20:25:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:25:27: #1 finished! INFO @ Sun, 02 Jun 2019 20:25:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:25:28: #2 number of paired peaks: 3889 INFO @ Sun, 02 Jun 2019 20:25:28: start model_add_line... INFO @ Sun, 02 Jun 2019 20:25:28: 4000000 INFO @ Sun, 02 Jun 2019 20:25:28: start X-correlation... INFO @ Sun, 02 Jun 2019 20:25:28: end of X-cor INFO @ Sun, 02 Jun 2019 20:25:28: #2 finished! INFO @ Sun, 02 Jun 2019 20:25:28: #2 predicted fragment length is 284 bps INFO @ Sun, 02 Jun 2019 20:25:28: #2 alternative fragment length(s) may be 284 bps INFO @ Sun, 02 Jun 2019 20:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.20_model.r INFO @ Sun, 02 Jun 2019 20:25:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:25:33: 4000000 INFO @ Sun, 02 Jun 2019 20:25:35: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:25:35: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:25:35: #1 total tags in treatment: 4876421 INFO @ Sun, 02 Jun 2019 20:25:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:25:35: #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 20:25:35: #1 tags after filtering in treatment: 4876421 INFO @ Sun, 02 Jun 2019 20:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:25:35: #1 finished! INFO @ Sun, 02 Jun 2019 20:25:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:25:36: #2 number of paired peaks: 3889 INFO @ Sun, 02 Jun 2019 20:25:36: start model_add_line... INFO @ Sun, 02 Jun 2019 20:25:36: start X-correlation... INFO @ Sun, 02 Jun 2019 20:25:36: end of X-cor INFO @ Sun, 02 Jun 2019 20:25:36: #2 finished! INFO @ Sun, 02 Jun 2019 20:25:36: #2 predicted fragment length is 284 bps INFO @ Sun, 02 Jun 2019 20:25:36: #2 alternative fragment length(s) may be 284 bps INFO @ Sun, 02 Jun 2019 20:25:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.05_model.r INFO @ Sun, 02 Jun 2019 20:25:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:25:42: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:25:42: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:25:42: #1 total tags in treatment: 4876421 INFO @ Sun, 02 Jun 2019 20:25:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:25:42: #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 20:25:42: #1 tags after filtering in treatment: 4876421 INFO @ Sun, 02 Jun 2019 20:25:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:25:42: #1 finished! INFO @ Sun, 02 Jun 2019 20:25:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:25:43: #2 number of paired peaks: 3889 INFO @ Sun, 02 Jun 2019 20:25:43: start model_add_line... INFO @ Sun, 02 Jun 2019 20:25:43: start X-correlation... INFO @ Sun, 02 Jun 2019 20:25:43: end of X-cor INFO @ Sun, 02 Jun 2019 20:25:43: #2 finished! INFO @ Sun, 02 Jun 2019 20:25:43: #2 predicted fragment length is 284 bps INFO @ Sun, 02 Jun 2019 20:25:43: #2 alternative fragment length(s) may be 284 bps INFO @ Sun, 02 Jun 2019 20:25:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.10_model.r INFO @ Sun, 02 Jun 2019 20:25:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:25:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:25:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.20_summits.bed INFO @ Sun, 02 Jun 2019 20:25:57: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1436 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:25:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:26:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.05_summits.bed INFO @ Sun, 02 Jun 2019 20:26:06: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6210 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:26:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:26:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:26:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495003/SRX495003.10_summits.bed INFO @ Sun, 02 Jun 2019 20:26:13: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3403 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。