Job ID = 1292988 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,732,587 reads read : 16,732,587 reads written : 16,732,587 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: 00:04:00 16732587 reads; of these: 16732587 (100.00%) were unpaired; of these: 1332473 (7.96%) aligned 0 times 12892493 (77.05%) aligned exactly 1 time 2507621 (14.99%) aligned >1 times 92.04% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 8434515 / 15400114 = 0.5477 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 21:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.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 21:23:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:23:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.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 21:23:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:23:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:23:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.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 21:23:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:23:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:23:48: 1000000 INFO @ Sun, 02 Jun 2019 21:23:49: 1000000 INFO @ Sun, 02 Jun 2019 21:23:50: 1000000 INFO @ Sun, 02 Jun 2019 21:23:55: 2000000 INFO @ Sun, 02 Jun 2019 21:23:56: 2000000 INFO @ Sun, 02 Jun 2019 21:23:58: 2000000 INFO @ Sun, 02 Jun 2019 21:24:01: 3000000 INFO @ Sun, 02 Jun 2019 21:24:03: 3000000 INFO @ Sun, 02 Jun 2019 21:24:06: 3000000 INFO @ Sun, 02 Jun 2019 21:24:08: 4000000 INFO @ Sun, 02 Jun 2019 21:24:10: 4000000 INFO @ Sun, 02 Jun 2019 21:24:14: 5000000 INFO @ Sun, 02 Jun 2019 21:24:15: 4000000 INFO @ Sun, 02 Jun 2019 21:24:17: 5000000 INFO @ Sun, 02 Jun 2019 21:24:21: 6000000 INFO @ Sun, 02 Jun 2019 21:24:23: 5000000 INFO @ Sun, 02 Jun 2019 21:24:25: 6000000 INFO @ Sun, 02 Jun 2019 21:24:27: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:24:27: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:24:27: #1 total tags in treatment: 6965599 INFO @ Sun, 02 Jun 2019 21:24:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:24:27: #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 21:24:28: #1 tags after filtering in treatment: 6965599 INFO @ Sun, 02 Jun 2019 21:24:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:24:28: #1 finished! INFO @ Sun, 02 Jun 2019 21:24:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:24:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:24:28: #2 number of paired peaks: 1067 INFO @ Sun, 02 Jun 2019 21:24:28: start model_add_line... INFO @ Sun, 02 Jun 2019 21:24:28: start X-correlation... INFO @ Sun, 02 Jun 2019 21:24:28: end of X-cor INFO @ Sun, 02 Jun 2019 21:24:28: #2 finished! INFO @ Sun, 02 Jun 2019 21:24:28: #2 predicted fragment length is 116 bps INFO @ Sun, 02 Jun 2019 21:24:28: #2 alternative fragment length(s) may be 4,116 bps INFO @ Sun, 02 Jun 2019 21:24:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.05_model.r INFO @ Sun, 02 Jun 2019 21:24:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:24:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:24:31: 6000000 INFO @ Sun, 02 Jun 2019 21:24:32: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:24:32: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:24:32: #1 total tags in treatment: 6965599 INFO @ Sun, 02 Jun 2019 21:24:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:24:32: #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 21:24:32: #1 tags after filtering in treatment: 6965599 INFO @ Sun, 02 Jun 2019 21:24:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:24:32: #1 finished! INFO @ Sun, 02 Jun 2019 21:24:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:24:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:24:33: #2 number of paired peaks: 1067 INFO @ Sun, 02 Jun 2019 21:24:33: start model_add_line... INFO @ Sun, 02 Jun 2019 21:24:33: start X-correlation... INFO @ Sun, 02 Jun 2019 21:24:33: end of X-cor INFO @ Sun, 02 Jun 2019 21:24:33: #2 finished! INFO @ Sun, 02 Jun 2019 21:24:33: #2 predicted fragment length is 116 bps INFO @ Sun, 02 Jun 2019 21:24:33: #2 alternative fragment length(s) may be 4,116 bps INFO @ Sun, 02 Jun 2019 21:24:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.20_model.r INFO @ Sun, 02 Jun 2019 21:24:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:24:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:24:39: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:24:39: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:24:39: #1 total tags in treatment: 6965599 INFO @ Sun, 02 Jun 2019 21:24:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:24:39: #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 21:24:39: #1 tags after filtering in treatment: 6965599 INFO @ Sun, 02 Jun 2019 21:24:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:24:39: #1 finished! INFO @ Sun, 02 Jun 2019 21:24:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:24:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:24:40: #2 number of paired peaks: 1067 INFO @ Sun, 02 Jun 2019 21:24:40: start model_add_line... INFO @ Sun, 02 Jun 2019 21:24:40: start X-correlation... INFO @ Sun, 02 Jun 2019 21:24:40: end of X-cor INFO @ Sun, 02 Jun 2019 21:24:40: #2 finished! INFO @ Sun, 02 Jun 2019 21:24:40: #2 predicted fragment length is 116 bps INFO @ Sun, 02 Jun 2019 21:24:40: #2 alternative fragment length(s) may be 4,116 bps INFO @ Sun, 02 Jun 2019 21:24:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.10_model.r INFO @ Sun, 02 Jun 2019 21:24:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:24:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:24:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:24:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:25:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:25:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:25:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.05_summits.bed INFO @ Sun, 02 Jun 2019 21:25:00: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2228 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:25:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:25:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:25:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:25:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.20_summits.bed INFO @ Sun, 02 Jun 2019 21:25:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (588 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020764/SRX5020764.10_summits.bed INFO @ Sun, 02 Jun 2019 21:25:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1153 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。