Job ID = 4178224 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,715,159 reads read : 14,715,159 reads written : 14,715,159 rm: cannot remove ‘[DSE]RR*’: 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: 00:02:24 14715159 reads; of these: 14715159 (100.00%) were unpaired; of these: 7055372 (47.95%) aligned 0 times 6125411 (41.63%) aligned exactly 1 time 1534376 (10.43%) aligned >1 times 52.05% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 1554038 / 7659787 = 0.2029 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:28:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.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 @ Thu, 05 Dec 2019 12:28:49: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:28:49: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:28:57: 1000000 INFO @ Thu, 05 Dec 2019 12:29:05: 2000000 INFO @ Thu, 05 Dec 2019 12:29:13: 3000000 INFO @ Thu, 05 Dec 2019 12:29:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.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 @ Thu, 05 Dec 2019 12:29:15: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:15: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:20: 4000000 INFO @ Thu, 05 Dec 2019 12:29:24: 1000000 INFO @ Thu, 05 Dec 2019 12:29:28: 5000000 INFO @ Thu, 05 Dec 2019 12:29:33: 2000000 INFO @ Thu, 05 Dec 2019 12:29:36: 6000000 INFO @ Thu, 05 Dec 2019 12:29:37: #1 tag size is determined as 49 bps INFO @ Thu, 05 Dec 2019 12:29:37: #1 tag size = 49 INFO @ Thu, 05 Dec 2019 12:29:37: #1 total tags in treatment: 6105749 INFO @ Thu, 05 Dec 2019 12:29:37: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:29:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:29:37: #1 tags after filtering in treatment: 6105749 INFO @ Thu, 05 Dec 2019 12:29:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:29:37: #1 finished! INFO @ Thu, 05 Dec 2019 12:29:37: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:29:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:29:38: #2 number of paired peaks: 2511 INFO @ Thu, 05 Dec 2019 12:29:38: start model_add_line... INFO @ Thu, 05 Dec 2019 12:29:38: start X-correlation... INFO @ Thu, 05 Dec 2019 12:29:38: end of X-cor INFO @ Thu, 05 Dec 2019 12:29:38: #2 finished! INFO @ Thu, 05 Dec 2019 12:29:38: #2 predicted fragment length is 153 bps INFO @ Thu, 05 Dec 2019 12:29:38: #2 alternative fragment length(s) may be 153 bps INFO @ Thu, 05 Dec 2019 12:29:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.05_model.r INFO @ Thu, 05 Dec 2019 12:29:38: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:29:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:29:42: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:29:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.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 @ Thu, 05 Dec 2019 12:29:45: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:45: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:50: 4000000 INFO @ Thu, 05 Dec 2019 12:29:54: 1000000 INFO @ Thu, 05 Dec 2019 12:29:59: 5000000 INFO @ Thu, 05 Dec 2019 12:29:59: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:30:03: 2000000 INFO @ Thu, 05 Dec 2019 12:30:08: 6000000 INFO @ Thu, 05 Dec 2019 12:30:09: #1 tag size is determined as 49 bps INFO @ Thu, 05 Dec 2019 12:30:09: #1 tag size = 49 INFO @ Thu, 05 Dec 2019 12:30:09: #1 total tags in treatment: 6105749 INFO @ Thu, 05 Dec 2019 12:30:09: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:30:09: #1 tags after filtering in treatment: 6105749 INFO @ Thu, 05 Dec 2019 12:30:09: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:30:09: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:09: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:10: #2 number of paired peaks: 2511 INFO @ Thu, 05 Dec 2019 12:30:10: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:10: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:10: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:10: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:10: #2 predicted fragment length is 153 bps INFO @ Thu, 05 Dec 2019 12:30:10: #2 alternative fragment length(s) may be 153 bps INFO @ Thu, 05 Dec 2019 12:30:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.10_model.r INFO @ Thu, 05 Dec 2019 12:30:10: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:30:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:30:11: 3000000 INFO @ Thu, 05 Dec 2019 12:30:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:30:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.05_summits.bed INFO @ Thu, 05 Dec 2019 12:30:14: Done! pass1 - making usageList (7 chroms): 11 millis pass2 - checking and writing primary data (6371 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:30:20: 4000000 INFO @ Thu, 05 Dec 2019 12:30:28: 5000000 INFO @ Thu, 05 Dec 2019 12:30:30: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:30:37: 6000000 INFO @ Thu, 05 Dec 2019 12:30:38: #1 tag size is determined as 49 bps INFO @ Thu, 05 Dec 2019 12:30:38: #1 tag size = 49 INFO @ Thu, 05 Dec 2019 12:30:38: #1 total tags in treatment: 6105749 INFO @ Thu, 05 Dec 2019 12:30:38: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:30:38: #1 tags after filtering in treatment: 6105749 INFO @ Thu, 05 Dec 2019 12:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:30:38: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:38: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:38: #2 number of paired peaks: 2511 INFO @ Thu, 05 Dec 2019 12:30:38: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:39: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:39: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:39: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:39: #2 predicted fragment length is 153 bps INFO @ Thu, 05 Dec 2019 12:30:39: #2 alternative fragment length(s) may be 153 bps INFO @ Thu, 05 Dec 2019 12:30:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.20_model.r INFO @ Thu, 05 Dec 2019 12:30:39: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:30:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:30:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:30:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.10_summits.bed INFO @ Thu, 05 Dec 2019 12:30:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3757 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:30:59: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107864/SRX4107864.20_summits.bed INFO @ Thu, 05 Dec 2019 12:31:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1485 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。