Job ID = 1294009 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,522,976 reads read : 11,522,976 reads written : 11,522,976 spots read : 11,522,976 reads read : 11,522,976 reads written : 11,522,976 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: 00:03:24 23045952 reads; of these: 23045952 (100.00%) were unpaired; of these: 19142492 (83.06%) aligned 0 times 2817527 (12.23%) aligned exactly 1 time 1085933 (4.71%) aligned >1 times 16.94% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2138707 / 3903460 = 0.5479 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 @ Mon, 03 Jun 2019 04:13:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 04:13:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:13:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:13:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 04:13:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:13:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:13:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 04:13:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:13:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:13:32: 1000000 INFO @ Mon, 03 Jun 2019 04:13:32: 1000000 INFO @ Mon, 03 Jun 2019 04:13:32: 1000000 INFO @ Mon, 03 Jun 2019 04:13:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:13:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:13:40: #1 total tags in treatment: 1764753 INFO @ Mon, 03 Jun 2019 04:13:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:13:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:13:40: #1 tags after filtering in treatment: 1764753 INFO @ Mon, 03 Jun 2019 04:13:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:13:40: #1 finished! INFO @ Mon, 03 Jun 2019 04:13:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:13:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:13:41: #2 number of paired peaks: 2705 INFO @ Mon, 03 Jun 2019 04:13:41: start model_add_line... INFO @ Mon, 03 Jun 2019 04:13:41: start X-correlation... INFO @ Mon, 03 Jun 2019 04:13:41: end of X-cor INFO @ Mon, 03 Jun 2019 04:13:41: #2 finished! INFO @ Mon, 03 Jun 2019 04:13:41: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 04:13:41: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 03 Jun 2019 04:13:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.05_model.r INFO @ Mon, 03 Jun 2019 04:13:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:13:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:13:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:13:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:13:41: #1 total tags in treatment: 1764753 INFO @ Mon, 03 Jun 2019 04:13:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:13:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:13:42: #1 tags after filtering in treatment: 1764753 INFO @ Mon, 03 Jun 2019 04:13:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:13:42: #1 finished! INFO @ Mon, 03 Jun 2019 04:13:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:13:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:13:42: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:13:42: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:13:42: #1 total tags in treatment: 1764753 INFO @ Mon, 03 Jun 2019 04:13:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:13:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:13:42: #1 tags after filtering in treatment: 1764753 INFO @ Mon, 03 Jun 2019 04:13:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:13:42: #1 finished! INFO @ Mon, 03 Jun 2019 04:13:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:13:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:13:42: #2 number of paired peaks: 2705 INFO @ Mon, 03 Jun 2019 04:13:42: start model_add_line... INFO @ Mon, 03 Jun 2019 04:13:42: start X-correlation... INFO @ Mon, 03 Jun 2019 04:13:42: end of X-cor INFO @ Mon, 03 Jun 2019 04:13:42: #2 finished! INFO @ Mon, 03 Jun 2019 04:13:42: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 04:13:42: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 03 Jun 2019 04:13:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.20_model.r INFO @ Mon, 03 Jun 2019 04:13:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:13:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:13:42: #2 number of paired peaks: 2705 INFO @ Mon, 03 Jun 2019 04:13:42: start model_add_line... INFO @ Mon, 03 Jun 2019 04:13:42: start X-correlation... INFO @ Mon, 03 Jun 2019 04:13:42: end of X-cor INFO @ Mon, 03 Jun 2019 04:13:42: #2 finished! INFO @ Mon, 03 Jun 2019 04:13:42: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 04:13:42: #2 alternative fragment length(s) may be 114 bps INFO @ Mon, 03 Jun 2019 04:13:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.10_model.r INFO @ Mon, 03 Jun 2019 04:13:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:13:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:13:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:13:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:13:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:13:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:13:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:13:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.05_summits.bed BedGraph に変換しました。 INFO @ Mon, 03 Jun 2019 04:13:49: Done! BigWig に変換中... pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3376 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:13:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.20_summits.bed INFO @ Mon, 03 Jun 2019 04:13:50: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1226 records, 4 fields): 5 millis INFO @ Mon, 03 Jun 2019 04:13:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.10_peaks.xls CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX160968/SRX160968.10_summits.bed INFO @ Mon, 03 Jun 2019 04:13:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2097 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。