Job ID = 1293974 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,526,261 reads read : 1,526,261 reads written : 1,526,261 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: 00:00:22 1526261 reads; of these: 1526261 (100.00%) were unpaired; of these: 978617 (64.12%) aligned 0 times 428148 (28.05%) aligned exactly 1 time 119496 (7.83%) aligned >1 times 35.88% overall alignment rate Time searching: 00:00:22 Overall time: 00:00:22 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] 106805 / 547644 = 0.1950 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 03:37:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.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 03:37:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:37:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:37:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.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 03:37:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:37:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:37:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.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 03:37:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:37:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:37:41: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:37:41: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:37:41: #1 total tags in treatment: 440839 INFO @ Mon, 03 Jun 2019 03:37:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:37:41: #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 03:37:41: #1 tags after filtering in treatment: 440839 INFO @ Mon, 03 Jun 2019 03:37:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:37:41: #1 finished! INFO @ Mon, 03 Jun 2019 03:37:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:37:41: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:37:41: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:37:41: #1 total tags in treatment: 440839 INFO @ Mon, 03 Jun 2019 03:37:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:37:41: #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 03:37:41: #1 tags after filtering in treatment: 440839 INFO @ Mon, 03 Jun 2019 03:37:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:37:41: #1 finished! INFO @ Mon, 03 Jun 2019 03:37:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:37:41: #2 number of paired peaks: 1479 INFO @ Mon, 03 Jun 2019 03:37:41: start model_add_line... INFO @ Mon, 03 Jun 2019 03:37:41: start X-correlation... INFO @ Mon, 03 Jun 2019 03:37:41: end of X-cor INFO @ Mon, 03 Jun 2019 03:37:41: #2 finished! INFO @ Mon, 03 Jun 2019 03:37:41: #2 predicted fragment length is 109 bps INFO @ Mon, 03 Jun 2019 03:37:41: #2 alternative fragment length(s) may be 109 bps INFO @ Mon, 03 Jun 2019 03:37:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.05_model.r INFO @ Mon, 03 Jun 2019 03:37:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:37:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:37:41: #2 number of paired peaks: 1479 INFO @ Mon, 03 Jun 2019 03:37:41: start model_add_line... INFO @ Mon, 03 Jun 2019 03:37:41: start X-correlation... INFO @ Mon, 03 Jun 2019 03:37:41: end of X-cor INFO @ Mon, 03 Jun 2019 03:37:41: #2 finished! INFO @ Mon, 03 Jun 2019 03:37:41: #2 predicted fragment length is 109 bps INFO @ Mon, 03 Jun 2019 03:37:41: #2 alternative fragment length(s) may be 109 bps INFO @ Mon, 03 Jun 2019 03:37:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.10_model.r INFO @ Mon, 03 Jun 2019 03:37:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:37:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:37:42: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 03:37:42: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 03:37:42: #1 total tags in treatment: 440839 INFO @ Mon, 03 Jun 2019 03:37:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:37:42: #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 03:37:42: #1 tags after filtering in treatment: 440839 INFO @ Mon, 03 Jun 2019 03:37:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:37:42: #1 finished! INFO @ Mon, 03 Jun 2019 03:37:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:37:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:37:42: #2 number of paired peaks: 1479 INFO @ Mon, 03 Jun 2019 03:37:42: start model_add_line... INFO @ Mon, 03 Jun 2019 03:37:42: start X-correlation... INFO @ Mon, 03 Jun 2019 03:37:42: end of X-cor INFO @ Mon, 03 Jun 2019 03:37:42: #2 finished! INFO @ Mon, 03 Jun 2019 03:37:42: #2 predicted fragment length is 109 bps INFO @ Mon, 03 Jun 2019 03:37:42: #2 alternative fragment length(s) may be 109 bps INFO @ Mon, 03 Jun 2019 03:37:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.20_model.r INFO @ Mon, 03 Jun 2019 03:37:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:37:42: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 03:37:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:37:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:37:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:37:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:37:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:37:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.05_summits.bed INFO @ Mon, 03 Jun 2019 03:37:43: Done! INFO @ Mon, 03 Jun 2019 03:37:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:37:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:37:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.10_summits.bed INFO @ Mon, 03 Jun 2019 03:37:43: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (795 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (418 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 03:37:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:37:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:37:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550608/SRX1550608.20_summits.bed INFO @ Mon, 03 Jun 2019 03:37:44: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (198 records, 4 fields): 2 millis CompletedMACS2peakCalling