Job ID = 1295052 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,655,041 reads read : 3,655,041 reads written : 3,655,041 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: 00:00:01 Multiseed full-index search: 00:01:22 3655041 reads; of these: 3655041 (100.00%) were unpaired; of these: 325635 (8.91%) aligned 0 times 2495432 (68.27%) aligned exactly 1 time 833974 (22.82%) aligned >1 times 91.09% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 491538 / 3329406 = 0.1476 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 11:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.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 11:28:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:28:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.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 11:28:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:28:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.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 11:28:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:28:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:28:50: 1000000 INFO @ Mon, 03 Jun 2019 11:28:52: 1000000 INFO @ Mon, 03 Jun 2019 11:28:52: 1000000 INFO @ Mon, 03 Jun 2019 11:28:57: 2000000 INFO @ Mon, 03 Jun 2019 11:29:02: 2000000 INFO @ Mon, 03 Jun 2019 11:29:02: 2000000 INFO @ Mon, 03 Jun 2019 11:29:03: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:29:03: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:29:03: #1 total tags in treatment: 2837868 INFO @ Mon, 03 Jun 2019 11:29:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:29:03: #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 11:29:03: #1 tags after filtering in treatment: 2837868 INFO @ Mon, 03 Jun 2019 11:29:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:29:03: #1 finished! INFO @ Mon, 03 Jun 2019 11:29:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:29:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:29:04: #2 number of paired peaks: 5169 INFO @ Mon, 03 Jun 2019 11:29:04: start model_add_line... INFO @ Mon, 03 Jun 2019 11:29:04: start X-correlation... INFO @ Mon, 03 Jun 2019 11:29:04: end of X-cor INFO @ Mon, 03 Jun 2019 11:29:04: #2 finished! INFO @ Mon, 03 Jun 2019 11:29:04: #2 predicted fragment length is 331 bps INFO @ Mon, 03 Jun 2019 11:29:04: #2 alternative fragment length(s) may be 331 bps INFO @ Mon, 03 Jun 2019 11:29:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.20_model.r INFO @ Mon, 03 Jun 2019 11:29:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:29:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:29:10: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:29:10: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:29:10: #1 total tags in treatment: 2837868 INFO @ Mon, 03 Jun 2019 11:29:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:29:10: #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 11:29:10: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:29:10: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:29:10: #1 total tags in treatment: 2837868 INFO @ Mon, 03 Jun 2019 11:29:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:29:10: #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 11:29:10: #1 tags after filtering in treatment: 2837868 INFO @ Mon, 03 Jun 2019 11:29:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:29:10: #1 finished! INFO @ Mon, 03 Jun 2019 11:29:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:29:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:29:10: #1 tags after filtering in treatment: 2837868 INFO @ Mon, 03 Jun 2019 11:29:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:29:10: #1 finished! INFO @ Mon, 03 Jun 2019 11:29:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:29:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:29:11: #2 number of paired peaks: 5169 INFO @ Mon, 03 Jun 2019 11:29:11: start model_add_line... INFO @ Mon, 03 Jun 2019 11:29:11: #2 number of paired peaks: 5169 INFO @ Mon, 03 Jun 2019 11:29:11: start model_add_line... INFO @ Mon, 03 Jun 2019 11:29:11: start X-correlation... INFO @ Mon, 03 Jun 2019 11:29:11: end of X-cor INFO @ Mon, 03 Jun 2019 11:29:11: #2 finished! INFO @ Mon, 03 Jun 2019 11:29:11: #2 predicted fragment length is 331 bps INFO @ Mon, 03 Jun 2019 11:29:11: #2 alternative fragment length(s) may be 331 bps INFO @ Mon, 03 Jun 2019 11:29:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.05_model.r INFO @ Mon, 03 Jun 2019 11:29:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:29:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:29:11: start X-correlation... INFO @ Mon, 03 Jun 2019 11:29:11: end of X-cor INFO @ Mon, 03 Jun 2019 11:29:11: #2 finished! INFO @ Mon, 03 Jun 2019 11:29:11: #2 predicted fragment length is 331 bps INFO @ Mon, 03 Jun 2019 11:29:11: #2 alternative fragment length(s) may be 331 bps INFO @ Mon, 03 Jun 2019 11:29:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.10_model.r INFO @ Mon, 03 Jun 2019 11:29:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:29:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:29:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:29:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:29:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:29:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.20_summits.bed INFO @ Mon, 03 Jun 2019 11:29:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3157 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:29:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:29:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:29:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:29:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:29:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.05_summits.bed INFO @ Mon, 03 Jun 2019 11:29:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:29:27: Done! INFO @ Mon, 03 Jun 2019 11:29:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:29:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167247/SRX3167247.10_summits.bed INFO @ Mon, 03 Jun 2019 11:29:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5941 records, 4 fields): 15 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4585 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。