Job ID = 1295710 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,700,436 reads read : 21,400,872 reads written : 10,700,436 reads 0-length : 10,700,436 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: 00:03:55 10700436 reads; of these: 10700436 (100.00%) were unpaired; of these: 286690 (2.68%) aligned 0 times 7967494 (74.46%) aligned exactly 1 time 2446252 (22.86%) aligned >1 times 97.32% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3050822 / 10413746 = 0.2930 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 15:14:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.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 15:14:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:14:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:14:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.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 15:14:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:14:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:14:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.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 15:14:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:14:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:14:24: 1000000 INFO @ Mon, 03 Jun 2019 15:14:24: 1000000 INFO @ Mon, 03 Jun 2019 15:14:26: 1000000 INFO @ Mon, 03 Jun 2019 15:14:33: 2000000 INFO @ Mon, 03 Jun 2019 15:14:33: 2000000 INFO @ Mon, 03 Jun 2019 15:14:35: 2000000 INFO @ Mon, 03 Jun 2019 15:14:41: 3000000 INFO @ Mon, 03 Jun 2019 15:14:41: 3000000 INFO @ Mon, 03 Jun 2019 15:14:44: 3000000 INFO @ Mon, 03 Jun 2019 15:14:49: 4000000 INFO @ Mon, 03 Jun 2019 15:14:49: 4000000 INFO @ Mon, 03 Jun 2019 15:14:53: 4000000 INFO @ Mon, 03 Jun 2019 15:14:57: 5000000 INFO @ Mon, 03 Jun 2019 15:14:57: 5000000 INFO @ Mon, 03 Jun 2019 15:15:02: 5000000 INFO @ Mon, 03 Jun 2019 15:15:05: 6000000 INFO @ Mon, 03 Jun 2019 15:15:05: 6000000 INFO @ Mon, 03 Jun 2019 15:15:10: 6000000 INFO @ Mon, 03 Jun 2019 15:15:13: 7000000 INFO @ Mon, 03 Jun 2019 15:15:13: 7000000 INFO @ Mon, 03 Jun 2019 15:15:16: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 15:15:16: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 15:15:16: #1 total tags in treatment: 7362924 INFO @ Mon, 03 Jun 2019 15:15:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:15:16: #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 15:15:16: #1 tags after filtering in treatment: 7362924 INFO @ Mon, 03 Jun 2019 15:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:15:16: #1 finished! INFO @ Mon, 03 Jun 2019 15:15:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:15:16: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 15:15:16: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 15:15:16: #1 total tags in treatment: 7362924 INFO @ Mon, 03 Jun 2019 15:15:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:15:16: #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 15:15:16: #1 tags after filtering in treatment: 7362924 INFO @ Mon, 03 Jun 2019 15:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:15:16: #1 finished! INFO @ Mon, 03 Jun 2019 15:15:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:15:17: #2 number of paired peaks: 5354 INFO @ Mon, 03 Jun 2019 15:15:17: start model_add_line... INFO @ Mon, 03 Jun 2019 15:15:17: start X-correlation... INFO @ Mon, 03 Jun 2019 15:15:17: end of X-cor INFO @ Mon, 03 Jun 2019 15:15:17: #2 finished! INFO @ Mon, 03 Jun 2019 15:15:17: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 15:15:17: #2 alternative fragment length(s) may be 3,103 bps INFO @ Mon, 03 Jun 2019 15:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.05_model.r INFO @ Mon, 03 Jun 2019 15:15:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:15:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:15:17: #2 number of paired peaks: 5354 INFO @ Mon, 03 Jun 2019 15:15:17: start model_add_line... INFO @ Mon, 03 Jun 2019 15:15:17: start X-correlation... INFO @ Mon, 03 Jun 2019 15:15:17: end of X-cor INFO @ Mon, 03 Jun 2019 15:15:17: #2 finished! INFO @ Mon, 03 Jun 2019 15:15:17: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 15:15:17: #2 alternative fragment length(s) may be 3,103 bps INFO @ Mon, 03 Jun 2019 15:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.10_model.r INFO @ Mon, 03 Jun 2019 15:15:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:15:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:15:18: 7000000 INFO @ Mon, 03 Jun 2019 15:15:22: #1 tag size is determined as 49 bps INFO @ Mon, 03 Jun 2019 15:15:22: #1 tag size = 49 INFO @ Mon, 03 Jun 2019 15:15:22: #1 total tags in treatment: 7362924 INFO @ Mon, 03 Jun 2019 15:15:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:15:22: #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 15:15:22: #1 tags after filtering in treatment: 7362924 INFO @ Mon, 03 Jun 2019 15:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:15:22: #1 finished! INFO @ Mon, 03 Jun 2019 15:15:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:15:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:15:23: #2 number of paired peaks: 5354 INFO @ Mon, 03 Jun 2019 15:15:23: start model_add_line... INFO @ Mon, 03 Jun 2019 15:15:23: start X-correlation... INFO @ Mon, 03 Jun 2019 15:15:23: end of X-cor INFO @ Mon, 03 Jun 2019 15:15:23: #2 finished! INFO @ Mon, 03 Jun 2019 15:15:23: #2 predicted fragment length is 103 bps INFO @ Mon, 03 Jun 2019 15:15:23: #2 alternative fragment length(s) may be 3,103 bps INFO @ Mon, 03 Jun 2019 15:15:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.20_model.r INFO @ Mon, 03 Jun 2019 15:15:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:15:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:15:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:15:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:15:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:15:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:15:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:15:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.05_summits.bed INFO @ Mon, 03 Jun 2019 15:15:53: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5009 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:15:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:15:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:15:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.10_summits.bed INFO @ Mon, 03 Jun 2019 15:15:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2599 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:15:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:15:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:15:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4370072/SRX4370072.20_summits.bed INFO @ Mon, 03 Jun 2019 15:15:59: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1156 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。