Job ID = 1300766 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,650,788 reads read : 32,650,788 reads written : 32,650,788 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: 00:08:14 32650788 reads; of these: 32650788 (100.00%) were unpaired; of these: 11577359 (35.46%) aligned 0 times 15595477 (47.76%) aligned exactly 1 time 5477952 (16.78%) aligned >1 times 64.54% overall alignment rate Time searching: 00:08:14 Overall time: 00:08:14 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 12 files... [bam_rmdupse_core] 9035140 / 21073429 = 0.4287 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 19:44:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.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 19:44:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:44:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:44:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.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 19:44:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:44:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:44:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.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 19:44:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:44:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:44:36: 1000000 INFO @ Mon, 03 Jun 2019 19:44:37: 1000000 INFO @ Mon, 03 Jun 2019 19:44:37: 1000000 INFO @ Mon, 03 Jun 2019 19:44:44: 2000000 INFO @ Mon, 03 Jun 2019 19:44:45: 2000000 INFO @ Mon, 03 Jun 2019 19:44:46: 2000000 INFO @ Mon, 03 Jun 2019 19:44:51: 3000000 INFO @ Mon, 03 Jun 2019 19:44:53: 3000000 INFO @ Mon, 03 Jun 2019 19:44:54: 3000000 INFO @ Mon, 03 Jun 2019 19:44:58: 4000000 INFO @ Mon, 03 Jun 2019 19:45:01: 4000000 INFO @ Mon, 03 Jun 2019 19:45:02: 4000000 INFO @ Mon, 03 Jun 2019 19:45:05: 5000000 INFO @ Mon, 03 Jun 2019 19:45:08: 5000000 INFO @ Mon, 03 Jun 2019 19:45:10: 5000000 INFO @ Mon, 03 Jun 2019 19:45:12: 6000000 INFO @ Mon, 03 Jun 2019 19:45:15: 6000000 INFO @ Mon, 03 Jun 2019 19:45:17: 6000000 INFO @ Mon, 03 Jun 2019 19:45:19: 7000000 INFO @ Mon, 03 Jun 2019 19:45:22: 7000000 INFO @ Mon, 03 Jun 2019 19:45:25: 7000000 INFO @ Mon, 03 Jun 2019 19:45:26: 8000000 INFO @ Mon, 03 Jun 2019 19:45:29: 8000000 INFO @ Mon, 03 Jun 2019 19:45:33: 8000000 INFO @ Mon, 03 Jun 2019 19:45:34: 9000000 INFO @ Mon, 03 Jun 2019 19:45:36: 9000000 INFO @ Mon, 03 Jun 2019 19:45:41: 10000000 INFO @ Mon, 03 Jun 2019 19:45:42: 9000000 INFO @ Mon, 03 Jun 2019 19:45:44: 10000000 INFO @ Mon, 03 Jun 2019 19:45:48: 11000000 INFO @ Mon, 03 Jun 2019 19:45:50: 10000000 INFO @ Mon, 03 Jun 2019 19:45:51: 11000000 INFO @ Mon, 03 Jun 2019 19:45:56: 12000000 INFO @ Mon, 03 Jun 2019 19:45:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:45:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:45:56: #1 total tags in treatment: 12038289 INFO @ Mon, 03 Jun 2019 19:45:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:45:56: #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 19:45:56: #1 tags after filtering in treatment: 12038289 INFO @ Mon, 03 Jun 2019 19:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:45:56: #1 finished! INFO @ Mon, 03 Jun 2019 19:45:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:45:58: #2 number of paired peaks: 2683 INFO @ Mon, 03 Jun 2019 19:45:58: start model_add_line... INFO @ Mon, 03 Jun 2019 19:45:58: start X-correlation... INFO @ Mon, 03 Jun 2019 19:45:58: end of X-cor INFO @ Mon, 03 Jun 2019 19:45:58: #2 finished! INFO @ Mon, 03 Jun 2019 19:45:58: #2 predicted fragment length is 205 bps INFO @ Mon, 03 Jun 2019 19:45:58: #2 alternative fragment length(s) may be 205 bps INFO @ Mon, 03 Jun 2019 19:45:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.10_model.r INFO @ Mon, 03 Jun 2019 19:45:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:45:58: 11000000 INFO @ Mon, 03 Jun 2019 19:45:59: 12000000 INFO @ Mon, 03 Jun 2019 19:45:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:45:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:45:59: #1 total tags in treatment: 12038289 INFO @ Mon, 03 Jun 2019 19:45:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:45:59: #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 19:45:59: #1 tags after filtering in treatment: 12038289 INFO @ Mon, 03 Jun 2019 19:45:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:45:59: #1 finished! INFO @ Mon, 03 Jun 2019 19:45:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:45:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:46:01: #2 number of paired peaks: 2683 INFO @ Mon, 03 Jun 2019 19:46:01: start model_add_line... INFO @ Mon, 03 Jun 2019 19:46:01: start X-correlation... INFO @ Mon, 03 Jun 2019 19:46:01: end of X-cor INFO @ Mon, 03 Jun 2019 19:46:01: #2 finished! INFO @ Mon, 03 Jun 2019 19:46:01: #2 predicted fragment length is 205 bps INFO @ Mon, 03 Jun 2019 19:46:01: #2 alternative fragment length(s) may be 205 bps INFO @ Mon, 03 Jun 2019 19:46:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.05_model.r INFO @ Mon, 03 Jun 2019 19:46:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:46:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:46:06: 12000000 INFO @ Mon, 03 Jun 2019 19:46:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:46:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:46:06: #1 total tags in treatment: 12038289 INFO @ Mon, 03 Jun 2019 19:46:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:46:06: #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 19:46:06: #1 tags after filtering in treatment: 12038289 INFO @ Mon, 03 Jun 2019 19:46:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:46:06: #1 finished! INFO @ Mon, 03 Jun 2019 19:46:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:46:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:46:08: #2 number of paired peaks: 2683 INFO @ Mon, 03 Jun 2019 19:46:08: start model_add_line... INFO @ Mon, 03 Jun 2019 19:46:08: start X-correlation... INFO @ Mon, 03 Jun 2019 19:46:08: end of X-cor INFO @ Mon, 03 Jun 2019 19:46:08: #2 finished! INFO @ Mon, 03 Jun 2019 19:46:08: #2 predicted fragment length is 205 bps INFO @ Mon, 03 Jun 2019 19:46:08: #2 alternative fragment length(s) may be 205 bps INFO @ Mon, 03 Jun 2019 19:46:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.20_model.r INFO @ Mon, 03 Jun 2019 19:46:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:46:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:46:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:46:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:46:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.10_summits.bed INFO @ Mon, 03 Jun 2019 19:46:53: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6627 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:46:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:46:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:46:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.05_summits.bed INFO @ Mon, 03 Jun 2019 19:46:57: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7986 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:47:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:47:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:47:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823793/SRX4823793.20_summits.bed INFO @ Mon, 03 Jun 2019 19:47:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5208 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。