Job ID = 1300225 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,961,446 reads read : 13,961,446 reads written : 13,961,446 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: 00:06:12 13961446 reads; of these: 13961446 (100.00%) were unpaired; of these: 365726 (2.62%) aligned 0 times 9569800 (68.54%) aligned exactly 1 time 4025920 (28.84%) aligned >1 times 97.38% overall alignment rate Time searching: 00:06:12 Overall time: 00:06:12 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] 1638924 / 13595720 = 0.1205 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 19:13:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.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 19:13:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:13:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:13:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.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 19:13:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:13:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:13:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.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 19:13:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:13:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:14:04: 1000000 INFO @ Mon, 03 Jun 2019 19:14:04: 1000000 INFO @ Mon, 03 Jun 2019 19:14:04: 1000000 INFO @ Mon, 03 Jun 2019 19:14:12: 2000000 INFO @ Mon, 03 Jun 2019 19:14:13: 2000000 INFO @ Mon, 03 Jun 2019 19:14:13: 2000000 INFO @ Mon, 03 Jun 2019 19:14:22: 3000000 INFO @ Mon, 03 Jun 2019 19:14:22: 3000000 INFO @ Mon, 03 Jun 2019 19:14:23: 3000000 INFO @ Mon, 03 Jun 2019 19:14:32: 4000000 INFO @ Mon, 03 Jun 2019 19:14:32: 4000000 INFO @ Mon, 03 Jun 2019 19:14:34: 4000000 INFO @ Mon, 03 Jun 2019 19:14:41: 5000000 INFO @ Mon, 03 Jun 2019 19:14:42: 5000000 INFO @ Mon, 03 Jun 2019 19:14:44: 5000000 INFO @ Mon, 03 Jun 2019 19:14:50: 6000000 INFO @ Mon, 03 Jun 2019 19:14:52: 6000000 INFO @ Mon, 03 Jun 2019 19:14:53: 6000000 INFO @ Mon, 03 Jun 2019 19:14:58: 7000000 INFO @ Mon, 03 Jun 2019 19:15:02: 7000000 INFO @ Mon, 03 Jun 2019 19:15:03: 7000000 INFO @ Mon, 03 Jun 2019 19:15:07: 8000000 INFO @ Mon, 03 Jun 2019 19:15:11: 8000000 INFO @ Mon, 03 Jun 2019 19:15:13: 8000000 INFO @ Mon, 03 Jun 2019 19:15:15: 9000000 INFO @ Mon, 03 Jun 2019 19:15:21: 9000000 INFO @ Mon, 03 Jun 2019 19:15:22: 9000000 INFO @ Mon, 03 Jun 2019 19:15:24: 10000000 INFO @ Mon, 03 Jun 2019 19:15:30: 10000000 INFO @ Mon, 03 Jun 2019 19:15:31: 10000000 INFO @ Mon, 03 Jun 2019 19:15:32: 11000000 INFO @ Mon, 03 Jun 2019 19:15:40: 11000000 INFO @ Mon, 03 Jun 2019 19:15:41: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:15:41: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:15:41: #1 total tags in treatment: 11956796 INFO @ Mon, 03 Jun 2019 19:15:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:15:41: #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 19:15:41: 11000000 INFO @ Mon, 03 Jun 2019 19:15:41: #1 tags after filtering in treatment: 11956796 INFO @ Mon, 03 Jun 2019 19:15:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:15:41: #1 finished! INFO @ Mon, 03 Jun 2019 19:15:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:15:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:15:42: #2 number of paired peaks: 1959 INFO @ Mon, 03 Jun 2019 19:15:42: start model_add_line... INFO @ Mon, 03 Jun 2019 19:15:42: start X-correlation... INFO @ Mon, 03 Jun 2019 19:15:43: end of X-cor INFO @ Mon, 03 Jun 2019 19:15:43: #2 finished! INFO @ Mon, 03 Jun 2019 19:15:43: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 19:15:43: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 19:15:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.05_model.r INFO @ Mon, 03 Jun 2019 19:15:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:15:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:15:48: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:15:48: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:15:48: #1 total tags in treatment: 11956796 INFO @ Mon, 03 Jun 2019 19:15:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:15:48: #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 19:15:48: #1 tags after filtering in treatment: 11956796 INFO @ Mon, 03 Jun 2019 19:15:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:15:48: #1 finished! INFO @ Mon, 03 Jun 2019 19:15:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:15:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:15:49: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:15:49: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:15:49: #1 total tags in treatment: 11956796 INFO @ Mon, 03 Jun 2019 19:15:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:15:49: #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 19:15:50: #1 tags after filtering in treatment: 11956796 INFO @ Mon, 03 Jun 2019 19:15:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:15:50: #1 finished! INFO @ Mon, 03 Jun 2019 19:15:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:15:50: #2 number of paired peaks: 1959 INFO @ Mon, 03 Jun 2019 19:15:50: start model_add_line... INFO @ Mon, 03 Jun 2019 19:15:50: start X-correlation... INFO @ Mon, 03 Jun 2019 19:15:50: end of X-cor INFO @ Mon, 03 Jun 2019 19:15:50: #2 finished! INFO @ Mon, 03 Jun 2019 19:15:50: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 19:15:50: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 19:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.10_model.r INFO @ Mon, 03 Jun 2019 19:15:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:15:51: #2 number of paired peaks: 1959 INFO @ Mon, 03 Jun 2019 19:15:51: start model_add_line... INFO @ Mon, 03 Jun 2019 19:15:51: start X-correlation... INFO @ Mon, 03 Jun 2019 19:15:51: end of X-cor INFO @ Mon, 03 Jun 2019 19:15:51: #2 finished! INFO @ Mon, 03 Jun 2019 19:15:51: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 19:15:51: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 19:15:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.20_model.r INFO @ Mon, 03 Jun 2019 19:15:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:15:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:16:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:16:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:16:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:16:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:16:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:16:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.05_summits.bed INFO @ Mon, 03 Jun 2019 19:16:36: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7433 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:16:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:16:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:16:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.10_summits.bed INFO @ Mon, 03 Jun 2019 19:16:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5271 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:16:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:16:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:16:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801814/SRX4801814.20_summits.bed INFO @ Mon, 03 Jun 2019 19:16:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3249 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。