Job ID = 2590309 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,174,194 reads read : 16,174,194 reads written : 16,174,194 rm: cannot remove ‘[DSE]RR*’: 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: 00:04:57 16174194 reads; of these: 16174194 (100.00%) were unpaired; of these: 2244535 (13.88%) aligned 0 times 11115032 (68.72%) aligned exactly 1 time 2814627 (17.40%) aligned >1 times 86.12% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 3135783 / 13929659 = 0.2251 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, 12 Aug 2019 20:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.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, 12 Aug 2019 20:51:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:51:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.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, 12 Aug 2019 20:51:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:51:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:51:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.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, 12 Aug 2019 20:51:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:51:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:51:47: 1000000 INFO @ Mon, 12 Aug 2019 20:51:48: 1000000 INFO @ Mon, 12 Aug 2019 20:51:50: 1000000 INFO @ Mon, 12 Aug 2019 20:51:54: 2000000 INFO @ Mon, 12 Aug 2019 20:51:55: 2000000 INFO @ Mon, 12 Aug 2019 20:51:57: 2000000 INFO @ Mon, 12 Aug 2019 20:52:01: 3000000 INFO @ Mon, 12 Aug 2019 20:52:03: 3000000 INFO @ Mon, 12 Aug 2019 20:52:05: 3000000 INFO @ Mon, 12 Aug 2019 20:52:07: 4000000 INFO @ Mon, 12 Aug 2019 20:52:11: 4000000 INFO @ Mon, 12 Aug 2019 20:52:13: 4000000 INFO @ Mon, 12 Aug 2019 20:52:14: 5000000 INFO @ Mon, 12 Aug 2019 20:52:19: 5000000 INFO @ Mon, 12 Aug 2019 20:52:20: 6000000 INFO @ Mon, 12 Aug 2019 20:52:21: 5000000 INFO @ Mon, 12 Aug 2019 20:52:26: 6000000 INFO @ Mon, 12 Aug 2019 20:52:27: 7000000 INFO @ Mon, 12 Aug 2019 20:52:29: 6000000 INFO @ Mon, 12 Aug 2019 20:52:34: 8000000 INFO @ Mon, 12 Aug 2019 20:52:34: 7000000 INFO @ Mon, 12 Aug 2019 20:52:36: 7000000 INFO @ Mon, 12 Aug 2019 20:52:40: 9000000 INFO @ Mon, 12 Aug 2019 20:52:42: 8000000 INFO @ Mon, 12 Aug 2019 20:52:44: 8000000 INFO @ Mon, 12 Aug 2019 20:52:47: 10000000 INFO @ Mon, 12 Aug 2019 20:52:50: 9000000 INFO @ Mon, 12 Aug 2019 20:52:52: 9000000 INFO @ Mon, 12 Aug 2019 20:52:52: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:52:52: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:52:52: #1 total tags in treatment: 10793876 INFO @ Mon, 12 Aug 2019 20:52:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:52:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:52:52: #1 tags after filtering in treatment: 10793876 INFO @ Mon, 12 Aug 2019 20:52:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:52:52: #1 finished! INFO @ Mon, 12 Aug 2019 20:52:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:52:54: #2 number of paired peaks: 8204 INFO @ Mon, 12 Aug 2019 20:52:54: start model_add_line... INFO @ Mon, 12 Aug 2019 20:52:55: start X-correlation... INFO @ Mon, 12 Aug 2019 20:52:55: end of X-cor INFO @ Mon, 12 Aug 2019 20:52:55: #2 finished! INFO @ Mon, 12 Aug 2019 20:52:55: #2 predicted fragment length is 208 bps INFO @ Mon, 12 Aug 2019 20:52:55: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 12 Aug 2019 20:52:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.10_model.r INFO @ Mon, 12 Aug 2019 20:52:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:52:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:52:57: 10000000 INFO @ Mon, 12 Aug 2019 20:52:59: 10000000 INFO @ Mon, 12 Aug 2019 20:53:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:53:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:53:03: #1 total tags in treatment: 10793876 INFO @ Mon, 12 Aug 2019 20:53:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:53:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:53:04: #1 tags after filtering in treatment: 10793876 INFO @ Mon, 12 Aug 2019 20:53:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:53:04: #1 finished! INFO @ Mon, 12 Aug 2019 20:53:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:53:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:53:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:53:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:53:05: #1 total tags in treatment: 10793876 INFO @ Mon, 12 Aug 2019 20:53:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:53:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:53:05: #2 number of paired peaks: 8204 INFO @ Mon, 12 Aug 2019 20:53:05: start model_add_line... INFO @ Mon, 12 Aug 2019 20:53:06: #1 tags after filtering in treatment: 10793876 INFO @ Mon, 12 Aug 2019 20:53:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:53:06: #1 finished! INFO @ Mon, 12 Aug 2019 20:53:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:53:06: start X-correlation... INFO @ Mon, 12 Aug 2019 20:53:06: end of X-cor INFO @ Mon, 12 Aug 2019 20:53:06: #2 finished! INFO @ Mon, 12 Aug 2019 20:53:06: #2 predicted fragment length is 208 bps INFO @ Mon, 12 Aug 2019 20:53:06: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 12 Aug 2019 20:53:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.05_model.r INFO @ Mon, 12 Aug 2019 20:53:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:53:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:53:07: #2 number of paired peaks: 8204 INFO @ Mon, 12 Aug 2019 20:53:07: start model_add_line... INFO @ Mon, 12 Aug 2019 20:53:08: start X-correlation... INFO @ Mon, 12 Aug 2019 20:53:08: end of X-cor INFO @ Mon, 12 Aug 2019 20:53:08: #2 finished! INFO @ Mon, 12 Aug 2019 20:53:08: #2 predicted fragment length is 208 bps INFO @ Mon, 12 Aug 2019 20:53:08: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 12 Aug 2019 20:53:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.20_model.r INFO @ Mon, 12 Aug 2019 20:53:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:53:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:53:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:53:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:53:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:53:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:53:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:53:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.10_summits.bed INFO @ Mon, 12 Aug 2019 20:53:52: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8409 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:54:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:54:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:54:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.05_summits.bed INFO @ Mon, 12 Aug 2019 20:54:04: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10314 records, 4 fields): 76 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:54:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:54:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:54:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331415/SRX331415.20_summits.bed INFO @ Mon, 12 Aug 2019 20:54:06: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6196 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。