Job ID = 1294956 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,892,995 reads read : 15,892,995 reads written : 15,892,995 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: 00:06:32 15892995 reads; of these: 15892995 (100.00%) were unpaired; of these: 776100 (4.88%) aligned 0 times 10295250 (64.78%) aligned exactly 1 time 4821645 (30.34%) aligned >1 times 95.12% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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] 1655184 / 15116895 = 0.1095 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 11:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.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 11:12:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:12:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.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 11:12:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:12:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.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 11:12:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:12:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:12:40: 1000000 INFO @ Mon, 03 Jun 2019 11:12:41: 1000000 INFO @ Mon, 03 Jun 2019 11:12:42: 1000000 INFO @ Mon, 03 Jun 2019 11:12:47: 2000000 INFO @ Mon, 03 Jun 2019 11:12:48: 2000000 INFO @ Mon, 03 Jun 2019 11:12:51: 2000000 INFO @ Mon, 03 Jun 2019 11:12:54: 3000000 INFO @ Mon, 03 Jun 2019 11:12:56: 3000000 INFO @ Mon, 03 Jun 2019 11:13:00: 3000000 INFO @ Mon, 03 Jun 2019 11:13:01: 4000000 INFO @ Mon, 03 Jun 2019 11:13:03: 4000000 INFO @ Mon, 03 Jun 2019 11:13:08: 5000000 INFO @ Mon, 03 Jun 2019 11:13:08: 4000000 INFO @ Mon, 03 Jun 2019 11:13:11: 5000000 INFO @ Mon, 03 Jun 2019 11:13:15: 6000000 INFO @ Mon, 03 Jun 2019 11:13:18: 5000000 INFO @ Mon, 03 Jun 2019 11:13:19: 6000000 INFO @ Mon, 03 Jun 2019 11:13:22: 7000000 INFO @ Mon, 03 Jun 2019 11:13:26: 7000000 INFO @ Mon, 03 Jun 2019 11:13:27: 6000000 INFO @ Mon, 03 Jun 2019 11:13:29: 8000000 INFO @ Mon, 03 Jun 2019 11:13:34: 8000000 INFO @ Mon, 03 Jun 2019 11:13:36: 9000000 INFO @ Mon, 03 Jun 2019 11:13:36: 7000000 INFO @ Mon, 03 Jun 2019 11:13:41: 9000000 INFO @ Mon, 03 Jun 2019 11:13:43: 10000000 INFO @ Mon, 03 Jun 2019 11:13:45: 8000000 INFO @ Mon, 03 Jun 2019 11:13:49: 10000000 INFO @ Mon, 03 Jun 2019 11:13:50: 11000000 INFO @ Mon, 03 Jun 2019 11:13:54: 9000000 INFO @ Mon, 03 Jun 2019 11:13:56: 11000000 INFO @ Mon, 03 Jun 2019 11:13:57: 12000000 INFO @ Mon, 03 Jun 2019 11:14:02: 10000000 INFO @ Mon, 03 Jun 2019 11:14:04: 13000000 INFO @ Mon, 03 Jun 2019 11:14:04: 12000000 INFO @ Mon, 03 Jun 2019 11:14:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:14:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:14:07: #1 total tags in treatment: 13461711 INFO @ Mon, 03 Jun 2019 11:14:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:14:07: #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 11:14:07: #1 tags after filtering in treatment: 13461711 INFO @ Mon, 03 Jun 2019 11:14:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:14:07: #1 finished! INFO @ Mon, 03 Jun 2019 11:14:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:14:09: #2 number of paired peaks: 941 WARNING @ Mon, 03 Jun 2019 11:14:09: Fewer paired peaks (941) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 941 pairs to build model! INFO @ Mon, 03 Jun 2019 11:14:09: start model_add_line... INFO @ Mon, 03 Jun 2019 11:14:09: start X-correlation... INFO @ Mon, 03 Jun 2019 11:14:09: end of X-cor INFO @ Mon, 03 Jun 2019 11:14:09: #2 finished! INFO @ Mon, 03 Jun 2019 11:14:09: #2 predicted fragment length is 178 bps INFO @ Mon, 03 Jun 2019 11:14:09: #2 alternative fragment length(s) may be 178 bps INFO @ Mon, 03 Jun 2019 11:14:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.05_model.r INFO @ Mon, 03 Jun 2019 11:14:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:14:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:14:11: 11000000 INFO @ Mon, 03 Jun 2019 11:14:12: 13000000 INFO @ Mon, 03 Jun 2019 11:14:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:14:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:14:15: #1 total tags in treatment: 13461711 INFO @ Mon, 03 Jun 2019 11:14:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:14:15: #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 11:14:15: #1 tags after filtering in treatment: 13461711 INFO @ Mon, 03 Jun 2019 11:14:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:14:15: #1 finished! INFO @ Mon, 03 Jun 2019 11:14:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:14:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:14:17: #2 number of paired peaks: 941 WARNING @ Mon, 03 Jun 2019 11:14:17: Fewer paired peaks (941) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 941 pairs to build model! INFO @ Mon, 03 Jun 2019 11:14:17: start model_add_line... INFO @ Mon, 03 Jun 2019 11:14:17: start X-correlation... INFO @ Mon, 03 Jun 2019 11:14:17: end of X-cor INFO @ Mon, 03 Jun 2019 11:14:17: #2 finished! INFO @ Mon, 03 Jun 2019 11:14:17: #2 predicted fragment length is 178 bps INFO @ Mon, 03 Jun 2019 11:14:17: #2 alternative fragment length(s) may be 178 bps INFO @ Mon, 03 Jun 2019 11:14:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.20_model.r INFO @ Mon, 03 Jun 2019 11:14:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:14:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:14:20: 12000000 INFO @ Mon, 03 Jun 2019 11:14:29: 13000000 INFO @ Mon, 03 Jun 2019 11:14:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:14:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:14:33: #1 total tags in treatment: 13461711 INFO @ Mon, 03 Jun 2019 11:14:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:14:33: #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 11:14:33: #1 tags after filtering in treatment: 13461711 INFO @ Mon, 03 Jun 2019 11:14:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:14:33: #1 finished! INFO @ Mon, 03 Jun 2019 11:14:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:14:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:14:35: #2 number of paired peaks: 941 WARNING @ Mon, 03 Jun 2019 11:14:35: Fewer paired peaks (941) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 941 pairs to build model! INFO @ Mon, 03 Jun 2019 11:14:35: start model_add_line... INFO @ Mon, 03 Jun 2019 11:14:35: start X-correlation... INFO @ Mon, 03 Jun 2019 11:14:35: end of X-cor INFO @ Mon, 03 Jun 2019 11:14:35: #2 finished! INFO @ Mon, 03 Jun 2019 11:14:35: #2 predicted fragment length is 178 bps INFO @ Mon, 03 Jun 2019 11:14:35: #2 alternative fragment length(s) may be 178 bps INFO @ Mon, 03 Jun 2019 11:14:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.10_model.r INFO @ Mon, 03 Jun 2019 11:14:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:14:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:14:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:15:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.05_summits.bed INFO @ Mon, 03 Jun 2019 11:15:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4189 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:15:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:15:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.20_summits.bed INFO @ Mon, 03 Jun 2019 11:15:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1933 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:15:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288018/SRX288018.10_summits.bed INFO @ Mon, 03 Jun 2019 11:15:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2914 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。