Job ID = 1294860 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,623,531 reads read : 17,623,531 reads written : 17,623,531 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: 00:05:10 17623531 reads; of these: 17623531 (100.00%) were unpaired; of these: 817772 (4.64%) aligned 0 times 14814130 (84.06%) aligned exactly 1 time 1991629 (11.30%) aligned >1 times 95.36% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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] 1669975 / 16805759 = 0.0994 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 10:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.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 10:47:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:47:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:47:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.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 10:47:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:47:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:47:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.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 10:47:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:47:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:47:24: 1000000 INFO @ Mon, 03 Jun 2019 10:47:24: 1000000 INFO @ Mon, 03 Jun 2019 10:47:27: 1000000 INFO @ Mon, 03 Jun 2019 10:47:33: 2000000 INFO @ Mon, 03 Jun 2019 10:47:33: 2000000 INFO @ Mon, 03 Jun 2019 10:47:38: 2000000 INFO @ Mon, 03 Jun 2019 10:47:42: 3000000 INFO @ Mon, 03 Jun 2019 10:47:42: 3000000 INFO @ Mon, 03 Jun 2019 10:47:49: 3000000 INFO @ Mon, 03 Jun 2019 10:47:51: 4000000 INFO @ Mon, 03 Jun 2019 10:47:51: 4000000 INFO @ Mon, 03 Jun 2019 10:48:00: 4000000 INFO @ Mon, 03 Jun 2019 10:48:01: 5000000 INFO @ Mon, 03 Jun 2019 10:48:01: 5000000 INFO @ Mon, 03 Jun 2019 10:48:10: 6000000 INFO @ Mon, 03 Jun 2019 10:48:12: 6000000 INFO @ Mon, 03 Jun 2019 10:48:12: 5000000 INFO @ Mon, 03 Jun 2019 10:48:20: 7000000 INFO @ Mon, 03 Jun 2019 10:48:22: 7000000 INFO @ Mon, 03 Jun 2019 10:48:22: 6000000 INFO @ Mon, 03 Jun 2019 10:48:29: 8000000 INFO @ Mon, 03 Jun 2019 10:48:31: 8000000 INFO @ Mon, 03 Jun 2019 10:48:32: 7000000 INFO @ Mon, 03 Jun 2019 10:48:37: 9000000 INFO @ Mon, 03 Jun 2019 10:48:40: 9000000 INFO @ Mon, 03 Jun 2019 10:48:41: 8000000 INFO @ Mon, 03 Jun 2019 10:48:47: 10000000 INFO @ Mon, 03 Jun 2019 10:48:49: 10000000 INFO @ Mon, 03 Jun 2019 10:48:51: 9000000 INFO @ Mon, 03 Jun 2019 10:48:56: 11000000 INFO @ Mon, 03 Jun 2019 10:48:58: 11000000 INFO @ Mon, 03 Jun 2019 10:49:01: 10000000 INFO @ Mon, 03 Jun 2019 10:49:06: 12000000 INFO @ Mon, 03 Jun 2019 10:49:07: 12000000 INFO @ Mon, 03 Jun 2019 10:49:10: 11000000 INFO @ Mon, 03 Jun 2019 10:49:16: 13000000 INFO @ Mon, 03 Jun 2019 10:49:16: 13000000 INFO @ Mon, 03 Jun 2019 10:49:20: 12000000 INFO @ Mon, 03 Jun 2019 10:49:25: 14000000 INFO @ Mon, 03 Jun 2019 10:49:25: 14000000 INFO @ Mon, 03 Jun 2019 10:49:29: 13000000 INFO @ Mon, 03 Jun 2019 10:49:33: 15000000 INFO @ Mon, 03 Jun 2019 10:49:34: 15000000 INFO @ Mon, 03 Jun 2019 10:49:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:49:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:49:35: #1 total tags in treatment: 15135784 INFO @ Mon, 03 Jun 2019 10:49:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:49:35: #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 10:49:35: #1 tags after filtering in treatment: 15135784 INFO @ Mon, 03 Jun 2019 10:49:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:49:35: #1 finished! INFO @ Mon, 03 Jun 2019 10:49:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:49:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:49:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:49:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:49:35: #1 total tags in treatment: 15135784 INFO @ Mon, 03 Jun 2019 10:49:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:49:35: #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 10:49:36: #1 tags after filtering in treatment: 15135784 INFO @ Mon, 03 Jun 2019 10:49:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:49:36: #1 finished! INFO @ Mon, 03 Jun 2019 10:49:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:49:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:49:36: #2 number of paired peaks: 126 WARNING @ Mon, 03 Jun 2019 10:49:36: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 03 Jun 2019 10:49:36: start model_add_line... INFO @ Mon, 03 Jun 2019 10:49:36: start X-correlation... INFO @ Mon, 03 Jun 2019 10:49:36: end of X-cor INFO @ Mon, 03 Jun 2019 10:49:36: #2 finished! INFO @ Mon, 03 Jun 2019 10:49:36: #2 predicted fragment length is 165 bps INFO @ Mon, 03 Jun 2019 10:49:36: #2 alternative fragment length(s) may be 165 bps INFO @ Mon, 03 Jun 2019 10:49:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.20_model.r INFO @ Mon, 03 Jun 2019 10:49:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:49:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:49:37: #2 number of paired peaks: 126 WARNING @ Mon, 03 Jun 2019 10:49:37: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 03 Jun 2019 10:49:37: start model_add_line... INFO @ Mon, 03 Jun 2019 10:49:37: start X-correlation... INFO @ Mon, 03 Jun 2019 10:49:37: end of X-cor INFO @ Mon, 03 Jun 2019 10:49:37: #2 finished! INFO @ Mon, 03 Jun 2019 10:49:37: #2 predicted fragment length is 165 bps INFO @ Mon, 03 Jun 2019 10:49:37: #2 alternative fragment length(s) may be 165 bps INFO @ Mon, 03 Jun 2019 10:49:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.05_model.r INFO @ Mon, 03 Jun 2019 10:49:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:49:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:49:38: 14000000 INFO @ Mon, 03 Jun 2019 10:49:45: 15000000 INFO @ Mon, 03 Jun 2019 10:49:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:49:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:49:46: #1 total tags in treatment: 15135784 INFO @ Mon, 03 Jun 2019 10:49:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:49:46: #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 10:49:47: #1 tags after filtering in treatment: 15135784 INFO @ Mon, 03 Jun 2019 10:49:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:49:47: #1 finished! INFO @ Mon, 03 Jun 2019 10:49:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:49:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:49:48: #2 number of paired peaks: 126 WARNING @ Mon, 03 Jun 2019 10:49:48: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 03 Jun 2019 10:49:48: start model_add_line... INFO @ Mon, 03 Jun 2019 10:49:48: start X-correlation... INFO @ Mon, 03 Jun 2019 10:49:48: end of X-cor INFO @ Mon, 03 Jun 2019 10:49:48: #2 finished! INFO @ Mon, 03 Jun 2019 10:49:48: #2 predicted fragment length is 165 bps INFO @ Mon, 03 Jun 2019 10:49:48: #2 alternative fragment length(s) may be 165 bps INFO @ Mon, 03 Jun 2019 10:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.10_model.r INFO @ Mon, 03 Jun 2019 10:49:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:50:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:50:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:50:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:50:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:50:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:50:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.20_summits.bed INFO @ Mon, 03 Jun 2019 10:50:42: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (727 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.05_summits.bed INFO @ Mon, 03 Jun 2019 10:50:43: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4562 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:50:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:50:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:50:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287953/SRX287953.10_summits.bed INFO @ Mon, 03 Jun 2019 10:50:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1951 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。