Job ID = 1307482 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,058,556 reads read : 48,117,112 reads written : 24,058,556 reads 0-length : 24,058,556 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: 00:08:09 24058556 reads; of these: 24058556 (100.00%) were unpaired; of these: 2043585 (8.49%) aligned 0 times 19148689 (79.59%) aligned exactly 1 time 2866282 (11.91%) aligned >1 times 91.51% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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] 8270061 / 22014971 = 0.3757 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 22:44:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.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 22:44:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:44:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:44:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.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 22:44:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:44:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:44:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.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 22:44:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:44:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:44:21: 1000000 INFO @ Mon, 03 Jun 2019 22:44:21: 1000000 INFO @ Mon, 03 Jun 2019 22:44:23: 1000000 INFO @ Mon, 03 Jun 2019 22:44:29: 2000000 INFO @ Mon, 03 Jun 2019 22:44:30: 2000000 INFO @ Mon, 03 Jun 2019 22:44:34: 2000000 INFO @ Mon, 03 Jun 2019 22:44:38: 3000000 INFO @ Mon, 03 Jun 2019 22:44:39: 3000000 INFO @ Mon, 03 Jun 2019 22:44:46: 4000000 INFO @ Mon, 03 Jun 2019 22:44:47: 3000000 INFO @ Mon, 03 Jun 2019 22:44:48: 4000000 INFO @ Mon, 03 Jun 2019 22:44:55: 5000000 INFO @ Mon, 03 Jun 2019 22:44:57: 5000000 INFO @ Mon, 03 Jun 2019 22:44:58: 4000000 INFO @ Mon, 03 Jun 2019 22:45:03: 6000000 INFO @ Mon, 03 Jun 2019 22:45:06: 6000000 INFO @ Mon, 03 Jun 2019 22:45:10: 5000000 INFO @ Mon, 03 Jun 2019 22:45:12: 7000000 INFO @ Mon, 03 Jun 2019 22:45:15: 7000000 INFO @ Mon, 03 Jun 2019 22:45:21: 8000000 INFO @ Mon, 03 Jun 2019 22:45:23: 6000000 INFO @ Mon, 03 Jun 2019 22:45:25: 8000000 INFO @ Mon, 03 Jun 2019 22:45:30: 9000000 INFO @ Mon, 03 Jun 2019 22:45:34: 9000000 INFO @ Mon, 03 Jun 2019 22:45:34: 7000000 INFO @ Mon, 03 Jun 2019 22:45:39: 10000000 INFO @ Mon, 03 Jun 2019 22:45:43: 10000000 INFO @ Mon, 03 Jun 2019 22:45:46: 8000000 INFO @ Mon, 03 Jun 2019 22:45:47: 11000000 INFO @ Mon, 03 Jun 2019 22:45:51: 11000000 INFO @ Mon, 03 Jun 2019 22:45:56: 12000000 INFO @ Mon, 03 Jun 2019 22:45:57: 9000000 INFO @ Mon, 03 Jun 2019 22:46:00: 12000000 INFO @ Mon, 03 Jun 2019 22:46:04: 13000000 INFO @ Mon, 03 Jun 2019 22:46:08: 10000000 INFO @ Mon, 03 Jun 2019 22:46:09: 13000000 INFO @ Mon, 03 Jun 2019 22:46:10: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:46:10: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:46:10: #1 total tags in treatment: 13744910 INFO @ Mon, 03 Jun 2019 22:46:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:46:10: #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 22:46:11: #1 tags after filtering in treatment: 13744910 INFO @ Mon, 03 Jun 2019 22:46:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:46:11: #1 finished! INFO @ Mon, 03 Jun 2019 22:46:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:46:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:46:12: #2 number of paired peaks: 140 WARNING @ Mon, 03 Jun 2019 22:46:12: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Mon, 03 Jun 2019 22:46:12: start model_add_line... INFO @ Mon, 03 Jun 2019 22:46:12: start X-correlation... INFO @ Mon, 03 Jun 2019 22:46:12: end of X-cor INFO @ Mon, 03 Jun 2019 22:46:12: #2 finished! INFO @ Mon, 03 Jun 2019 22:46:12: #2 predicted fragment length is 131 bps INFO @ Mon, 03 Jun 2019 22:46:12: #2 alternative fragment length(s) may be 131 bps INFO @ Mon, 03 Jun 2019 22:46:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.05_model.r INFO @ Mon, 03 Jun 2019 22:46:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:46:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:46:16: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:46:16: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:46:16: #1 total tags in treatment: 13744910 INFO @ Mon, 03 Jun 2019 22:46:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:46:16: #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 22:46:16: #1 tags after filtering in treatment: 13744910 INFO @ Mon, 03 Jun 2019 22:46:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:46:16: #1 finished! INFO @ Mon, 03 Jun 2019 22:46:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:46:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:46:17: #2 number of paired peaks: 140 WARNING @ Mon, 03 Jun 2019 22:46:17: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Mon, 03 Jun 2019 22:46:17: start model_add_line... INFO @ Mon, 03 Jun 2019 22:46:17: start X-correlation... INFO @ Mon, 03 Jun 2019 22:46:17: end of X-cor INFO @ Mon, 03 Jun 2019 22:46:17: #2 finished! INFO @ Mon, 03 Jun 2019 22:46:17: #2 predicted fragment length is 131 bps INFO @ Mon, 03 Jun 2019 22:46:17: #2 alternative fragment length(s) may be 131 bps INFO @ Mon, 03 Jun 2019 22:46:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.20_model.r INFO @ Mon, 03 Jun 2019 22:46:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:46:19: 11000000 INFO @ Mon, 03 Jun 2019 22:46:30: 12000000 INFO @ Mon, 03 Jun 2019 22:46:41: 13000000 INFO @ Mon, 03 Jun 2019 22:46:50: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:46:50: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:46:50: #1 total tags in treatment: 13744910 INFO @ Mon, 03 Jun 2019 22:46:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:46:50: #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 22:46:51: #1 tags after filtering in treatment: 13744910 INFO @ Mon, 03 Jun 2019 22:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:46:51: #1 finished! INFO @ Mon, 03 Jun 2019 22:46:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:46:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:46:52: #2 number of paired peaks: 140 WARNING @ Mon, 03 Jun 2019 22:46:52: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Mon, 03 Jun 2019 22:46:52: start model_add_line... INFO @ Mon, 03 Jun 2019 22:46:52: start X-correlation... INFO @ Mon, 03 Jun 2019 22:46:52: end of X-cor INFO @ Mon, 03 Jun 2019 22:46:52: #2 finished! INFO @ Mon, 03 Jun 2019 22:46:52: #2 predicted fragment length is 131 bps INFO @ Mon, 03 Jun 2019 22:46:52: #2 alternative fragment length(s) may be 131 bps INFO @ Mon, 03 Jun 2019 22:46:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.10_model.r INFO @ Mon, 03 Jun 2019 22:46:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:46:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:47:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:47:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.05_summits.bed INFO @ Mon, 03 Jun 2019 22:47:11: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (5879 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:47:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:47:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:47:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.20_summits.bed INFO @ Mon, 03 Jun 2019 22:47:14: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1397 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:47:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:47:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343086/SRX5343086.10_summits.bed INFO @ Mon, 03 Jun 2019 22:47:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3556 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。