Job ID = 2590260 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,638,531 reads read : 33,638,531 reads written : 33,638,531 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR100229.sra.cache’: 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: 00:15:07 33638531 reads; of these: 33638531 (100.00%) were unpaired; of these: 9528595 (28.33%) aligned 0 times 19805095 (58.88%) aligned exactly 1 time 4304841 (12.80%) aligned >1 times 71.67% overall alignment rate Time searching: 00:15:07 Overall time: 00:15:07 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] 7802860 / 24109936 = 0.3236 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 20:43:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.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 20:43:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:43:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:44:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.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 20:44:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:44:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:44:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.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 20:44:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:44:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:44:10: 1000000 INFO @ Mon, 12 Aug 2019 20:44:11: 1000000 INFO @ Mon, 12 Aug 2019 20:44:15: 1000000 INFO @ Mon, 12 Aug 2019 20:44:20: 2000000 INFO @ Mon, 12 Aug 2019 20:44:22: 2000000 INFO @ Mon, 12 Aug 2019 20:44:29: 2000000 INFO @ Mon, 12 Aug 2019 20:44:31: 3000000 INFO @ Mon, 12 Aug 2019 20:44:32: 3000000 INFO @ Mon, 12 Aug 2019 20:44:42: 4000000 INFO @ Mon, 12 Aug 2019 20:44:42: 3000000 INFO @ Mon, 12 Aug 2019 20:44:43: 4000000 INFO @ Mon, 12 Aug 2019 20:44:52: 5000000 INFO @ Mon, 12 Aug 2019 20:44:53: 5000000 INFO @ Mon, 12 Aug 2019 20:44:55: 4000000 INFO @ Mon, 12 Aug 2019 20:45:02: 6000000 INFO @ Mon, 12 Aug 2019 20:45:04: 6000000 INFO @ Mon, 12 Aug 2019 20:45:08: 5000000 INFO @ Mon, 12 Aug 2019 20:45:12: 7000000 INFO @ Mon, 12 Aug 2019 20:45:14: 7000000 INFO @ Mon, 12 Aug 2019 20:45:21: 6000000 INFO @ Mon, 12 Aug 2019 20:45:22: 8000000 INFO @ Mon, 12 Aug 2019 20:45:23: 8000000 INFO @ Mon, 12 Aug 2019 20:45:32: 9000000 INFO @ Mon, 12 Aug 2019 20:45:33: 9000000 INFO @ Mon, 12 Aug 2019 20:45:34: 7000000 INFO @ Mon, 12 Aug 2019 20:45:42: 10000000 INFO @ Mon, 12 Aug 2019 20:45:43: 10000000 INFO @ Mon, 12 Aug 2019 20:45:46: 8000000 INFO @ Mon, 12 Aug 2019 20:45:52: 11000000 INFO @ Mon, 12 Aug 2019 20:45:53: 11000000 INFO @ Mon, 12 Aug 2019 20:45:58: 9000000 INFO @ Mon, 12 Aug 2019 20:46:02: 12000000 INFO @ Mon, 12 Aug 2019 20:46:03: 12000000 INFO @ Mon, 12 Aug 2019 20:46:10: 10000000 INFO @ Mon, 12 Aug 2019 20:46:12: 13000000 INFO @ Mon, 12 Aug 2019 20:46:14: 13000000 INFO @ Mon, 12 Aug 2019 20:46:22: 14000000 INFO @ Mon, 12 Aug 2019 20:46:22: 11000000 INFO @ Mon, 12 Aug 2019 20:46:24: 14000000 INFO @ Mon, 12 Aug 2019 20:46:32: 15000000 INFO @ Mon, 12 Aug 2019 20:46:34: 15000000 INFO @ Mon, 12 Aug 2019 20:46:35: 12000000 INFO @ Mon, 12 Aug 2019 20:46:42: 16000000 INFO @ Mon, 12 Aug 2019 20:46:44: 16000000 INFO @ Mon, 12 Aug 2019 20:46:45: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:46:45: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:46:45: #1 total tags in treatment: 16307076 INFO @ Mon, 12 Aug 2019 20:46:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:46:45: #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 20:46:45: #1 tags after filtering in treatment: 16307076 INFO @ Mon, 12 Aug 2019 20:46:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:46:45: #1 finished! INFO @ Mon, 12 Aug 2019 20:46:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:46:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:46:47: #2 number of paired peaks: 112 WARNING @ Mon, 12 Aug 2019 20:46:47: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Mon, 12 Aug 2019 20:46:47: start model_add_line... INFO @ Mon, 12 Aug 2019 20:46:47: start X-correlation... INFO @ Mon, 12 Aug 2019 20:46:47: end of X-cor INFO @ Mon, 12 Aug 2019 20:46:47: #2 finished! INFO @ Mon, 12 Aug 2019 20:46:47: #2 predicted fragment length is 214 bps INFO @ Mon, 12 Aug 2019 20:46:47: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 12 Aug 2019 20:46:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.05_model.r INFO @ Mon, 12 Aug 2019 20:46:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:46:47: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:46:47: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:46:47: #1 total tags in treatment: 16307076 INFO @ Mon, 12 Aug 2019 20:46:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:46:47: #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 20:46:47: #1 tags after filtering in treatment: 16307076 INFO @ Mon, 12 Aug 2019 20:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:46:47: #1 finished! INFO @ Mon, 12 Aug 2019 20:46:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:46:48: 13000000 INFO @ Mon, 12 Aug 2019 20:46:49: #2 number of paired peaks: 112 WARNING @ Mon, 12 Aug 2019 20:46:49: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Mon, 12 Aug 2019 20:46:49: start model_add_line... INFO @ Mon, 12 Aug 2019 20:46:49: start X-correlation... INFO @ Mon, 12 Aug 2019 20:46:49: end of X-cor INFO @ Mon, 12 Aug 2019 20:46:49: #2 finished! INFO @ Mon, 12 Aug 2019 20:46:49: #2 predicted fragment length is 214 bps INFO @ Mon, 12 Aug 2019 20:46:49: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 12 Aug 2019 20:46:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.10_model.r INFO @ Mon, 12 Aug 2019 20:46:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:46:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:47:00: 14000000 INFO @ Mon, 12 Aug 2019 20:47:12: 15000000 INFO @ Mon, 12 Aug 2019 20:47:24: 16000000 INFO @ Mon, 12 Aug 2019 20:47:28: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:47:28: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:47:28: #1 total tags in treatment: 16307076 INFO @ Mon, 12 Aug 2019 20:47:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:47:28: #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 20:47:28: #1 tags after filtering in treatment: 16307076 INFO @ Mon, 12 Aug 2019 20:47:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:47:28: #1 finished! INFO @ Mon, 12 Aug 2019 20:47:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:47:30: #2 number of paired peaks: 112 WARNING @ Mon, 12 Aug 2019 20:47:30: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Mon, 12 Aug 2019 20:47:30: start model_add_line... INFO @ Mon, 12 Aug 2019 20:47:30: start X-correlation... INFO @ Mon, 12 Aug 2019 20:47:30: end of X-cor INFO @ Mon, 12 Aug 2019 20:47:30: #2 finished! INFO @ Mon, 12 Aug 2019 20:47:30: #2 predicted fragment length is 214 bps INFO @ Mon, 12 Aug 2019 20:47:30: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 12 Aug 2019 20:47:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.20_model.r INFO @ Mon, 12 Aug 2019 20:47:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:47:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:47:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:47:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:48:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:48:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:48:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.05_summits.bed INFO @ Mon, 12 Aug 2019 20:48:00: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (18053 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:48:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:48:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:48:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.10_summits.bed INFO @ Mon, 12 Aug 2019 20:48:01: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9505 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:48:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:48:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:48:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:48:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX042248/SRX042248.20_summits.bed INFO @ Mon, 12 Aug 2019 20:48:42: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3431 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。