Job ID = 1294820 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,226,423 reads read : 16,226,423 reads written : 16,226,423 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: 00:06:11 16226423 reads; of these: 16226423 (100.00%) were unpaired; of these: 905351 (5.58%) aligned 0 times 12585231 (77.56%) aligned exactly 1 time 2735841 (16.86%) aligned >1 times 94.42% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 3438767 / 15321072 = 0.2244 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 10:33:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.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 10:33:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:33:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:33:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.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 10:33:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:33:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:33:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.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 10:33:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:33:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:33:11: 1000000 INFO @ Mon, 03 Jun 2019 10:33:11: 1000000 INFO @ Mon, 03 Jun 2019 10:33:12: 1000000 INFO @ Mon, 03 Jun 2019 10:33:20: 2000000 INFO @ Mon, 03 Jun 2019 10:33:21: 2000000 INFO @ Mon, 03 Jun 2019 10:33:22: 2000000 INFO @ Mon, 03 Jun 2019 10:33:28: 3000000 INFO @ Mon, 03 Jun 2019 10:33:30: 3000000 INFO @ Mon, 03 Jun 2019 10:33:33: 3000000 INFO @ Mon, 03 Jun 2019 10:33:36: 4000000 INFO @ Mon, 03 Jun 2019 10:33:38: 4000000 INFO @ Mon, 03 Jun 2019 10:33:43: 4000000 INFO @ Mon, 03 Jun 2019 10:33:44: 5000000 INFO @ Mon, 03 Jun 2019 10:33:47: 5000000 INFO @ Mon, 03 Jun 2019 10:33:52: 6000000 INFO @ Mon, 03 Jun 2019 10:33:53: 5000000 INFO @ Mon, 03 Jun 2019 10:33:56: 6000000 INFO @ Mon, 03 Jun 2019 10:34:00: 7000000 INFO @ Mon, 03 Jun 2019 10:34:04: 6000000 INFO @ Mon, 03 Jun 2019 10:34:05: 7000000 INFO @ Mon, 03 Jun 2019 10:34:08: 8000000 INFO @ Mon, 03 Jun 2019 10:34:14: 7000000 INFO @ Mon, 03 Jun 2019 10:34:14: 8000000 INFO @ Mon, 03 Jun 2019 10:34:16: 9000000 INFO @ Mon, 03 Jun 2019 10:34:24: 9000000 INFO @ Mon, 03 Jun 2019 10:34:24: 8000000 INFO @ Mon, 03 Jun 2019 10:34:24: 10000000 INFO @ Mon, 03 Jun 2019 10:34:32: 11000000 INFO @ Mon, 03 Jun 2019 10:34:33: 10000000 INFO @ Mon, 03 Jun 2019 10:34:34: 9000000 INFO @ Mon, 03 Jun 2019 10:34:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:34:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:34:39: #1 total tags in treatment: 11882305 INFO @ Mon, 03 Jun 2019 10:34:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:34:39: #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 10:34:39: #1 tags after filtering in treatment: 11882305 INFO @ Mon, 03 Jun 2019 10:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:34:39: #1 finished! INFO @ Mon, 03 Jun 2019 10:34:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:34:40: #2 number of paired peaks: 676 WARNING @ Mon, 03 Jun 2019 10:34:40: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Mon, 03 Jun 2019 10:34:40: start model_add_line... INFO @ Mon, 03 Jun 2019 10:34:40: start X-correlation... INFO @ Mon, 03 Jun 2019 10:34:40: end of X-cor INFO @ Mon, 03 Jun 2019 10:34:40: #2 finished! INFO @ Mon, 03 Jun 2019 10:34:40: #2 predicted fragment length is 182 bps INFO @ Mon, 03 Jun 2019 10:34:40: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 03 Jun 2019 10:34:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.05_model.r INFO @ Mon, 03 Jun 2019 10:34:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:34:42: 11000000 INFO @ Mon, 03 Jun 2019 10:34:44: 10000000 INFO @ Mon, 03 Jun 2019 10:34:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:34:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:34:49: #1 total tags in treatment: 11882305 INFO @ Mon, 03 Jun 2019 10:34:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:34:49: #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 10:34:50: #1 tags after filtering in treatment: 11882305 INFO @ Mon, 03 Jun 2019 10:34:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:34:50: #1 finished! INFO @ Mon, 03 Jun 2019 10:34:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:34:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:34:51: #2 number of paired peaks: 676 WARNING @ Mon, 03 Jun 2019 10:34:51: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Mon, 03 Jun 2019 10:34:51: start model_add_line... INFO @ Mon, 03 Jun 2019 10:34:51: start X-correlation... INFO @ Mon, 03 Jun 2019 10:34:51: end of X-cor INFO @ Mon, 03 Jun 2019 10:34:51: #2 finished! INFO @ Mon, 03 Jun 2019 10:34:51: #2 predicted fragment length is 182 bps INFO @ Mon, 03 Jun 2019 10:34:51: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 03 Jun 2019 10:34:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.10_model.r INFO @ Mon, 03 Jun 2019 10:34:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:34:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:34:54: 11000000 INFO @ Mon, 03 Jun 2019 10:35:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:35:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:35:03: #1 total tags in treatment: 11882305 INFO @ Mon, 03 Jun 2019 10:35:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:35:03: #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 10:35:03: #1 tags after filtering in treatment: 11882305 INFO @ Mon, 03 Jun 2019 10:35:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:35:03: #1 finished! INFO @ Mon, 03 Jun 2019 10:35:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:35:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:35:04: #2 number of paired peaks: 676 WARNING @ Mon, 03 Jun 2019 10:35:04: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Mon, 03 Jun 2019 10:35:04: start model_add_line... INFO @ Mon, 03 Jun 2019 10:35:04: start X-correlation... INFO @ Mon, 03 Jun 2019 10:35:04: end of X-cor INFO @ Mon, 03 Jun 2019 10:35:04: #2 finished! INFO @ Mon, 03 Jun 2019 10:35:04: #2 predicted fragment length is 182 bps INFO @ Mon, 03 Jun 2019 10:35:04: #2 alternative fragment length(s) may be 182 bps INFO @ Mon, 03 Jun 2019 10:35:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.20_model.r INFO @ Mon, 03 Jun 2019 10:35:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:35:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:35:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:35:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:35:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:35:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:35:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.05_summits.bed INFO @ Mon, 03 Jun 2019 10:35:34: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5640 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:35:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:35:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:35:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:35:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.10_summits.bed INFO @ Mon, 03 Jun 2019 10:35:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3896 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:35:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:35:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:35:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287919/SRX287919.20_summits.bed INFO @ Mon, 03 Jun 2019 10:35:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2166 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。