Job ID = 1294067 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,968,817 reads read : 19,968,817 reads written : 19,968,817 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: 00:04:19 19968817 reads; of these: 19968817 (100.00%) were unpaired; of these: 1994047 (9.99%) aligned 0 times 15675051 (78.50%) aligned exactly 1 time 2299719 (11.52%) aligned >1 times 90.01% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 10238494 / 17974770 = 0.5696 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 04:41:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.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 04:41:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:41:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:41:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.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 04:41:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:41:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:41:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.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 04:41:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:41:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:41:30: 1000000 INFO @ Mon, 03 Jun 2019 04:41:30: 1000000 INFO @ Mon, 03 Jun 2019 04:41:30: 1000000 INFO @ Mon, 03 Jun 2019 04:41:37: 2000000 INFO @ Mon, 03 Jun 2019 04:41:38: 2000000 INFO @ Mon, 03 Jun 2019 04:41:38: 2000000 INFO @ Mon, 03 Jun 2019 04:41:44: 3000000 INFO @ Mon, 03 Jun 2019 04:41:45: 3000000 INFO @ Mon, 03 Jun 2019 04:41:45: 3000000 INFO @ Mon, 03 Jun 2019 04:41:51: 4000000 INFO @ Mon, 03 Jun 2019 04:41:52: 4000000 INFO @ Mon, 03 Jun 2019 04:41:52: 4000000 INFO @ Mon, 03 Jun 2019 04:41:58: 5000000 INFO @ Mon, 03 Jun 2019 04:42:00: 5000000 INFO @ Mon, 03 Jun 2019 04:42:00: 5000000 INFO @ Mon, 03 Jun 2019 04:42:05: 6000000 INFO @ Mon, 03 Jun 2019 04:42:07: 6000000 INFO @ Mon, 03 Jun 2019 04:42:07: 6000000 INFO @ Mon, 03 Jun 2019 04:42:12: 7000000 INFO @ Mon, 03 Jun 2019 04:42:15: 7000000 INFO @ Mon, 03 Jun 2019 04:42:15: 7000000 INFO @ Mon, 03 Jun 2019 04:42:17: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:42:17: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:42:17: #1 total tags in treatment: 7736276 INFO @ Mon, 03 Jun 2019 04:42:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:42:17: #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 04:42:17: #1 tags after filtering in treatment: 7736276 INFO @ Mon, 03 Jun 2019 04:42:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:42:17: #1 finished! INFO @ Mon, 03 Jun 2019 04:42:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:42:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:42:18: #2 number of paired peaks: 413 WARNING @ Mon, 03 Jun 2019 04:42:18: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Mon, 03 Jun 2019 04:42:18: start model_add_line... INFO @ Mon, 03 Jun 2019 04:42:18: start X-correlation... INFO @ Mon, 03 Jun 2019 04:42:18: end of X-cor INFO @ Mon, 03 Jun 2019 04:42:18: #2 finished! INFO @ Mon, 03 Jun 2019 04:42:18: #2 predicted fragment length is 144 bps INFO @ Mon, 03 Jun 2019 04:42:18: #2 alternative fragment length(s) may be 144 bps INFO @ Mon, 03 Jun 2019 04:42:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.20_model.r INFO @ Mon, 03 Jun 2019 04:42:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:42:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:42:20: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:42:20: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:42:20: #1 total tags in treatment: 7736276 INFO @ Mon, 03 Jun 2019 04:42:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:42:20: #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 04:42:20: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 04:42:20: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 04:42:20: #1 total tags in treatment: 7736276 INFO @ Mon, 03 Jun 2019 04:42:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:42:20: #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 04:42:20: #1 tags after filtering in treatment: 7736276 INFO @ Mon, 03 Jun 2019 04:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:42:20: #1 finished! INFO @ Mon, 03 Jun 2019 04:42:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:42:20: #1 tags after filtering in treatment: 7736276 INFO @ Mon, 03 Jun 2019 04:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:42:20: #1 finished! INFO @ Mon, 03 Jun 2019 04:42:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:42:21: #2 number of paired peaks: 413 WARNING @ Mon, 03 Jun 2019 04:42:21: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Mon, 03 Jun 2019 04:42:21: start model_add_line... INFO @ Mon, 03 Jun 2019 04:42:21: #2 number of paired peaks: 413 WARNING @ Mon, 03 Jun 2019 04:42:21: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Mon, 03 Jun 2019 04:42:21: start model_add_line... INFO @ Mon, 03 Jun 2019 04:42:21: start X-correlation... INFO @ Mon, 03 Jun 2019 04:42:21: start X-correlation... INFO @ Mon, 03 Jun 2019 04:42:21: end of X-cor INFO @ Mon, 03 Jun 2019 04:42:21: #2 finished! INFO @ Mon, 03 Jun 2019 04:42:21: #2 predicted fragment length is 144 bps INFO @ Mon, 03 Jun 2019 04:42:21: #2 alternative fragment length(s) may be 144 bps INFO @ Mon, 03 Jun 2019 04:42:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.05_model.r INFO @ Mon, 03 Jun 2019 04:42:21: end of X-cor INFO @ Mon, 03 Jun 2019 04:42:21: #2 finished! INFO @ Mon, 03 Jun 2019 04:42:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:42:21: #2 predicted fragment length is 144 bps INFO @ Mon, 03 Jun 2019 04:42:21: #2 alternative fragment length(s) may be 144 bps INFO @ Mon, 03 Jun 2019 04:42:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.10_model.r INFO @ Mon, 03 Jun 2019 04:42:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:42:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:42:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:42:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:42:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:42:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:42:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:42:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:42:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.20_summits.bed INFO @ Mon, 03 Jun 2019 04:42:53: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (554 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:42:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:42:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:42:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.10_summits.bed INFO @ Mon, 03 Jun 2019 04:42:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1523 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:42:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:42:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:42:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX181425/SRX181425.05_summits.bed INFO @ Mon, 03 Jun 2019 04:42:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3662 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。