Job ID = 1294829 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,744,483 reads read : 19,744,483 reads written : 19,744,483 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: 00:08:13 19744483 reads; of these: 19744483 (100.00%) were unpaired; of these: 1190622 (6.03%) aligned 0 times 13056939 (66.13%) aligned exactly 1 time 5496922 (27.84%) aligned >1 times 93.97% overall alignment rate Time searching: 00:08:13 Overall time: 00:08:13 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] 4771673 / 18553861 = 0.2572 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 10:39:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.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 10:39:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:39:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:39:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.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 10:39:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:39:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:39:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.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 10:39:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:39:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:40:03: 1000000 INFO @ Mon, 03 Jun 2019 10:40:03: 1000000 INFO @ Mon, 03 Jun 2019 10:40:04: 1000000 INFO @ Mon, 03 Jun 2019 10:40:11: 2000000 INFO @ Mon, 03 Jun 2019 10:40:12: 2000000 INFO @ Mon, 03 Jun 2019 10:40:13: 2000000 INFO @ Mon, 03 Jun 2019 10:40:19: 3000000 INFO @ Mon, 03 Jun 2019 10:40:20: 3000000 INFO @ Mon, 03 Jun 2019 10:40:23: 3000000 INFO @ Mon, 03 Jun 2019 10:40:27: 4000000 INFO @ Mon, 03 Jun 2019 10:40:29: 4000000 INFO @ Mon, 03 Jun 2019 10:40:32: 4000000 INFO @ Mon, 03 Jun 2019 10:40:35: 5000000 INFO @ Mon, 03 Jun 2019 10:40:38: 5000000 INFO @ Mon, 03 Jun 2019 10:40:42: 5000000 INFO @ Mon, 03 Jun 2019 10:40:44: 6000000 INFO @ Mon, 03 Jun 2019 10:40:46: 6000000 INFO @ Mon, 03 Jun 2019 10:40:51: 6000000 INFO @ Mon, 03 Jun 2019 10:40:51: 7000000 INFO @ Mon, 03 Jun 2019 10:40:55: 7000000 INFO @ Mon, 03 Jun 2019 10:40:59: 8000000 INFO @ Mon, 03 Jun 2019 10:41:01: 7000000 INFO @ Mon, 03 Jun 2019 10:41:03: 8000000 INFO @ Mon, 03 Jun 2019 10:41:07: 9000000 INFO @ Mon, 03 Jun 2019 10:41:10: 8000000 INFO @ Mon, 03 Jun 2019 10:41:12: 9000000 INFO @ Mon, 03 Jun 2019 10:41:16: 10000000 INFO @ Mon, 03 Jun 2019 10:41:19: 9000000 INFO @ Mon, 03 Jun 2019 10:41:20: 10000000 INFO @ Mon, 03 Jun 2019 10:41:24: 11000000 INFO @ Mon, 03 Jun 2019 10:41:28: 11000000 INFO @ Mon, 03 Jun 2019 10:41:28: 10000000 INFO @ Mon, 03 Jun 2019 10:41:33: 12000000 INFO @ Mon, 03 Jun 2019 10:41:37: 12000000 INFO @ Mon, 03 Jun 2019 10:41:38: 11000000 INFO @ Mon, 03 Jun 2019 10:41:41: 13000000 INFO @ Mon, 03 Jun 2019 10:41:45: 13000000 INFO @ Mon, 03 Jun 2019 10:41:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:41:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:41:47: #1 total tags in treatment: 13782188 INFO @ Mon, 03 Jun 2019 10:41:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:41:47: #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 10:41:48: #1 tags after filtering in treatment: 13782188 INFO @ Mon, 03 Jun 2019 10:41:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:41:48: #1 finished! INFO @ Mon, 03 Jun 2019 10:41:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:41:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:41:48: 12000000 INFO @ Mon, 03 Jun 2019 10:41:49: #2 number of paired peaks: 575 WARNING @ Mon, 03 Jun 2019 10:41:49: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Mon, 03 Jun 2019 10:41:49: start model_add_line... INFO @ Mon, 03 Jun 2019 10:41:49: start X-correlation... INFO @ Mon, 03 Jun 2019 10:41:49: end of X-cor INFO @ Mon, 03 Jun 2019 10:41:49: #2 finished! INFO @ Mon, 03 Jun 2019 10:41:49: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 10:41:49: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 10:41:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.10_model.r INFO @ Mon, 03 Jun 2019 10:41:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:41:52: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:41:52: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:41:52: #1 total tags in treatment: 13782188 INFO @ Mon, 03 Jun 2019 10:41:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:41:52: #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 10:41:52: #1 tags after filtering in treatment: 13782188 INFO @ Mon, 03 Jun 2019 10:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:41:52: #1 finished! INFO @ Mon, 03 Jun 2019 10:41:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:41:53: #2 number of paired peaks: 575 WARNING @ Mon, 03 Jun 2019 10:41:53: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Mon, 03 Jun 2019 10:41:53: start model_add_line... INFO @ Mon, 03 Jun 2019 10:41:53: start X-correlation... INFO @ Mon, 03 Jun 2019 10:41:53: end of X-cor INFO @ Mon, 03 Jun 2019 10:41:53: #2 finished! INFO @ Mon, 03 Jun 2019 10:41:53: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 10:41:53: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 10:41:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.20_model.r INFO @ Mon, 03 Jun 2019 10:41:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:41:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:41:58: 13000000 INFO @ Mon, 03 Jun 2019 10:42:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:42:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:42:05: #1 total tags in treatment: 13782188 INFO @ Mon, 03 Jun 2019 10:42:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:42:05: #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 10:42:05: #1 tags after filtering in treatment: 13782188 INFO @ Mon, 03 Jun 2019 10:42:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:42:05: #1 finished! INFO @ Mon, 03 Jun 2019 10:42:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:42:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:42:07: #2 number of paired peaks: 575 WARNING @ Mon, 03 Jun 2019 10:42:07: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Mon, 03 Jun 2019 10:42:07: start model_add_line... INFO @ Mon, 03 Jun 2019 10:42:07: start X-correlation... INFO @ Mon, 03 Jun 2019 10:42:07: end of X-cor INFO @ Mon, 03 Jun 2019 10:42:07: #2 finished! INFO @ Mon, 03 Jun 2019 10:42:07: #2 predicted fragment length is 191 bps INFO @ Mon, 03 Jun 2019 10:42:07: #2 alternative fragment length(s) may be 191 bps INFO @ Mon, 03 Jun 2019 10:42:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.05_model.r INFO @ Mon, 03 Jun 2019 10:42:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:42:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:42:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:42:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:42:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:42:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:42:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:42:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.10_summits.bed INFO @ Mon, 03 Jun 2019 10:42:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1323 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:42:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:42:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:42:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.20_summits.bed INFO @ Mon, 03 Jun 2019 10:42:53: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (940 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:43:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:43:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:43:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287928/SRX287928.05_summits.bed INFO @ Mon, 03 Jun 2019 10:43:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1761 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。