Job ID = 1306748 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,241,558 reads read : 7,241,558 reads written : 7,241,558 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: 00:02:21 7241558 reads; of these: 7241558 (100.00%) were unpaired; of these: 380089 (5.25%) aligned 0 times 5438439 (75.10%) aligned exactly 1 time 1423030 (19.65%) aligned >1 times 94.75% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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_rmdupse_core] 2788428 / 6861469 = 0.4064 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 22:02:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.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 22:02:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:02:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:02:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.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 22:02:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:02:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:02:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.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 22:02:16: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:02:16: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:02:24: 1000000 INFO @ Mon, 03 Jun 2019 22:02:24: 1000000 INFO @ Mon, 03 Jun 2019 22:02:24: 1000000 INFO @ Mon, 03 Jun 2019 22:02:31: 2000000 INFO @ Mon, 03 Jun 2019 22:02:32: 2000000 INFO @ Mon, 03 Jun 2019 22:02:32: 2000000 INFO @ Mon, 03 Jun 2019 22:02:39: 3000000 INFO @ Mon, 03 Jun 2019 22:02:40: 3000000 INFO @ Mon, 03 Jun 2019 22:02:40: 3000000 INFO @ Mon, 03 Jun 2019 22:02:45: 4000000 INFO @ Mon, 03 Jun 2019 22:02:46: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:02:46: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:02:46: #1 total tags in treatment: 4073041 INFO @ Mon, 03 Jun 2019 22:02:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:02:46: #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 22:02:46: #1 tags after filtering in treatment: 4073041 INFO @ Mon, 03 Jun 2019 22:02:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:02:46: #1 finished! INFO @ Mon, 03 Jun 2019 22:02:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:02:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:02:47: #2 number of paired peaks: 115 WARNING @ Mon, 03 Jun 2019 22:02:47: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Mon, 03 Jun 2019 22:02:47: start model_add_line... INFO @ Mon, 03 Jun 2019 22:02:47: start X-correlation... INFO @ Mon, 03 Jun 2019 22:02:47: end of X-cor INFO @ Mon, 03 Jun 2019 22:02:47: #2 finished! INFO @ Mon, 03 Jun 2019 22:02:47: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 22:02:47: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 22:02:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.10_model.r WARNING @ Mon, 03 Jun 2019 22:02:47: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:02:47: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 22:02:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:02:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:02:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:02:48: 4000000 INFO @ Mon, 03 Jun 2019 22:02:48: 4000000 INFO @ Mon, 03 Jun 2019 22:02:48: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:02:48: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:02:48: #1 total tags in treatment: 4073041 INFO @ Mon, 03 Jun 2019 22:02:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:02:48: #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 22:02:48: #1 tags after filtering in treatment: 4073041 INFO @ Mon, 03 Jun 2019 22:02:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:02:48: #1 finished! INFO @ Mon, 03 Jun 2019 22:02:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:02:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:02:49: #1 tag size is determined as 44 bps INFO @ Mon, 03 Jun 2019 22:02:49: #1 tag size = 44 INFO @ Mon, 03 Jun 2019 22:02:49: #1 total tags in treatment: 4073041 INFO @ Mon, 03 Jun 2019 22:02:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:02:49: #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 22:02:49: #1 tags after filtering in treatment: 4073041 INFO @ Mon, 03 Jun 2019 22:02:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:02:49: #1 finished! INFO @ Mon, 03 Jun 2019 22:02:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:02:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:02:49: #2 number of paired peaks: 115 WARNING @ Mon, 03 Jun 2019 22:02:49: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Mon, 03 Jun 2019 22:02:49: start model_add_line... INFO @ Mon, 03 Jun 2019 22:02:49: start X-correlation... INFO @ Mon, 03 Jun 2019 22:02:49: end of X-cor INFO @ Mon, 03 Jun 2019 22:02:49: #2 finished! INFO @ Mon, 03 Jun 2019 22:02:49: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 22:02:49: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 22:02:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.05_model.r WARNING @ Mon, 03 Jun 2019 22:02:49: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:02:49: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 22:02:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:02:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:02:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:02:49: #2 number of paired peaks: 115 WARNING @ Mon, 03 Jun 2019 22:02:49: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Mon, 03 Jun 2019 22:02:49: start model_add_line... INFO @ Mon, 03 Jun 2019 22:02:49: start X-correlation... INFO @ Mon, 03 Jun 2019 22:02:49: end of X-cor INFO @ Mon, 03 Jun 2019 22:02:49: #2 finished! INFO @ Mon, 03 Jun 2019 22:02:49: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 22:02:49: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 22:02:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.20_model.r WARNING @ Mon, 03 Jun 2019 22:02:49: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:02:49: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 22:02:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 22:02:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:02:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:02:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:03:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:03:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:03:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:03:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:03:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.10_summits.bed INFO @ Mon, 03 Jun 2019 22:03:05: Done! pass1 - making usageList (5 chroms): 2 millis pass2 - checking and writing primary data (171 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:03:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:03:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.05_summits.bed INFO @ Mon, 03 Jun 2019 22:03:07: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (562 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:03:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:03:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507386/SRX507386.20_summits.bed INFO @ Mon, 03 Jun 2019 22:03:07: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。