Job ID = 1293622 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,777,089 reads read : 9,777,089 reads written : 9,777,089 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: 00:04:06 9777089 reads; of these: 9777089 (100.00%) were unpaired; of these: 551849 (5.64%) aligned 0 times 6295834 (64.39%) aligned exactly 1 time 2929406 (29.96%) aligned >1 times 94.36% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 894199 / 9225240 = 0.0969 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 01:00:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.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 01:00:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:00:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:00:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.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 01:00:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:00:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:00:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.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 01:00:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:00:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:00:52: 1000000 INFO @ Mon, 03 Jun 2019 01:00:53: 1000000 INFO @ Mon, 03 Jun 2019 01:00:54: 1000000 INFO @ Mon, 03 Jun 2019 01:00:59: 2000000 INFO @ Mon, 03 Jun 2019 01:01:00: 2000000 INFO @ Mon, 03 Jun 2019 01:01:01: 2000000 INFO @ Mon, 03 Jun 2019 01:01:05: 3000000 INFO @ Mon, 03 Jun 2019 01:01:07: 3000000 INFO @ Mon, 03 Jun 2019 01:01:09: 3000000 INFO @ Mon, 03 Jun 2019 01:01:11: 4000000 INFO @ Mon, 03 Jun 2019 01:01:14: 4000000 INFO @ Mon, 03 Jun 2019 01:01:16: 4000000 INFO @ Mon, 03 Jun 2019 01:01:17: 5000000 INFO @ Mon, 03 Jun 2019 01:01:22: 5000000 INFO @ Mon, 03 Jun 2019 01:01:23: 6000000 INFO @ Mon, 03 Jun 2019 01:01:23: 5000000 INFO @ Mon, 03 Jun 2019 01:01:29: 6000000 INFO @ Mon, 03 Jun 2019 01:01:29: 7000000 INFO @ Mon, 03 Jun 2019 01:01:31: 6000000 INFO @ Mon, 03 Jun 2019 01:01:35: 8000000 INFO @ Mon, 03 Jun 2019 01:01:36: 7000000 INFO @ Mon, 03 Jun 2019 01:01:37: #1 tag size is determined as 33 bps INFO @ Mon, 03 Jun 2019 01:01:37: #1 tag size = 33 INFO @ Mon, 03 Jun 2019 01:01:37: #1 total tags in treatment: 8331041 INFO @ Mon, 03 Jun 2019 01:01:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:01:37: #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 01:01:38: #1 tags after filtering in treatment: 8331041 INFO @ Mon, 03 Jun 2019 01:01:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:01:38: #1 finished! INFO @ Mon, 03 Jun 2019 01:01:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:01:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:01:38: 7000000 INFO @ Mon, 03 Jun 2019 01:01:38: #2 number of paired peaks: 494 WARNING @ Mon, 03 Jun 2019 01:01:38: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Mon, 03 Jun 2019 01:01:38: start model_add_line... INFO @ Mon, 03 Jun 2019 01:01:39: start X-correlation... INFO @ Mon, 03 Jun 2019 01:01:39: end of X-cor INFO @ Mon, 03 Jun 2019 01:01:39: #2 finished! INFO @ Mon, 03 Jun 2019 01:01:39: #2 predicted fragment length is 29 bps INFO @ Mon, 03 Jun 2019 01:01:39: #2 alternative fragment length(s) may be 29 bps INFO @ Mon, 03 Jun 2019 01:01:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.20_model.r WARNING @ Mon, 03 Jun 2019 01:01:39: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:01:39: #2 You may need to consider one of the other alternative d(s): 29 WARNING @ Mon, 03 Jun 2019 01:01:39: #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 01:01:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:01:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:01:43: 8000000 INFO @ Mon, 03 Jun 2019 01:01:45: 8000000 INFO @ Mon, 03 Jun 2019 01:01:45: #1 tag size is determined as 33 bps INFO @ Mon, 03 Jun 2019 01:01:45: #1 tag size = 33 INFO @ Mon, 03 Jun 2019 01:01:45: #1 total tags in treatment: 8331041 INFO @ Mon, 03 Jun 2019 01:01:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:01:45: #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 01:01:45: #1 tags after filtering in treatment: 8331041 INFO @ Mon, 03 Jun 2019 01:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:01:45: #1 finished! INFO @ Mon, 03 Jun 2019 01:01:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:01:46: #2 number of paired peaks: 494 WARNING @ Mon, 03 Jun 2019 01:01:46: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Mon, 03 Jun 2019 01:01:46: start model_add_line... INFO @ Mon, 03 Jun 2019 01:01:46: start X-correlation... INFO @ Mon, 03 Jun 2019 01:01:46: end of X-cor INFO @ Mon, 03 Jun 2019 01:01:46: #2 finished! INFO @ Mon, 03 Jun 2019 01:01:46: #2 predicted fragment length is 29 bps INFO @ Mon, 03 Jun 2019 01:01:46: #2 alternative fragment length(s) may be 29 bps INFO @ Mon, 03 Jun 2019 01:01:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.10_model.r WARNING @ Mon, 03 Jun 2019 01:01:46: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:01:46: #2 You may need to consider one of the other alternative d(s): 29 WARNING @ Mon, 03 Jun 2019 01:01:46: #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 01:01:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:01:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:01:48: #1 tag size is determined as 33 bps INFO @ Mon, 03 Jun 2019 01:01:48: #1 tag size = 33 INFO @ Mon, 03 Jun 2019 01:01:48: #1 total tags in treatment: 8331041 INFO @ Mon, 03 Jun 2019 01:01:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:01:48: #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 01:01:48: #1 tags after filtering in treatment: 8331041 INFO @ Mon, 03 Jun 2019 01:01:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:01:48: #1 finished! INFO @ Mon, 03 Jun 2019 01:01:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:01:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:01:49: #2 number of paired peaks: 494 WARNING @ Mon, 03 Jun 2019 01:01:49: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Mon, 03 Jun 2019 01:01:49: start model_add_line... INFO @ Mon, 03 Jun 2019 01:01:49: start X-correlation... INFO @ Mon, 03 Jun 2019 01:01:49: end of X-cor INFO @ Mon, 03 Jun 2019 01:01:49: #2 finished! INFO @ Mon, 03 Jun 2019 01:01:49: #2 predicted fragment length is 29 bps INFO @ Mon, 03 Jun 2019 01:01:49: #2 alternative fragment length(s) may be 29 bps INFO @ Mon, 03 Jun 2019 01:01:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.05_model.r WARNING @ Mon, 03 Jun 2019 01:01:49: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:01:49: #2 You may need to consider one of the other alternative d(s): 29 WARNING @ Mon, 03 Jun 2019 01:01:49: #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 01:01:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:01:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:02:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:02:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:02:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:02:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:02:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:02:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.20_summits.bed INFO @ Mon, 03 Jun 2019 01:02:14: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (888 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:02:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:02:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:02:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.10_summits.bed INFO @ Mon, 03 Jun 2019 01:02:22: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1453 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032396/SRX1032396.05_summits.bed INFO @ Mon, 03 Jun 2019 01:02:24: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1747 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。