Job ID = 1300230 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,967,021 reads read : 10,967,021 reads written : 10,967,021 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: 00:05:41 10967021 reads; of these: 10967021 (100.00%) were unpaired; of these: 286670 (2.61%) aligned 0 times 6943227 (63.31%) aligned exactly 1 time 3737124 (34.08%) aligned >1 times 97.39% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 1044593 / 10680351 = 0.0978 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 19:13:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.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 19:13:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:13:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:13:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.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 19:13:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.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 19:13:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:13:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:13:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:13:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:13:38: 1000000 INFO @ Mon, 03 Jun 2019 19:13:40: 1000000 INFO @ Mon, 03 Jun 2019 19:13:40: 1000000 INFO @ Mon, 03 Jun 2019 19:13:46: 2000000 INFO @ Mon, 03 Jun 2019 19:13:50: 2000000 INFO @ Mon, 03 Jun 2019 19:13:50: 2000000 INFO @ Mon, 03 Jun 2019 19:13:54: 3000000 INFO @ Mon, 03 Jun 2019 19:14:00: 3000000 INFO @ Mon, 03 Jun 2019 19:14:00: 3000000 INFO @ Mon, 03 Jun 2019 19:14:02: 4000000 INFO @ Mon, 03 Jun 2019 19:14:10: 4000000 INFO @ Mon, 03 Jun 2019 19:14:10: 4000000 INFO @ Mon, 03 Jun 2019 19:14:10: 5000000 INFO @ Mon, 03 Jun 2019 19:14:18: 6000000 INFO @ Mon, 03 Jun 2019 19:14:20: 5000000 INFO @ Mon, 03 Jun 2019 19:14:20: 5000000 INFO @ Mon, 03 Jun 2019 19:14:26: 7000000 INFO @ Mon, 03 Jun 2019 19:14:30: 6000000 INFO @ Mon, 03 Jun 2019 19:14:30: 6000000 INFO @ Mon, 03 Jun 2019 19:14:34: 8000000 INFO @ Mon, 03 Jun 2019 19:14:40: 7000000 INFO @ Mon, 03 Jun 2019 19:14:40: 7000000 INFO @ Mon, 03 Jun 2019 19:14:42: 9000000 INFO @ Mon, 03 Jun 2019 19:14:47: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:14:47: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:14:47: #1 total tags in treatment: 9635758 INFO @ Mon, 03 Jun 2019 19:14:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:14:47: #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 19:14:47: #1 tags after filtering in treatment: 9635758 INFO @ Mon, 03 Jun 2019 19:14:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:14:47: #1 finished! INFO @ Mon, 03 Jun 2019 19:14:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:14:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:14:48: #2 number of paired peaks: 1243 INFO @ Mon, 03 Jun 2019 19:14:48: start model_add_line... INFO @ Mon, 03 Jun 2019 19:14:49: start X-correlation... INFO @ Mon, 03 Jun 2019 19:14:49: end of X-cor INFO @ Mon, 03 Jun 2019 19:14:49: #2 finished! INFO @ Mon, 03 Jun 2019 19:14:49: #2 predicted fragment length is 72 bps INFO @ Mon, 03 Jun 2019 19:14:49: #2 alternative fragment length(s) may be 4,72 bps INFO @ Mon, 03 Jun 2019 19:14:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.05_model.r WARNING @ Mon, 03 Jun 2019 19:14:49: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:14:49: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Mon, 03 Jun 2019 19:14:49: #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 19:14:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:14:49: 8000000 INFO @ Mon, 03 Jun 2019 19:14:49: 8000000 INFO @ Mon, 03 Jun 2019 19:14:59: 9000000 INFO @ Mon, 03 Jun 2019 19:14:59: 9000000 INFO @ Mon, 03 Jun 2019 19:15:05: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:15:05: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:15:05: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:15:05: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:15:05: #1 total tags in treatment: 9635758 INFO @ Mon, 03 Jun 2019 19:15:05: #1 total tags in treatment: 9635758 INFO @ Mon, 03 Jun 2019 19:15:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:15:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:15:05: #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 19:15:05: #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 19:15:05: #1 tags after filtering in treatment: 9635758 INFO @ Mon, 03 Jun 2019 19:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:15:05: #1 finished! INFO @ Mon, 03 Jun 2019 19:15:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:15:05: #1 tags after filtering in treatment: 9635758 INFO @ Mon, 03 Jun 2019 19:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:15:05: #1 finished! INFO @ Mon, 03 Jun 2019 19:15:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:15:06: #2 number of paired peaks: 1243 INFO @ Mon, 03 Jun 2019 19:15:06: start model_add_line... INFO @ Mon, 03 Jun 2019 19:15:06: #2 number of paired peaks: 1243 INFO @ Mon, 03 Jun 2019 19:15:06: start model_add_line... INFO @ Mon, 03 Jun 2019 19:15:06: start X-correlation... INFO @ Mon, 03 Jun 2019 19:15:06: start X-correlation... INFO @ Mon, 03 Jun 2019 19:15:06: end of X-cor INFO @ Mon, 03 Jun 2019 19:15:06: #2 finished! INFO @ Mon, 03 Jun 2019 19:15:06: #2 predicted fragment length is 72 bps INFO @ Mon, 03 Jun 2019 19:15:06: #2 alternative fragment length(s) may be 4,72 bps INFO @ Mon, 03 Jun 2019 19:15:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.20_model.r INFO @ Mon, 03 Jun 2019 19:15:06: end of X-cor INFO @ Mon, 03 Jun 2019 19:15:06: #2 finished! INFO @ Mon, 03 Jun 2019 19:15:06: #2 predicted fragment length is 72 bps INFO @ Mon, 03 Jun 2019 19:15:06: #2 alternative fragment length(s) may be 4,72 bps INFO @ Mon, 03 Jun 2019 19:15:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.10_model.r WARNING @ Mon, 03 Jun 2019 19:15:06: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:15:06: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Mon, 03 Jun 2019 19:15:06: #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 19:15:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:15:06: #3 Pre-compute pvalue-qvalue table... WARNING @ Mon, 03 Jun 2019 19:15:06: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:15:06: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Mon, 03 Jun 2019 19:15:06: #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 19:15:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:15:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:15:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:15:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:15:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:15:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.05_summits.bed INFO @ Mon, 03 Jun 2019 19:15:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2920 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:15:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:15:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:15:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:15:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:15:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.20_summits.bed INFO @ Mon, 03 Jun 2019 19:15:48: Done! INFO @ Mon, 03 Jun 2019 19:15:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:15:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:15:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801815/SRX4801815.10_summits.bed INFO @ Mon, 03 Jun 2019 19:15:48: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1031 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1950 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。