Job ID = 1294939 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,570,684 reads read : 17,570,684 reads written : 17,570,684 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: 00:08:37 17570684 reads; of these: 17570684 (100.00%) were unpaired; of these: 850007 (4.84%) aligned 0 times 11024847 (62.75%) aligned exactly 1 time 5695830 (32.42%) aligned >1 times 95.16% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 2898238 / 16720677 = 0.1733 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 11:09:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.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 11:09:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:09:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:09:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.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 11:09:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:09:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:09:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.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 11:09:06: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:09:06: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:09:14: 1000000 INFO @ Mon, 03 Jun 2019 11:09:15: 1000000 INFO @ Mon, 03 Jun 2019 11:09:17: 1000000 INFO @ Mon, 03 Jun 2019 11:09:22: 2000000 INFO @ Mon, 03 Jun 2019 11:09:23: 2000000 INFO @ Mon, 03 Jun 2019 11:09:27: 2000000 INFO @ Mon, 03 Jun 2019 11:09:29: 3000000 INFO @ Mon, 03 Jun 2019 11:09:32: 3000000 INFO @ Mon, 03 Jun 2019 11:09:37: 4000000 INFO @ Mon, 03 Jun 2019 11:09:37: 3000000 INFO @ Mon, 03 Jun 2019 11:09:41: 4000000 INFO @ Mon, 03 Jun 2019 11:09:45: 5000000 INFO @ Mon, 03 Jun 2019 11:09:47: 4000000 INFO @ Mon, 03 Jun 2019 11:09:49: 5000000 INFO @ Mon, 03 Jun 2019 11:09:52: 6000000 INFO @ Mon, 03 Jun 2019 11:09:57: 5000000 INFO @ Mon, 03 Jun 2019 11:09:58: 6000000 INFO @ Mon, 03 Jun 2019 11:10:00: 7000000 INFO @ Mon, 03 Jun 2019 11:10:06: 7000000 INFO @ Mon, 03 Jun 2019 11:10:07: 8000000 INFO @ Mon, 03 Jun 2019 11:10:08: 6000000 INFO @ Mon, 03 Jun 2019 11:10:14: 8000000 INFO @ Mon, 03 Jun 2019 11:10:15: 9000000 INFO @ Mon, 03 Jun 2019 11:10:18: 7000000 INFO @ Mon, 03 Jun 2019 11:10:22: 10000000 INFO @ Mon, 03 Jun 2019 11:10:23: 9000000 INFO @ Mon, 03 Jun 2019 11:10:28: 8000000 INFO @ Mon, 03 Jun 2019 11:10:30: 11000000 INFO @ Mon, 03 Jun 2019 11:10:31: 10000000 INFO @ Mon, 03 Jun 2019 11:10:37: 12000000 INFO @ Mon, 03 Jun 2019 11:10:38: 9000000 INFO @ Mon, 03 Jun 2019 11:10:39: 11000000 INFO @ Mon, 03 Jun 2019 11:10:45: 13000000 INFO @ Mon, 03 Jun 2019 11:10:48: 12000000 INFO @ Mon, 03 Jun 2019 11:10:48: 10000000 INFO @ Mon, 03 Jun 2019 11:10:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:10:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:10:51: #1 total tags in treatment: 13822439 INFO @ Mon, 03 Jun 2019 11:10:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:10:51: #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 11:10:51: #1 tags after filtering in treatment: 13822439 INFO @ Mon, 03 Jun 2019 11:10:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:10:51: #1 finished! INFO @ Mon, 03 Jun 2019 11:10:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:10:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:10:53: #2 number of paired peaks: 456 WARNING @ Mon, 03 Jun 2019 11:10:53: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Mon, 03 Jun 2019 11:10:53: start model_add_line... INFO @ Mon, 03 Jun 2019 11:10:53: start X-correlation... INFO @ Mon, 03 Jun 2019 11:10:53: end of X-cor INFO @ Mon, 03 Jun 2019 11:10:53: #2 finished! INFO @ Mon, 03 Jun 2019 11:10:53: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 11:10:53: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 11:10:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.05_model.r WARNING @ Mon, 03 Jun 2019 11:10:53: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:10:53: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 11:10:53: #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 11:10:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:10:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:10:56: 13000000 INFO @ Mon, 03 Jun 2019 11:10:58: 11000000 INFO @ Mon, 03 Jun 2019 11:11:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:11:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:11:03: #1 total tags in treatment: 13822439 INFO @ Mon, 03 Jun 2019 11:11:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:11:03: #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 11:11:03: #1 tags after filtering in treatment: 13822439 INFO @ Mon, 03 Jun 2019 11:11:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:11:03: #1 finished! INFO @ Mon, 03 Jun 2019 11:11:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:11:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:11:04: #2 number of paired peaks: 456 WARNING @ Mon, 03 Jun 2019 11:11:04: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Mon, 03 Jun 2019 11:11:04: start model_add_line... INFO @ Mon, 03 Jun 2019 11:11:05: start X-correlation... INFO @ Mon, 03 Jun 2019 11:11:05: end of X-cor INFO @ Mon, 03 Jun 2019 11:11:05: #2 finished! INFO @ Mon, 03 Jun 2019 11:11:05: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 11:11:05: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 11:11:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.10_model.r WARNING @ Mon, 03 Jun 2019 11:11:05: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:11:05: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 11:11:05: #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 11:11:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:11:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:11:07: 12000000 INFO @ Mon, 03 Jun 2019 11:11:17: 13000000 INFO @ Mon, 03 Jun 2019 11:11:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:11:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:11:25: #1 total tags in treatment: 13822439 INFO @ Mon, 03 Jun 2019 11:11:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:11:25: #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 11:11:25: #1 tags after filtering in treatment: 13822439 INFO @ Mon, 03 Jun 2019 11:11:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:11:25: #1 finished! INFO @ Mon, 03 Jun 2019 11:11:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:11:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:11:26: #2 number of paired peaks: 456 WARNING @ Mon, 03 Jun 2019 11:11:26: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Mon, 03 Jun 2019 11:11:26: start model_add_line... INFO @ Mon, 03 Jun 2019 11:11:27: start X-correlation... INFO @ Mon, 03 Jun 2019 11:11:27: end of X-cor INFO @ Mon, 03 Jun 2019 11:11:27: #2 finished! INFO @ Mon, 03 Jun 2019 11:11:27: #2 predicted fragment length is 42 bps INFO @ Mon, 03 Jun 2019 11:11:27: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 03 Jun 2019 11:11:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.20_model.r WARNING @ Mon, 03 Jun 2019 11:11:27: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:11:27: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 03 Jun 2019 11:11:27: #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 11:11:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:11:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:11:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:11:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:11:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:11:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:11:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.05_summits.bed INFO @ Mon, 03 Jun 2019 11:11:48: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2161 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:12:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:12:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:12:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.10_summits.bed INFO @ Mon, 03 Jun 2019 11:12:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1903 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:12:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:12:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:12:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:12:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288003/SRX288003.20_summits.bed INFO @ Mon, 03 Jun 2019 11:12:22: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1494 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。