Job ID = 1294696 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,133,552 reads read : 17,133,552 reads written : 17,133,552 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: 00:08:17 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 669303 (3.91%) aligned 0 times 11145629 (65.05%) aligned exactly 1 time 5318620 (31.04%) aligned >1 times 96.09% overall alignment rate Time searching: 00:08:17 Overall time: 00:08:17 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] 2378876 / 16464249 = 0.1445 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 09:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.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 09:57:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:57:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.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 09:57:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:57:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.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 09:57:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:57:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:57:55: 1000000 INFO @ Mon, 03 Jun 2019 09:57:56: 1000000 INFO @ Mon, 03 Jun 2019 09:57:57: 1000000 INFO @ Mon, 03 Jun 2019 09:58:03: 2000000 INFO @ Mon, 03 Jun 2019 09:58:05: 2000000 INFO @ Mon, 03 Jun 2019 09:58:06: 2000000 INFO @ Mon, 03 Jun 2019 09:58:10: 3000000 INFO @ Mon, 03 Jun 2019 09:58:13: 3000000 INFO @ Mon, 03 Jun 2019 09:58:15: 3000000 INFO @ Mon, 03 Jun 2019 09:58:17: 4000000 INFO @ Mon, 03 Jun 2019 09:58:21: 4000000 INFO @ Mon, 03 Jun 2019 09:58:23: 4000000 INFO @ Mon, 03 Jun 2019 09:58:25: 5000000 INFO @ Mon, 03 Jun 2019 09:58:29: 5000000 INFO @ Mon, 03 Jun 2019 09:58:32: 5000000 INFO @ Mon, 03 Jun 2019 09:58:32: 6000000 INFO @ Mon, 03 Jun 2019 09:58:36: 6000000 INFO @ Mon, 03 Jun 2019 09:58:39: 7000000 INFO @ Mon, 03 Jun 2019 09:58:40: 6000000 INFO @ Mon, 03 Jun 2019 09:58:44: 7000000 INFO @ Mon, 03 Jun 2019 09:58:46: 8000000 INFO @ Mon, 03 Jun 2019 09:58:48: 7000000 INFO @ Mon, 03 Jun 2019 09:58:52: 8000000 INFO @ Mon, 03 Jun 2019 09:58:53: 9000000 INFO @ Mon, 03 Jun 2019 09:58:57: 8000000 INFO @ Mon, 03 Jun 2019 09:59:00: 9000000 INFO @ Mon, 03 Jun 2019 09:59:01: 10000000 INFO @ Mon, 03 Jun 2019 09:59:05: 9000000 INFO @ Mon, 03 Jun 2019 09:59:08: 11000000 INFO @ Mon, 03 Jun 2019 09:59:08: 10000000 INFO @ Mon, 03 Jun 2019 09:59:13: 10000000 INFO @ Mon, 03 Jun 2019 09:59:15: 12000000 INFO @ Mon, 03 Jun 2019 09:59:16: 11000000 INFO @ Mon, 03 Jun 2019 09:59:22: 11000000 INFO @ Mon, 03 Jun 2019 09:59:23: 13000000 INFO @ Mon, 03 Jun 2019 09:59:24: 12000000 INFO @ Mon, 03 Jun 2019 09:59:30: 12000000 INFO @ Mon, 03 Jun 2019 09:59:31: 14000000 INFO @ Mon, 03 Jun 2019 09:59:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:59:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:59:31: #1 total tags in treatment: 14085373 INFO @ Mon, 03 Jun 2019 09:59:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:59:31: #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 09:59:32: #1 tags after filtering in treatment: 14085373 INFO @ Mon, 03 Jun 2019 09:59:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:59:32: #1 finished! INFO @ Mon, 03 Jun 2019 09:59:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:59:32: 13000000 INFO @ Mon, 03 Jun 2019 09:59:33: #2 number of paired peaks: 340 WARNING @ Mon, 03 Jun 2019 09:59:33: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Mon, 03 Jun 2019 09:59:33: start model_add_line... INFO @ Mon, 03 Jun 2019 09:59:33: start X-correlation... INFO @ Mon, 03 Jun 2019 09:59:33: end of X-cor INFO @ Mon, 03 Jun 2019 09:59:33: #2 finished! INFO @ Mon, 03 Jun 2019 09:59:33: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:59:33: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:59:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.10_model.r WARNING @ Mon, 03 Jun 2019 09:59:33: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:59:33: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:59:33: #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 09:59:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:59:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:59:39: 13000000 INFO @ Mon, 03 Jun 2019 09:59:40: 14000000 INFO @ Mon, 03 Jun 2019 09:59:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:59:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:59:41: #1 total tags in treatment: 14085373 INFO @ Mon, 03 Jun 2019 09:59:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:59:41: #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 09:59:41: #1 tags after filtering in treatment: 14085373 INFO @ Mon, 03 Jun 2019 09:59:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:59:41: #1 finished! INFO @ Mon, 03 Jun 2019 09:59:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:59:42: #2 number of paired peaks: 340 WARNING @ Mon, 03 Jun 2019 09:59:42: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Mon, 03 Jun 2019 09:59:42: start model_add_line... INFO @ Mon, 03 Jun 2019 09:59:42: start X-correlation... INFO @ Mon, 03 Jun 2019 09:59:42: end of X-cor INFO @ Mon, 03 Jun 2019 09:59:42: #2 finished! INFO @ Mon, 03 Jun 2019 09:59:42: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:59:42: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:59:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.20_model.r WARNING @ Mon, 03 Jun 2019 09:59:42: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:59:42: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:59:42: #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 09:59:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:59:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:59:47: 14000000 INFO @ Mon, 03 Jun 2019 09:59:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:59:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:59:48: #1 total tags in treatment: 14085373 INFO @ Mon, 03 Jun 2019 09:59:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:59:48: #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 09:59:48: #1 tags after filtering in treatment: 14085373 INFO @ Mon, 03 Jun 2019 09:59:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:59:48: #1 finished! INFO @ Mon, 03 Jun 2019 09:59:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:59:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:59:49: #2 number of paired peaks: 340 WARNING @ Mon, 03 Jun 2019 09:59:49: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Mon, 03 Jun 2019 09:59:49: start model_add_line... INFO @ Mon, 03 Jun 2019 09:59:49: start X-correlation... INFO @ Mon, 03 Jun 2019 09:59:49: end of X-cor INFO @ Mon, 03 Jun 2019 09:59:49: #2 finished! INFO @ Mon, 03 Jun 2019 09:59:49: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:59:49: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.05_model.r WARNING @ Mon, 03 Jun 2019 09:59:49: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:59:49: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:59:49: #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 09:59:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:59:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:00:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:00:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:00:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:00:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:00:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:00:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.10_summits.bed INFO @ Mon, 03 Jun 2019 10:00:30: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1912 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:00:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:00:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:00:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.20_summits.bed INFO @ Mon, 03 Jun 2019 10:00:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1469 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287826/SRX287826.05_summits.bed INFO @ Mon, 03 Jun 2019 10:00:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2217 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。