Job ID = 1293632 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,955,656 reads read : 18,955,656 reads written : 18,955,656 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: 00:08:29 18955656 reads; of these: 18955656 (100.00%) were unpaired; of these: 1292089 (6.82%) aligned 0 times 11534751 (60.85%) aligned exactly 1 time 6128816 (32.33%) aligned >1 times 93.18% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 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] 2089276 / 17663567 = 0.1183 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 01:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.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 01:20:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:20:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.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 01:20:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:20:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.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 01:20:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:20:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:20:20: 1000000 INFO @ Mon, 03 Jun 2019 01:20:21: 1000000 INFO @ Mon, 03 Jun 2019 01:20:22: 1000000 INFO @ Mon, 03 Jun 2019 01:20:27: 2000000 INFO @ Mon, 03 Jun 2019 01:20:28: 2000000 INFO @ Mon, 03 Jun 2019 01:20:30: 2000000 INFO @ Mon, 03 Jun 2019 01:20:33: 3000000 INFO @ Mon, 03 Jun 2019 01:20:34: 3000000 INFO @ Mon, 03 Jun 2019 01:20:37: 3000000 INFO @ Mon, 03 Jun 2019 01:20:39: 4000000 INFO @ Mon, 03 Jun 2019 01:20:41: 4000000 INFO @ Mon, 03 Jun 2019 01:20:45: 4000000 INFO @ Mon, 03 Jun 2019 01:20:46: 5000000 INFO @ Mon, 03 Jun 2019 01:20:48: 5000000 INFO @ Mon, 03 Jun 2019 01:20:52: 6000000 INFO @ Mon, 03 Jun 2019 01:20:53: 5000000 INFO @ Mon, 03 Jun 2019 01:20:54: 6000000 INFO @ Mon, 03 Jun 2019 01:20:59: 7000000 INFO @ Mon, 03 Jun 2019 01:21:01: 6000000 INFO @ Mon, 03 Jun 2019 01:21:01: 7000000 INFO @ Mon, 03 Jun 2019 01:21:05: 8000000 INFO @ Mon, 03 Jun 2019 01:21:07: 8000000 INFO @ Mon, 03 Jun 2019 01:21:08: 7000000 INFO @ Mon, 03 Jun 2019 01:21:12: 9000000 INFO @ Mon, 03 Jun 2019 01:21:14: 9000000 INFO @ Mon, 03 Jun 2019 01:21:16: 8000000 INFO @ Mon, 03 Jun 2019 01:21:18: 10000000 INFO @ Mon, 03 Jun 2019 01:21:21: 10000000 INFO @ Mon, 03 Jun 2019 01:21:24: 9000000 INFO @ Mon, 03 Jun 2019 01:21:24: 11000000 INFO @ Mon, 03 Jun 2019 01:21:27: 11000000 INFO @ Mon, 03 Jun 2019 01:21:31: 12000000 INFO @ Mon, 03 Jun 2019 01:21:31: 10000000 INFO @ Mon, 03 Jun 2019 01:21:34: 12000000 INFO @ Mon, 03 Jun 2019 01:21:37: 13000000 INFO @ Mon, 03 Jun 2019 01:21:39: 11000000 INFO @ Mon, 03 Jun 2019 01:21:40: 13000000 INFO @ Mon, 03 Jun 2019 01:21:43: 14000000 INFO @ Mon, 03 Jun 2019 01:21:46: 14000000 INFO @ Mon, 03 Jun 2019 01:21:47: 12000000 INFO @ Mon, 03 Jun 2019 01:21:50: 15000000 INFO @ Mon, 03 Jun 2019 01:21:53: 15000000 INFO @ Mon, 03 Jun 2019 01:21:53: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:21:53: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:21:53: #1 total tags in treatment: 15574291 INFO @ Mon, 03 Jun 2019 01:21:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:21:53: #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 01:21:54: #1 tags after filtering in treatment: 15574291 INFO @ Mon, 03 Jun 2019 01:21:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:21:54: #1 finished! INFO @ Mon, 03 Jun 2019 01:21:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:21:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:21:54: 13000000 INFO @ Mon, 03 Jun 2019 01:21:55: #2 number of paired peaks: 236 WARNING @ Mon, 03 Jun 2019 01:21:55: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Mon, 03 Jun 2019 01:21:55: start model_add_line... INFO @ Mon, 03 Jun 2019 01:21:55: start X-correlation... INFO @ Mon, 03 Jun 2019 01:21:55: end of X-cor INFO @ Mon, 03 Jun 2019 01:21:55: #2 finished! INFO @ Mon, 03 Jun 2019 01:21:55: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 01:21:55: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 03 Jun 2019 01:21:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.20_model.r WARNING @ Mon, 03 Jun 2019 01:21:55: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:21:55: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 03 Jun 2019 01:21:55: #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 01:21:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:21:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:21:57: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:21:57: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:21:57: #1 total tags in treatment: 15574291 INFO @ Mon, 03 Jun 2019 01:21:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:21:57: #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 01:21:57: #1 tags after filtering in treatment: 15574291 INFO @ Mon, 03 Jun 2019 01:21:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:21:57: #1 finished! INFO @ Mon, 03 Jun 2019 01:21:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:21:59: #2 number of paired peaks: 236 WARNING @ Mon, 03 Jun 2019 01:21:59: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Mon, 03 Jun 2019 01:21:59: start model_add_line... INFO @ Mon, 03 Jun 2019 01:21:59: start X-correlation... INFO @ Mon, 03 Jun 2019 01:21:59: end of X-cor INFO @ Mon, 03 Jun 2019 01:21:59: #2 finished! INFO @ Mon, 03 Jun 2019 01:21:59: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 01:21:59: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 03 Jun 2019 01:21:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.10_model.r WARNING @ Mon, 03 Jun 2019 01:21:59: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:21:59: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 03 Jun 2019 01:21:59: #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 01:21:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:21:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:22:01: 14000000 INFO @ Mon, 03 Jun 2019 01:22:09: 15000000 INFO @ Mon, 03 Jun 2019 01:22:13: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:22:13: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:22:13: #1 total tags in treatment: 15574291 INFO @ Mon, 03 Jun 2019 01:22:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:22:13: #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 01:22:14: #1 tags after filtering in treatment: 15574291 INFO @ Mon, 03 Jun 2019 01:22:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:22:14: #1 finished! INFO @ Mon, 03 Jun 2019 01:22:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:22:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:22:15: #2 number of paired peaks: 236 WARNING @ Mon, 03 Jun 2019 01:22:15: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Mon, 03 Jun 2019 01:22:15: start model_add_line... INFO @ Mon, 03 Jun 2019 01:22:15: start X-correlation... INFO @ Mon, 03 Jun 2019 01:22:15: end of X-cor INFO @ Mon, 03 Jun 2019 01:22:15: #2 finished! INFO @ Mon, 03 Jun 2019 01:22:15: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 01:22:15: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 03 Jun 2019 01:22:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.05_model.r WARNING @ Mon, 03 Jun 2019 01:22:15: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:22:15: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 03 Jun 2019 01:22:15: #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 01:22:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:22:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:22:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:22:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:22:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:22:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:22:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:22:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.20_summits.bed INFO @ Mon, 03 Jun 2019 01:22:57: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1210 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:23:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:23:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:23:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.10_summits.bed INFO @ Mon, 03 Jun 2019 01:23:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1893 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:23:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:23:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:23:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032407/SRX1032407.05_summits.bed INFO @ Mon, 03 Jun 2019 01:23:18: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2840 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。