Job ID = 1295602 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 111,639,082 reads read : 111,639,082 reads written : 111,639,082 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: 00:23:27 111639082 reads; of these: 111639082 (100.00%) were unpaired; of these: 45342466 (40.62%) aligned 0 times 52433909 (46.97%) aligned exactly 1 time 13862707 (12.42%) aligned >1 times 59.38% overall alignment rate Time searching: 00:23:27 Overall time: 00:23:27 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 28 files... [bam_rmdupse_core] 45976467 / 66296616 = 0.6935 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 15:16:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.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 15:16:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:16:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:16:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.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 15:16:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:16:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:16:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.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 15:16:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:16:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:16:29: 1000000 INFO @ Mon, 03 Jun 2019 15:16:29: 1000000 INFO @ Mon, 03 Jun 2019 15:16:30: 1000000 INFO @ Mon, 03 Jun 2019 15:16:36: 2000000 INFO @ Mon, 03 Jun 2019 15:16:37: 2000000 INFO @ Mon, 03 Jun 2019 15:16:38: 2000000 INFO @ Mon, 03 Jun 2019 15:16:44: 3000000 INFO @ Mon, 03 Jun 2019 15:16:45: 3000000 INFO @ Mon, 03 Jun 2019 15:16:46: 3000000 INFO @ Mon, 03 Jun 2019 15:16:51: 4000000 INFO @ Mon, 03 Jun 2019 15:16:52: 4000000 INFO @ Mon, 03 Jun 2019 15:16:53: 4000000 INFO @ Mon, 03 Jun 2019 15:16:59: 5000000 INFO @ Mon, 03 Jun 2019 15:17:01: 5000000 INFO @ Mon, 03 Jun 2019 15:17:01: 5000000 INFO @ Mon, 03 Jun 2019 15:17:07: 6000000 INFO @ Mon, 03 Jun 2019 15:17:08: 6000000 INFO @ Mon, 03 Jun 2019 15:17:09: 6000000 INFO @ Mon, 03 Jun 2019 15:17:15: 7000000 INFO @ Mon, 03 Jun 2019 15:17:16: 7000000 INFO @ Mon, 03 Jun 2019 15:17:17: 7000000 INFO @ Mon, 03 Jun 2019 15:17:24: 8000000 INFO @ Mon, 03 Jun 2019 15:17:24: 8000000 INFO @ Mon, 03 Jun 2019 15:17:25: 8000000 INFO @ Mon, 03 Jun 2019 15:17:32: 9000000 INFO @ Mon, 03 Jun 2019 15:17:32: 9000000 INFO @ Mon, 03 Jun 2019 15:17:33: 9000000 INFO @ Mon, 03 Jun 2019 15:17:39: 10000000 INFO @ Mon, 03 Jun 2019 15:17:40: 10000000 INFO @ Mon, 03 Jun 2019 15:17:41: 10000000 INFO @ Mon, 03 Jun 2019 15:17:47: 11000000 INFO @ Mon, 03 Jun 2019 15:17:48: 11000000 INFO @ Mon, 03 Jun 2019 15:17:49: 11000000 INFO @ Mon, 03 Jun 2019 15:17:55: 12000000 INFO @ Mon, 03 Jun 2019 15:17:56: 12000000 INFO @ Mon, 03 Jun 2019 15:17:58: 12000000 INFO @ Mon, 03 Jun 2019 15:18:03: 13000000 INFO @ Mon, 03 Jun 2019 15:18:04: 13000000 INFO @ Mon, 03 Jun 2019 15:18:05: 13000000 INFO @ Mon, 03 Jun 2019 15:18:10: 14000000 INFO @ Mon, 03 Jun 2019 15:18:12: 14000000 INFO @ Mon, 03 Jun 2019 15:18:13: 14000000 INFO @ Mon, 03 Jun 2019 15:18:18: 15000000 INFO @ Mon, 03 Jun 2019 15:18:20: 15000000 INFO @ Mon, 03 Jun 2019 15:18:21: 15000000 INFO @ Mon, 03 Jun 2019 15:18:26: 16000000 INFO @ Mon, 03 Jun 2019 15:18:29: 16000000 INFO @ Mon, 03 Jun 2019 15:18:29: 16000000 INFO @ Mon, 03 Jun 2019 15:18:33: 17000000 INFO @ Mon, 03 Jun 2019 15:18:36: 17000000 INFO @ Mon, 03 Jun 2019 15:18:39: 17000000 INFO @ Mon, 03 Jun 2019 15:18:41: 18000000 INFO @ Mon, 03 Jun 2019 15:18:44: 18000000 INFO @ Mon, 03 Jun 2019 15:18:47: 18000000 INFO @ Mon, 03 Jun 2019 15:18:49: 19000000 INFO @ Mon, 03 Jun 2019 15:18:52: 19000000 INFO @ Mon, 03 Jun 2019 15:18:55: 19000000 INFO @ Mon, 03 Jun 2019 15:18:56: 20000000 INFO @ Mon, 03 Jun 2019 15:18:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 15:18:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 15:18:59: #1 total tags in treatment: 20320149 INFO @ Mon, 03 Jun 2019 15:18:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:18:59: #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 15:18:59: 20000000 INFO @ Mon, 03 Jun 2019 15:18:59: #1 tags after filtering in treatment: 20320149 INFO @ Mon, 03 Jun 2019 15:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:18:59: #1 finished! INFO @ Mon, 03 Jun 2019 15:18:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:18:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:19:01: #2 number of paired peaks: 334 WARNING @ Mon, 03 Jun 2019 15:19:01: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Mon, 03 Jun 2019 15:19:01: start model_add_line... INFO @ Mon, 03 Jun 2019 15:19:01: start X-correlation... INFO @ Mon, 03 Jun 2019 15:19:01: end of X-cor INFO @ Mon, 03 Jun 2019 15:19:01: #2 finished! INFO @ Mon, 03 Jun 2019 15:19:01: #2 predicted fragment length is 64 bps INFO @ Mon, 03 Jun 2019 15:19:01: #2 alternative fragment length(s) may be 3,64 bps INFO @ Mon, 03 Jun 2019 15:19:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.05_model.r WARNING @ Mon, 03 Jun 2019 15:19:01: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:19:01: #2 You may need to consider one of the other alternative d(s): 3,64 WARNING @ Mon, 03 Jun 2019 15:19:01: #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 15:19:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:19:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 15:19:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 15:19:02: #1 total tags in treatment: 20320149 INFO @ Mon, 03 Jun 2019 15:19:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:19:02: #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 15:19:02: #1 tags after filtering in treatment: 20320149 INFO @ Mon, 03 Jun 2019 15:19:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:19:02: #1 finished! INFO @ Mon, 03 Jun 2019 15:19:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:19:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:19:03: 20000000 INFO @ Mon, 03 Jun 2019 15:19:04: #2 number of paired peaks: 334 WARNING @ Mon, 03 Jun 2019 15:19:04: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Mon, 03 Jun 2019 15:19:04: start model_add_line... INFO @ Mon, 03 Jun 2019 15:19:04: start X-correlation... INFO @ Mon, 03 Jun 2019 15:19:04: end of X-cor INFO @ Mon, 03 Jun 2019 15:19:04: #2 finished! INFO @ Mon, 03 Jun 2019 15:19:04: #2 predicted fragment length is 64 bps INFO @ Mon, 03 Jun 2019 15:19:04: #2 alternative fragment length(s) may be 3,64 bps INFO @ Mon, 03 Jun 2019 15:19:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.20_model.r WARNING @ Mon, 03 Jun 2019 15:19:04: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:19:04: #2 You may need to consider one of the other alternative d(s): 3,64 WARNING @ Mon, 03 Jun 2019 15:19:04: #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 15:19:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:19:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:19:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 15:19:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 15:19:06: #1 total tags in treatment: 20320149 INFO @ Mon, 03 Jun 2019 15:19:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:19:06: #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 15:19:06: #1 tags after filtering in treatment: 20320149 INFO @ Mon, 03 Jun 2019 15:19:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:19:06: #1 finished! INFO @ Mon, 03 Jun 2019 15:19:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:19:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:19:08: #2 number of paired peaks: 334 WARNING @ Mon, 03 Jun 2019 15:19:08: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Mon, 03 Jun 2019 15:19:08: start model_add_line... INFO @ Mon, 03 Jun 2019 15:19:08: start X-correlation... INFO @ Mon, 03 Jun 2019 15:19:08: end of X-cor INFO @ Mon, 03 Jun 2019 15:19:08: #2 finished! INFO @ Mon, 03 Jun 2019 15:19:08: #2 predicted fragment length is 64 bps INFO @ Mon, 03 Jun 2019 15:19:08: #2 alternative fragment length(s) may be 3,64 bps INFO @ Mon, 03 Jun 2019 15:19:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.10_model.r WARNING @ Mon, 03 Jun 2019 15:19:08: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:19:08: #2 You may need to consider one of the other alternative d(s): 3,64 WARNING @ Mon, 03 Jun 2019 15:19:08: #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 15:19:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:19:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:19:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:19:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:20:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:20:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:20:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:20:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.05_summits.bed INFO @ Mon, 03 Jun 2019 15:20:21: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8605 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:20:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:20:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:20:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.20_summits.bed INFO @ Mon, 03 Jun 2019 15:20:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (747 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:20:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:20:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:20:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX373329/SRX373329.10_summits.bed INFO @ Mon, 03 Jun 2019 15:20:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2985 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。