Job ID = 2590605 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,917,825 reads read : 71,835,650 reads written : 35,917,825 reads 0-length : 35,917,825 rm: cannot remove ‘[DSE]RR*’: 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: 00:22:10 35917825 reads; of these: 35917825 (100.00%) were unpaired; of these: 664980 (1.85%) aligned 0 times 9952746 (27.71%) aligned exactly 1 time 25300099 (70.44%) aligned >1 times 98.15% overall alignment rate Time searching: 00:22:10 Overall time: 00:22:10 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 16 files... [bam_rmdupse_core] 15559728 / 35252845 = 0.4414 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, 12 Aug 2019 23:12:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.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, 12 Aug 2019 23:12:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:12:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:12:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.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, 12 Aug 2019 23:12:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:12:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:12:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.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, 12 Aug 2019 23:12:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:12:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:12:34: 1000000 INFO @ Mon, 12 Aug 2019 23:12:35: 1000000 INFO @ Mon, 12 Aug 2019 23:12:36: 1000000 INFO @ Mon, 12 Aug 2019 23:12:43: 2000000 INFO @ Mon, 12 Aug 2019 23:12:44: 2000000 INFO @ Mon, 12 Aug 2019 23:12:45: 2000000 INFO @ Mon, 12 Aug 2019 23:12:51: 3000000 INFO @ Mon, 12 Aug 2019 23:12:51: 3000000 INFO @ Mon, 12 Aug 2019 23:12:55: 3000000 INFO @ Mon, 12 Aug 2019 23:12:59: 4000000 INFO @ Mon, 12 Aug 2019 23:12:59: 4000000 INFO @ Mon, 12 Aug 2019 23:13:04: 4000000 INFO @ Mon, 12 Aug 2019 23:13:06: 5000000 INFO @ Mon, 12 Aug 2019 23:13:07: 5000000 INFO @ Mon, 12 Aug 2019 23:13:12: 5000000 INFO @ Mon, 12 Aug 2019 23:13:13: 6000000 INFO @ Mon, 12 Aug 2019 23:13:16: 6000000 INFO @ Mon, 12 Aug 2019 23:13:20: 7000000 INFO @ Mon, 12 Aug 2019 23:13:21: 6000000 INFO @ Mon, 12 Aug 2019 23:13:24: 7000000 INFO @ Mon, 12 Aug 2019 23:13:27: 8000000 INFO @ Mon, 12 Aug 2019 23:13:30: 7000000 INFO @ Mon, 12 Aug 2019 23:13:33: 8000000 INFO @ Mon, 12 Aug 2019 23:13:34: 9000000 INFO @ Mon, 12 Aug 2019 23:13:38: 8000000 INFO @ Mon, 12 Aug 2019 23:13:41: 9000000 INFO @ Mon, 12 Aug 2019 23:13:42: 10000000 INFO @ Mon, 12 Aug 2019 23:13:46: 9000000 INFO @ Mon, 12 Aug 2019 23:13:49: 11000000 INFO @ Mon, 12 Aug 2019 23:13:49: 10000000 INFO @ Mon, 12 Aug 2019 23:13:55: 10000000 INFO @ Mon, 12 Aug 2019 23:13:56: 12000000 INFO @ Mon, 12 Aug 2019 23:13:58: 11000000 INFO @ Mon, 12 Aug 2019 23:14:03: 11000000 INFO @ Mon, 12 Aug 2019 23:14:03: 13000000 INFO @ Mon, 12 Aug 2019 23:14:06: 12000000 INFO @ Mon, 12 Aug 2019 23:14:10: 14000000 INFO @ Mon, 12 Aug 2019 23:14:11: 12000000 INFO @ Mon, 12 Aug 2019 23:14:14: 13000000 INFO @ Mon, 12 Aug 2019 23:14:17: 15000000 INFO @ Mon, 12 Aug 2019 23:14:19: 13000000 INFO @ Mon, 12 Aug 2019 23:14:23: 14000000 INFO @ Mon, 12 Aug 2019 23:14:24: 16000000 INFO @ Mon, 12 Aug 2019 23:14:28: 14000000 INFO @ Mon, 12 Aug 2019 23:14:31: 15000000 INFO @ Mon, 12 Aug 2019 23:14:31: 17000000 INFO @ Mon, 12 Aug 2019 23:14:36: 15000000 INFO @ Mon, 12 Aug 2019 23:14:38: 18000000 INFO @ Mon, 12 Aug 2019 23:14:39: 16000000 INFO @ Mon, 12 Aug 2019 23:14:44: 16000000 INFO @ Mon, 12 Aug 2019 23:14:45: 19000000 INFO @ Mon, 12 Aug 2019 23:14:47: 17000000 INFO @ Mon, 12 Aug 2019 23:14:50: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:14:50: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:14:50: #1 total tags in treatment: 19693117 INFO @ Mon, 12 Aug 2019 23:14:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:14:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:14:51: #1 tags after filtering in treatment: 19693117 INFO @ Mon, 12 Aug 2019 23:14:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:14:51: #1 finished! INFO @ Mon, 12 Aug 2019 23:14:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:14:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:14:52: 17000000 INFO @ Mon, 12 Aug 2019 23:14:53: #2 number of paired peaks: 2453 INFO @ Mon, 12 Aug 2019 23:14:53: start model_add_line... INFO @ Mon, 12 Aug 2019 23:14:53: start X-correlation... INFO @ Mon, 12 Aug 2019 23:14:53: end of X-cor INFO @ Mon, 12 Aug 2019 23:14:53: #2 finished! INFO @ Mon, 12 Aug 2019 23:14:53: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 23:14:53: #2 alternative fragment length(s) may be 3,48 bps INFO @ Mon, 12 Aug 2019 23:14:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.20_model.r WARNING @ Mon, 12 Aug 2019 23:14:53: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:14:53: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Mon, 12 Aug 2019 23:14:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:14:53: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:14:56: 18000000 INFO @ Mon, 12 Aug 2019 23:15:01: 18000000 INFO @ Mon, 12 Aug 2019 23:15:04: 19000000 INFO @ Mon, 12 Aug 2019 23:15:09: 19000000 INFO @ Mon, 12 Aug 2019 23:15:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:15:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:15:10: #1 total tags in treatment: 19693117 INFO @ Mon, 12 Aug 2019 23:15:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:15:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:15:10: #1 tags after filtering in treatment: 19693117 INFO @ Mon, 12 Aug 2019 23:15:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:15:10: #1 finished! INFO @ Mon, 12 Aug 2019 23:15:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:15:12: #2 number of paired peaks: 2453 INFO @ Mon, 12 Aug 2019 23:15:12: start model_add_line... INFO @ Mon, 12 Aug 2019 23:15:12: start X-correlation... INFO @ Mon, 12 Aug 2019 23:15:12: end of X-cor INFO @ Mon, 12 Aug 2019 23:15:12: #2 finished! INFO @ Mon, 12 Aug 2019 23:15:12: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 23:15:12: #2 alternative fragment length(s) may be 3,48 bps INFO @ Mon, 12 Aug 2019 23:15:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.10_model.r WARNING @ Mon, 12 Aug 2019 23:15:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:15:12: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Mon, 12 Aug 2019 23:15:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:15:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:15:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:15:14: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:15:14: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:15:14: #1 total tags in treatment: 19693117 INFO @ Mon, 12 Aug 2019 23:15:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:15:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:15:15: #1 tags after filtering in treatment: 19693117 INFO @ Mon, 12 Aug 2019 23:15:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:15:15: #1 finished! INFO @ Mon, 12 Aug 2019 23:15:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:15:17: #2 number of paired peaks: 2453 INFO @ Mon, 12 Aug 2019 23:15:17: start model_add_line... INFO @ Mon, 12 Aug 2019 23:15:17: start X-correlation... INFO @ Mon, 12 Aug 2019 23:15:17: end of X-cor INFO @ Mon, 12 Aug 2019 23:15:17: #2 finished! INFO @ Mon, 12 Aug 2019 23:15:17: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 23:15:17: #2 alternative fragment length(s) may be 3,48 bps INFO @ Mon, 12 Aug 2019 23:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.05_model.r WARNING @ Mon, 12 Aug 2019 23:15:17: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:15:17: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Mon, 12 Aug 2019 23:15:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:15:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:15:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:15:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:15:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.20_summits.bed INFO @ Mon, 12 Aug 2019 23:16:03: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1859 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:16:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:16:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:16:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:16:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.10_summits.bed INFO @ Mon, 12 Aug 2019 23:16:23: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7969 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:16:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:16:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:16:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923189/SRX4923189.05_summits.bed INFO @ Mon, 12 Aug 2019 23:16:28: Done! pass1 - making usageList (14 chroms): 8 millis pass2 - checking and writing primary data (18059 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。