Job ID = 2590476 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,873,433 reads read : 15,746,866 reads written : 7,873,433 reads 0-length : 7,873,433 spots read : 7,862,744 reads read : 15,725,488 reads written : 7,862,744 reads 0-length : 7,862,744 spots read : 7,895,584 reads read : 15,791,168 reads written : 7,895,584 reads 0-length : 7,895,584 spots read : 7,931,868 reads read : 15,863,736 reads written : 7,931,868 reads 0-length : 7,931,868 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: 00:00:01 Multiseed full-index search: 00:10:00 31563629 reads; of these: 31563629 (100.00%) were unpaired; of these: 1426322 (4.52%) aligned 0 times 23424603 (74.21%) aligned exactly 1 time 6712704 (21.27%) aligned >1 times 95.48% overall alignment rate Time searching: 00:10:01 Overall time: 00:10:01 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] 4071204 / 30137307 = 0.1351 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 22:19:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.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 22:19:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:19:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:19:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.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 22:19:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:19:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:19:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.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 22:19:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:19:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:20:03: 1000000 INFO @ Mon, 12 Aug 2019 22:20:05: 1000000 INFO @ Mon, 12 Aug 2019 22:20:05: 1000000 INFO @ Mon, 12 Aug 2019 22:20:11: 2000000 INFO @ Mon, 12 Aug 2019 22:20:12: 2000000 INFO @ Mon, 12 Aug 2019 22:20:13: 2000000 INFO @ Mon, 12 Aug 2019 22:20:19: 3000000 INFO @ Mon, 12 Aug 2019 22:20:20: 3000000 INFO @ Mon, 12 Aug 2019 22:20:21: 3000000 INFO @ Mon, 12 Aug 2019 22:20:26: 4000000 INFO @ Mon, 12 Aug 2019 22:20:28: 4000000 INFO @ Mon, 12 Aug 2019 22:20:28: 4000000 INFO @ Mon, 12 Aug 2019 22:20:34: 5000000 INFO @ Mon, 12 Aug 2019 22:20:35: 5000000 INFO @ Mon, 12 Aug 2019 22:20:36: 5000000 INFO @ Mon, 12 Aug 2019 22:20:41: 6000000 INFO @ Mon, 12 Aug 2019 22:20:43: 6000000 INFO @ Mon, 12 Aug 2019 22:20:43: 6000000 INFO @ Mon, 12 Aug 2019 22:20:49: 7000000 INFO @ Mon, 12 Aug 2019 22:20:50: 7000000 INFO @ Mon, 12 Aug 2019 22:20:51: 7000000 INFO @ Mon, 12 Aug 2019 22:20:57: 8000000 INFO @ Mon, 12 Aug 2019 22:20:58: 8000000 INFO @ Mon, 12 Aug 2019 22:20:59: 8000000 INFO @ Mon, 12 Aug 2019 22:21:04: 9000000 INFO @ Mon, 12 Aug 2019 22:21:06: 9000000 INFO @ Mon, 12 Aug 2019 22:21:06: 9000000 INFO @ Mon, 12 Aug 2019 22:21:12: 10000000 INFO @ Mon, 12 Aug 2019 22:21:13: 10000000 INFO @ Mon, 12 Aug 2019 22:21:14: 10000000 INFO @ Mon, 12 Aug 2019 22:21:19: 11000000 INFO @ Mon, 12 Aug 2019 22:21:21: 11000000 INFO @ Mon, 12 Aug 2019 22:21:21: 11000000 INFO @ Mon, 12 Aug 2019 22:21:27: 12000000 INFO @ Mon, 12 Aug 2019 22:21:29: 12000000 INFO @ Mon, 12 Aug 2019 22:21:29: 12000000 INFO @ Mon, 12 Aug 2019 22:21:35: 13000000 INFO @ Mon, 12 Aug 2019 22:21:37: 13000000 INFO @ Mon, 12 Aug 2019 22:21:37: 13000000 INFO @ Mon, 12 Aug 2019 22:21:42: 14000000 INFO @ Mon, 12 Aug 2019 22:21:44: 14000000 INFO @ Mon, 12 Aug 2019 22:21:44: 14000000 INFO @ Mon, 12 Aug 2019 22:21:50: 15000000 INFO @ Mon, 12 Aug 2019 22:21:52: 15000000 INFO @ Mon, 12 Aug 2019 22:21:52: 15000000 INFO @ Mon, 12 Aug 2019 22:21:58: 16000000 INFO @ Mon, 12 Aug 2019 22:22:00: 16000000 INFO @ Mon, 12 Aug 2019 22:22:00: 16000000 INFO @ Mon, 12 Aug 2019 22:22:06: 17000000 INFO @ Mon, 12 Aug 2019 22:22:07: 17000000 INFO @ Mon, 12 Aug 2019 22:22:07: 17000000 INFO @ Mon, 12 Aug 2019 22:22:13: 18000000 INFO @ Mon, 12 Aug 2019 22:22:15: 18000000 INFO @ Mon, 12 Aug 2019 22:22:15: 18000000 INFO @ Mon, 12 Aug 2019 22:22:21: 19000000 INFO @ Mon, 12 Aug 2019 22:22:22: 19000000 INFO @ Mon, 12 Aug 2019 22:22:22: 19000000 INFO @ Mon, 12 Aug 2019 22:22:28: 20000000 INFO @ Mon, 12 Aug 2019 22:22:30: 20000000 INFO @ Mon, 12 Aug 2019 22:22:30: 20000000 INFO @ Mon, 12 Aug 2019 22:22:36: 21000000 INFO @ Mon, 12 Aug 2019 22:22:37: 21000000 INFO @ Mon, 12 Aug 2019 22:22:38: 21000000 INFO @ Mon, 12 Aug 2019 22:22:43: 22000000 INFO @ Mon, 12 Aug 2019 22:22:45: 22000000 INFO @ Mon, 12 Aug 2019 22:22:45: 22000000 INFO @ Mon, 12 Aug 2019 22:22:51: 23000000 INFO @ Mon, 12 Aug 2019 22:22:53: 23000000 INFO @ Mon, 12 Aug 2019 22:22:53: 23000000 INFO @ Mon, 12 Aug 2019 22:22:59: 24000000 INFO @ Mon, 12 Aug 2019 22:23:00: 24000000 INFO @ Mon, 12 Aug 2019 22:23:00: 24000000 INFO @ Mon, 12 Aug 2019 22:23:06: 25000000 INFO @ Mon, 12 Aug 2019 22:23:08: 25000000 INFO @ Mon, 12 Aug 2019 22:23:08: 25000000 INFO @ Mon, 12 Aug 2019 22:23:14: 26000000 INFO @ Mon, 12 Aug 2019 22:23:14: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:23:14: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:23:14: #1 total tags in treatment: 26066103 INFO @ Mon, 12 Aug 2019 22:23:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:23:14: #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 22:23:15: #1 tags after filtering in treatment: 26066103 INFO @ Mon, 12 Aug 2019 22:23:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:23:15: #1 finished! INFO @ Mon, 12 Aug 2019 22:23:15: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:23:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:23:15: 26000000 INFO @ Mon, 12 Aug 2019 22:23:15: 26000000 INFO @ Mon, 12 Aug 2019 22:23:16: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:23:16: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:23:16: #1 total tags in treatment: 26066103 INFO @ Mon, 12 Aug 2019 22:23:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:23:16: #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 22:23:16: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:23:16: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:23:16: #1 total tags in treatment: 26066103 INFO @ Mon, 12 Aug 2019 22:23:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:23:16: #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 22:23:17: #1 tags after filtering in treatment: 26066103 INFO @ Mon, 12 Aug 2019 22:23:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:23:17: #1 finished! INFO @ Mon, 12 Aug 2019 22:23:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:23:17: #1 tags after filtering in treatment: 26066103 INFO @ Mon, 12 Aug 2019 22:23:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:23:17: #1 finished! INFO @ Mon, 12 Aug 2019 22:23:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:23:17: #2 number of paired peaks: 271 WARNING @ Mon, 12 Aug 2019 22:23:17: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Mon, 12 Aug 2019 22:23:17: start model_add_line... INFO @ Mon, 12 Aug 2019 22:23:17: start X-correlation... INFO @ Mon, 12 Aug 2019 22:23:17: end of X-cor INFO @ Mon, 12 Aug 2019 22:23:17: #2 finished! INFO @ Mon, 12 Aug 2019 22:23:17: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 22:23:17: #2 alternative fragment length(s) may be 3,50,585 bps INFO @ Mon, 12 Aug 2019 22:23:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.05_model.r WARNING @ Mon, 12 Aug 2019 22:23:17: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:23:17: #2 You may need to consider one of the other alternative d(s): 3,50,585 WARNING @ Mon, 12 Aug 2019 22:23:17: #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 22:23:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:23:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:23:19: #2 number of paired peaks: 271 WARNING @ Mon, 12 Aug 2019 22:23:19: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Mon, 12 Aug 2019 22:23:19: start model_add_line... INFO @ Mon, 12 Aug 2019 22:23:19: #2 number of paired peaks: 271 WARNING @ Mon, 12 Aug 2019 22:23:19: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Mon, 12 Aug 2019 22:23:19: start model_add_line... INFO @ Mon, 12 Aug 2019 22:23:19: start X-correlation... INFO @ Mon, 12 Aug 2019 22:23:19: end of X-cor INFO @ Mon, 12 Aug 2019 22:23:19: #2 finished! INFO @ Mon, 12 Aug 2019 22:23:19: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 22:23:19: #2 alternative fragment length(s) may be 3,50,585 bps INFO @ Mon, 12 Aug 2019 22:23:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.20_model.r WARNING @ Mon, 12 Aug 2019 22:23:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:23:19: #2 You may need to consider one of the other alternative d(s): 3,50,585 WARNING @ Mon, 12 Aug 2019 22:23:19: #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 22:23:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:23:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:23:19: start X-correlation... INFO @ Mon, 12 Aug 2019 22:23:19: end of X-cor INFO @ Mon, 12 Aug 2019 22:23:19: #2 finished! INFO @ Mon, 12 Aug 2019 22:23:19: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 22:23:19: #2 alternative fragment length(s) may be 3,50,585 bps INFO @ Mon, 12 Aug 2019 22:23:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.10_model.r WARNING @ Mon, 12 Aug 2019 22:23:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:23:19: #2 You may need to consider one of the other alternative d(s): 3,50,585 WARNING @ Mon, 12 Aug 2019 22:23:19: #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 22:23:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:23:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:24:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:24:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:24:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:24:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.05_summits.bed INFO @ Mon, 12 Aug 2019 22:24:51: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3307 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:24:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:24:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:24:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.20_summits.bed INFO @ Mon, 12 Aug 2019 22:24:52: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (530 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:24:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:24:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:24:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981706/SRX3981706.10_summits.bed INFO @ Mon, 12 Aug 2019 22:24:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1499 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。