Job ID = 1294095 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,492,092 reads read : 32,492,092 reads written : 32,492,092 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: 00:09:34 32492092 reads; of these: 32492092 (100.00%) were unpaired; of these: 2355083 (7.25%) aligned 0 times 24326160 (74.87%) aligned exactly 1 time 5810849 (17.88%) aligned >1 times 92.75% overall alignment rate Time searching: 00:09:34 Overall time: 00:09:34 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] 16666439 / 30137009 = 0.5530 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 05:24:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.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 05:24:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:24:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:24:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.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 05:24:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:24:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:24:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.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 05:24:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:24:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:24:41: 1000000 INFO @ Mon, 03 Jun 2019 05:24:41: 1000000 INFO @ Mon, 03 Jun 2019 05:24:42: 1000000 INFO @ Mon, 03 Jun 2019 05:24:48: 2000000 INFO @ Mon, 03 Jun 2019 05:24:49: 2000000 INFO @ Mon, 03 Jun 2019 05:24:50: 2000000 INFO @ Mon, 03 Jun 2019 05:24:54: 3000000 INFO @ Mon, 03 Jun 2019 05:24:57: 3000000 INFO @ Mon, 03 Jun 2019 05:24:58: 3000000 INFO @ Mon, 03 Jun 2019 05:25:01: 4000000 INFO @ Mon, 03 Jun 2019 05:25:04: 4000000 INFO @ Mon, 03 Jun 2019 05:25:05: 4000000 INFO @ Mon, 03 Jun 2019 05:25:07: 5000000 INFO @ Mon, 03 Jun 2019 05:25:12: 5000000 INFO @ Mon, 03 Jun 2019 05:25:13: 5000000 INFO @ Mon, 03 Jun 2019 05:25:13: 6000000 INFO @ Mon, 03 Jun 2019 05:25:19: 6000000 INFO @ Mon, 03 Jun 2019 05:25:19: 7000000 INFO @ Mon, 03 Jun 2019 05:25:21: 6000000 INFO @ Mon, 03 Jun 2019 05:25:26: 8000000 INFO @ Mon, 03 Jun 2019 05:25:27: 7000000 INFO @ Mon, 03 Jun 2019 05:25:28: 7000000 INFO @ Mon, 03 Jun 2019 05:25:32: 9000000 INFO @ Mon, 03 Jun 2019 05:25:34: 8000000 INFO @ Mon, 03 Jun 2019 05:25:36: 8000000 INFO @ Mon, 03 Jun 2019 05:25:39: 10000000 INFO @ Mon, 03 Jun 2019 05:25:42: 9000000 INFO @ Mon, 03 Jun 2019 05:25:44: 9000000 INFO @ Mon, 03 Jun 2019 05:25:46: 11000000 INFO @ Mon, 03 Jun 2019 05:25:49: 10000000 INFO @ Mon, 03 Jun 2019 05:25:51: 10000000 INFO @ Mon, 03 Jun 2019 05:25:52: 12000000 INFO @ Mon, 03 Jun 2019 05:25:57: 11000000 INFO @ Mon, 03 Jun 2019 05:25:59: 13000000 INFO @ Mon, 03 Jun 2019 05:25:59: 11000000 INFO @ Mon, 03 Jun 2019 05:26:02: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:26:02: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:26:02: #1 total tags in treatment: 13470570 INFO @ Mon, 03 Jun 2019 05:26:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:26:02: #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 05:26:02: #1 tags after filtering in treatment: 13470570 INFO @ Mon, 03 Jun 2019 05:26:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:26:02: #1 finished! INFO @ Mon, 03 Jun 2019 05:26:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:26:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:26:03: #2 number of paired peaks: 302 WARNING @ Mon, 03 Jun 2019 05:26:03: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Mon, 03 Jun 2019 05:26:03: start model_add_line... INFO @ Mon, 03 Jun 2019 05:26:03: start X-correlation... INFO @ Mon, 03 Jun 2019 05:26:03: end of X-cor INFO @ Mon, 03 Jun 2019 05:26:03: #2 finished! INFO @ Mon, 03 Jun 2019 05:26:03: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 05:26:03: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 03 Jun 2019 05:26:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.20_model.r WARNING @ Mon, 03 Jun 2019 05:26:03: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:26:03: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 03 Jun 2019 05:26:03: #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 05:26:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:26:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:26:04: 12000000 INFO @ Mon, 03 Jun 2019 05:26:07: 12000000 INFO @ Mon, 03 Jun 2019 05:26:12: 13000000 INFO @ Mon, 03 Jun 2019 05:26:14: 13000000 INFO @ Mon, 03 Jun 2019 05:26:15: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:26:15: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:26:15: #1 total tags in treatment: 13470570 INFO @ Mon, 03 Jun 2019 05:26:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:26:15: #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 05:26:15: #1 tags after filtering in treatment: 13470570 INFO @ Mon, 03 Jun 2019 05:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:26:15: #1 finished! INFO @ Mon, 03 Jun 2019 05:26:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:26:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:26:17: #2 number of paired peaks: 302 WARNING @ Mon, 03 Jun 2019 05:26:17: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Mon, 03 Jun 2019 05:26:17: start model_add_line... INFO @ Mon, 03 Jun 2019 05:26:17: start X-correlation... INFO @ Mon, 03 Jun 2019 05:26:17: end of X-cor INFO @ Mon, 03 Jun 2019 05:26:17: #2 finished! INFO @ Mon, 03 Jun 2019 05:26:17: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 05:26:17: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 03 Jun 2019 05:26:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.05_model.r WARNING @ Mon, 03 Jun 2019 05:26:17: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:26:17: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 03 Jun 2019 05:26:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:26:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:26:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:26:18: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:26:18: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:26:18: #1 total tags in treatment: 13470570 INFO @ Mon, 03 Jun 2019 05:26:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:26:18: #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 05:26:18: #1 tags after filtering in treatment: 13470570 INFO @ Mon, 03 Jun 2019 05:26:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:26:18: #1 finished! INFO @ Mon, 03 Jun 2019 05:26:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:26:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:26:19: #2 number of paired peaks: 302 WARNING @ Mon, 03 Jun 2019 05:26:19: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Mon, 03 Jun 2019 05:26:19: start model_add_line... INFO @ Mon, 03 Jun 2019 05:26:19: start X-correlation... INFO @ Mon, 03 Jun 2019 05:26:19: end of X-cor INFO @ Mon, 03 Jun 2019 05:26:19: #2 finished! INFO @ Mon, 03 Jun 2019 05:26:19: #2 predicted fragment length is 63 bps INFO @ Mon, 03 Jun 2019 05:26:19: #2 alternative fragment length(s) may be 63 bps INFO @ Mon, 03 Jun 2019 05:26:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.10_model.r WARNING @ Mon, 03 Jun 2019 05:26:19: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:26:19: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Mon, 03 Jun 2019 05:26:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:26:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:26:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:26:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:26:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:26:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:26:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:26:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:26:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.20_summits.bed INFO @ Mon, 03 Jun 2019 05:26:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1822 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:27:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:27:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:27:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.05_summits.bed INFO @ Mon, 03 Jun 2019 05:27:11: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (14976 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:27:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:27:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:27:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX183884/SRX183884.10_summits.bed INFO @ Mon, 03 Jun 2019 05:27:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5570 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。