Job ID = 1306847 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,201,016 reads read : 15,201,016 reads written : 15,201,016 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: 00:17:45 15201016 reads; of these: 15201016 (100.00%) were unpaired; of these: 188688 (1.24%) aligned 0 times 3550938 (23.36%) aligned exactly 1 time 11461390 (75.40%) aligned >1 times 98.76% overall alignment rate Time searching: 00:17:45 Overall time: 00:17:45 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] 3713552 / 15012328 = 0.2474 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 22:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.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 22:31:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:31:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.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 22:31:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:31:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.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 22:31:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:31:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:31:39: 1000000 INFO @ Mon, 03 Jun 2019 22:31:40: 1000000 INFO @ Mon, 03 Jun 2019 22:31:40: 1000000 INFO @ Mon, 03 Jun 2019 22:31:48: 2000000 INFO @ Mon, 03 Jun 2019 22:31:50: 2000000 INFO @ Mon, 03 Jun 2019 22:31:50: 2000000 INFO @ Mon, 03 Jun 2019 22:31:57: 3000000 INFO @ Mon, 03 Jun 2019 22:32:00: 3000000 INFO @ Mon, 03 Jun 2019 22:32:01: 3000000 INFO @ Mon, 03 Jun 2019 22:32:07: 4000000 INFO @ Mon, 03 Jun 2019 22:32:10: 4000000 INFO @ Mon, 03 Jun 2019 22:32:11: 4000000 INFO @ Mon, 03 Jun 2019 22:32:17: 5000000 INFO @ Mon, 03 Jun 2019 22:32:19: 5000000 INFO @ Mon, 03 Jun 2019 22:32:21: 5000000 INFO @ Mon, 03 Jun 2019 22:32:27: 6000000 INFO @ Mon, 03 Jun 2019 22:32:30: 6000000 INFO @ Mon, 03 Jun 2019 22:32:32: 6000000 INFO @ Mon, 03 Jun 2019 22:32:35: 7000000 INFO @ Mon, 03 Jun 2019 22:32:40: 7000000 INFO @ Mon, 03 Jun 2019 22:32:42: 7000000 INFO @ Mon, 03 Jun 2019 22:32:44: 8000000 INFO @ Mon, 03 Jun 2019 22:32:51: 8000000 INFO @ Mon, 03 Jun 2019 22:32:53: 8000000 INFO @ Mon, 03 Jun 2019 22:32:53: 9000000 INFO @ Mon, 03 Jun 2019 22:33:02: 9000000 INFO @ Mon, 03 Jun 2019 22:33:02: 10000000 INFO @ Mon, 03 Jun 2019 22:33:04: 9000000 INFO @ Mon, 03 Jun 2019 22:33:12: 11000000 INFO @ Mon, 03 Jun 2019 22:33:12: 10000000 INFO @ Mon, 03 Jun 2019 22:33:14: 10000000 INFO @ Mon, 03 Jun 2019 22:33:14: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 22:33:14: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 22:33:14: #1 total tags in treatment: 11298776 INFO @ Mon, 03 Jun 2019 22:33:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:33:14: #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 22:33:15: #1 tags after filtering in treatment: 11298776 INFO @ Mon, 03 Jun 2019 22:33:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:33:15: #1 finished! INFO @ Mon, 03 Jun 2019 22:33:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:33:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:33:16: #2 number of paired peaks: 1614 INFO @ Mon, 03 Jun 2019 22:33:16: start model_add_line... INFO @ Mon, 03 Jun 2019 22:33:16: start X-correlation... INFO @ Mon, 03 Jun 2019 22:33:16: end of X-cor INFO @ Mon, 03 Jun 2019 22:33:16: #2 finished! INFO @ Mon, 03 Jun 2019 22:33:16: #2 predicted fragment length is 72 bps INFO @ Mon, 03 Jun 2019 22:33:16: #2 alternative fragment length(s) may be 72 bps INFO @ Mon, 03 Jun 2019 22:33:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.20_model.r WARNING @ Mon, 03 Jun 2019 22:33:16: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:33:16: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Mon, 03 Jun 2019 22:33:16: #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 22:33:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:33:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:33:23: 11000000 INFO @ Mon, 03 Jun 2019 22:33:25: 11000000 INFO @ Mon, 03 Jun 2019 22:33:26: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 22:33:26: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 22:33:26: #1 total tags in treatment: 11298776 INFO @ Mon, 03 Jun 2019 22:33:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:33:26: #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 22:33:26: #1 tags after filtering in treatment: 11298776 INFO @ Mon, 03 Jun 2019 22:33:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:33:26: #1 finished! INFO @ Mon, 03 Jun 2019 22:33:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:33:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:33:27: #2 number of paired peaks: 1614 INFO @ Mon, 03 Jun 2019 22:33:27: start model_add_line... INFO @ Mon, 03 Jun 2019 22:33:27: start X-correlation... INFO @ Mon, 03 Jun 2019 22:33:27: end of X-cor INFO @ Mon, 03 Jun 2019 22:33:27: #2 finished! INFO @ Mon, 03 Jun 2019 22:33:27: #2 predicted fragment length is 72 bps INFO @ Mon, 03 Jun 2019 22:33:27: #2 alternative fragment length(s) may be 72 bps INFO @ Mon, 03 Jun 2019 22:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.05_model.r WARNING @ Mon, 03 Jun 2019 22:33:27: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:33:27: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Mon, 03 Jun 2019 22:33:27: #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 22:33:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:33:27: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 22:33:27: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 22:33:27: #1 total tags in treatment: 11298776 INFO @ Mon, 03 Jun 2019 22:33:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:33:27: #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 22:33:27: #1 tags after filtering in treatment: 11298776 INFO @ Mon, 03 Jun 2019 22:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:33:27: #1 finished! INFO @ Mon, 03 Jun 2019 22:33:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:33:29: #2 number of paired peaks: 1614 INFO @ Mon, 03 Jun 2019 22:33:29: start model_add_line... INFO @ Mon, 03 Jun 2019 22:33:29: start X-correlation... INFO @ Mon, 03 Jun 2019 22:33:29: end of X-cor INFO @ Mon, 03 Jun 2019 22:33:29: #2 finished! INFO @ Mon, 03 Jun 2019 22:33:29: #2 predicted fragment length is 72 bps INFO @ Mon, 03 Jun 2019 22:33:29: #2 alternative fragment length(s) may be 72 bps INFO @ Mon, 03 Jun 2019 22:33:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.10_model.r WARNING @ Mon, 03 Jun 2019 22:33:29: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:33:29: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Mon, 03 Jun 2019 22:33:29: #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 22:33:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:33:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:33:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:34:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:34:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:34:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:34:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.20_summits.bed INFO @ Mon, 03 Jun 2019 22:34:05: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1302 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:34:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:34:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:34:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.05_summits.bed INFO @ Mon, 03 Jun 2019 22:34:18: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8297 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:34:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:34:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:34:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX511125/SRX511125.10_summits.bed INFO @ Mon, 03 Jun 2019 22:34:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3146 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。