Job ID = 2590834 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 39,031,841 reads read : 78,063,682 reads written : 39,031,841 reads 0-length : 39,031,841 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: 00:15:58 39031841 reads; of these: 39031841 (100.00%) were unpaired; of these: 3758666 (9.63%) aligned 0 times 25598076 (65.58%) aligned exactly 1 time 9675099 (24.79%) aligned >1 times 90.37% overall alignment rate Time searching: 00:15:58 Overall time: 00:15:58 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] 21359499 / 35273175 = 0.6055 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 23:59:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.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 23:59:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:59:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:59:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.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 23:59:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:59:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:59:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.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 23:59:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:59:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:59:55: 1000000 INFO @ Mon, 12 Aug 2019 23:59:56: 1000000 INFO @ Mon, 12 Aug 2019 23:59:57: 1000000 INFO @ Tue, 13 Aug 2019 00:00:04: 2000000 INFO @ Tue, 13 Aug 2019 00:00:05: 2000000 INFO @ Tue, 13 Aug 2019 00:00:06: 2000000 INFO @ Tue, 13 Aug 2019 00:00:12: 3000000 INFO @ Tue, 13 Aug 2019 00:00:14: 3000000 INFO @ Tue, 13 Aug 2019 00:00:15: 3000000 INFO @ Tue, 13 Aug 2019 00:00:19: 4000000 INFO @ Tue, 13 Aug 2019 00:00:24: 4000000 INFO @ Tue, 13 Aug 2019 00:00:25: 4000000 INFO @ Tue, 13 Aug 2019 00:00:27: 5000000 INFO @ Tue, 13 Aug 2019 00:00:33: 5000000 INFO @ Tue, 13 Aug 2019 00:00:34: 5000000 INFO @ Tue, 13 Aug 2019 00:00:35: 6000000 INFO @ Tue, 13 Aug 2019 00:00:42: 7000000 INFO @ Tue, 13 Aug 2019 00:00:43: 6000000 INFO @ Tue, 13 Aug 2019 00:00:44: 6000000 INFO @ Tue, 13 Aug 2019 00:00:50: 8000000 INFO @ Tue, 13 Aug 2019 00:00:52: 7000000 INFO @ Tue, 13 Aug 2019 00:00:53: 7000000 INFO @ Tue, 13 Aug 2019 00:00:58: 9000000 INFO @ Tue, 13 Aug 2019 00:01:02: 8000000 INFO @ Tue, 13 Aug 2019 00:01:03: 8000000 INFO @ Tue, 13 Aug 2019 00:01:05: 10000000 INFO @ Tue, 13 Aug 2019 00:01:11: 9000000 INFO @ Tue, 13 Aug 2019 00:01:12: 9000000 INFO @ Tue, 13 Aug 2019 00:01:13: 11000000 INFO @ Tue, 13 Aug 2019 00:01:21: 12000000 INFO @ Tue, 13 Aug 2019 00:01:21: 10000000 INFO @ Tue, 13 Aug 2019 00:01:22: 10000000 INFO @ Tue, 13 Aug 2019 00:01:28: 13000000 INFO @ Tue, 13 Aug 2019 00:01:30: 11000000 INFO @ Tue, 13 Aug 2019 00:01:31: 11000000 INFO @ Tue, 13 Aug 2019 00:01:35: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:01:35: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:01:35: #1 total tags in treatment: 13913676 INFO @ Tue, 13 Aug 2019 00:01:35: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:01:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:01:36: #1 tags after filtering in treatment: 13913676 INFO @ Tue, 13 Aug 2019 00:01:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:01:36: #1 finished! INFO @ Tue, 13 Aug 2019 00:01:36: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:01:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:01:37: #2 number of paired peaks: 1480 INFO @ Tue, 13 Aug 2019 00:01:37: start model_add_line... INFO @ Tue, 13 Aug 2019 00:01:37: start X-correlation... INFO @ Tue, 13 Aug 2019 00:01:37: end of X-cor INFO @ Tue, 13 Aug 2019 00:01:37: #2 finished! INFO @ Tue, 13 Aug 2019 00:01:37: #2 predicted fragment length is 53 bps INFO @ Tue, 13 Aug 2019 00:01:37: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 13 Aug 2019 00:01:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.20_model.r WARNING @ Tue, 13 Aug 2019 00:01:37: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:01:37: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 13 Aug 2019 00:01:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:01:37: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:01:40: 12000000 INFO @ Tue, 13 Aug 2019 00:01:41: 12000000 INFO @ Tue, 13 Aug 2019 00:01:49: 13000000 INFO @ Tue, 13 Aug 2019 00:01:50: 13000000 INFO @ Tue, 13 Aug 2019 00:01:58: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:01:58: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:01:58: #1 total tags in treatment: 13913676 INFO @ Tue, 13 Aug 2019 00:01:58: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:01:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:01:58: #1 tags after filtering in treatment: 13913676 INFO @ Tue, 13 Aug 2019 00:01:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:01:58: #1 finished! INFO @ Tue, 13 Aug 2019 00:01:58: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:01:59: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:01:59: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:01:59: #1 total tags in treatment: 13913676 INFO @ Tue, 13 Aug 2019 00:01:59: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:01:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:01:59: #1 tags after filtering in treatment: 13913676 INFO @ Tue, 13 Aug 2019 00:01:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:01:59: #1 finished! INFO @ Tue, 13 Aug 2019 00:01:59: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:01:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:01:59: #2 number of paired peaks: 1480 INFO @ Tue, 13 Aug 2019 00:01:59: start model_add_line... INFO @ Tue, 13 Aug 2019 00:02:00: start X-correlation... INFO @ Tue, 13 Aug 2019 00:02:00: end of X-cor INFO @ Tue, 13 Aug 2019 00:02:00: #2 finished! INFO @ Tue, 13 Aug 2019 00:02:00: #2 predicted fragment length is 53 bps INFO @ Tue, 13 Aug 2019 00:02:00: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 13 Aug 2019 00:02:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.05_model.r WARNING @ Tue, 13 Aug 2019 00:02:00: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:02:00: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 13 Aug 2019 00:02:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:02:00: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:02:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:02:00: #2 number of paired peaks: 1480 INFO @ Tue, 13 Aug 2019 00:02:00: start model_add_line... INFO @ Tue, 13 Aug 2019 00:02:00: start X-correlation... INFO @ Tue, 13 Aug 2019 00:02:00: end of X-cor INFO @ Tue, 13 Aug 2019 00:02:00: #2 finished! INFO @ Tue, 13 Aug 2019 00:02:00: #2 predicted fragment length is 53 bps INFO @ Tue, 13 Aug 2019 00:02:00: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 13 Aug 2019 00:02:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.10_model.r WARNING @ Tue, 13 Aug 2019 00:02:00: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:02:00: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 13 Aug 2019 00:02:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:02:00: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:02:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:02:14: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:02:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:02:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:02:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.20_summits.bed INFO @ Tue, 13 Aug 2019 00:02:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2361 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:02:36: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:02:37: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:02:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:02:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:02:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.05_summits.bed INFO @ Tue, 13 Aug 2019 00:02:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6499 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:02:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:02:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:02:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011071/SRX5011071.10_summits.bed INFO @ Tue, 13 Aug 2019 00:02:55: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (3995 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。