Job ID = 2590949 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,821,391 reads read : 51,642,782 reads written : 25,821,391 reads 0-length : 25,821,391 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: 00:14:02 25821391 reads; of these: 25821391 (100.00%) were unpaired; of these: 674438 (2.61%) aligned 0 times 9936883 (38.48%) aligned exactly 1 time 15210070 (58.90%) aligned >1 times 97.39% overall alignment rate Time searching: 00:14:02 Overall time: 00:14:02 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 12 files... [bam_rmdupse_core] 7259982 / 25146953 = 0.2887 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 @ Tue, 13 Aug 2019 00:25:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.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 @ Tue, 13 Aug 2019 00:25:10: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:25:10: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.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 @ Tue, 13 Aug 2019 00:25:11: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:25:11: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.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 @ Tue, 13 Aug 2019 00:25:11: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:25:11: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:25:17: 1000000 INFO @ Tue, 13 Aug 2019 00:25:19: 1000000 INFO @ Tue, 13 Aug 2019 00:25:19: 1000000 INFO @ Tue, 13 Aug 2019 00:25:24: 2000000 INFO @ Tue, 13 Aug 2019 00:25:26: 2000000 INFO @ Tue, 13 Aug 2019 00:25:27: 2000000 INFO @ Tue, 13 Aug 2019 00:25:31: 3000000 INFO @ Tue, 13 Aug 2019 00:25:33: 3000000 INFO @ Tue, 13 Aug 2019 00:25:36: 3000000 INFO @ Tue, 13 Aug 2019 00:25:37: 4000000 INFO @ Tue, 13 Aug 2019 00:25:40: 4000000 INFO @ Tue, 13 Aug 2019 00:25:44: 5000000 INFO @ Tue, 13 Aug 2019 00:25:44: 4000000 INFO @ Tue, 13 Aug 2019 00:25:47: 5000000 INFO @ Tue, 13 Aug 2019 00:25:50: 6000000 INFO @ Tue, 13 Aug 2019 00:25:52: 5000000 INFO @ Tue, 13 Aug 2019 00:25:54: 6000000 INFO @ Tue, 13 Aug 2019 00:25:57: 7000000 INFO @ Tue, 13 Aug 2019 00:26:01: 6000000 INFO @ Tue, 13 Aug 2019 00:26:01: 7000000 INFO @ Tue, 13 Aug 2019 00:26:03: 8000000 INFO @ Tue, 13 Aug 2019 00:26:09: 7000000 INFO @ Tue, 13 Aug 2019 00:26:10: 8000000 INFO @ Tue, 13 Aug 2019 00:26:10: 9000000 INFO @ Tue, 13 Aug 2019 00:26:16: 10000000 INFO @ Tue, 13 Aug 2019 00:26:17: 8000000 INFO @ Tue, 13 Aug 2019 00:26:18: 9000000 INFO @ Tue, 13 Aug 2019 00:26:23: 11000000 INFO @ Tue, 13 Aug 2019 00:26:25: 9000000 INFO @ Tue, 13 Aug 2019 00:26:26: 10000000 INFO @ Tue, 13 Aug 2019 00:26:29: 12000000 INFO @ Tue, 13 Aug 2019 00:26:34: 10000000 INFO @ Tue, 13 Aug 2019 00:26:34: 11000000 INFO @ Tue, 13 Aug 2019 00:26:36: 13000000 INFO @ Tue, 13 Aug 2019 00:26:42: 11000000 INFO @ Tue, 13 Aug 2019 00:26:42: 14000000 INFO @ Tue, 13 Aug 2019 00:26:42: 12000000 INFO @ Tue, 13 Aug 2019 00:26:49: 15000000 INFO @ Tue, 13 Aug 2019 00:26:50: 12000000 INFO @ Tue, 13 Aug 2019 00:26:51: 13000000 INFO @ Tue, 13 Aug 2019 00:26:55: 16000000 INFO @ Tue, 13 Aug 2019 00:26:58: 13000000 INFO @ Tue, 13 Aug 2019 00:26:59: 14000000 INFO @ Tue, 13 Aug 2019 00:27:02: 17000000 INFO @ Tue, 13 Aug 2019 00:27:07: 14000000 INFO @ Tue, 13 Aug 2019 00:27:07: 15000000 INFO @ Tue, 13 Aug 2019 00:27:08: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:27:08: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:27:08: #1 total tags in treatment: 17886971 INFO @ Tue, 13 Aug 2019 00:27:08: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:27:08: #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 00:27:08: #1 tags after filtering in treatment: 17886971 INFO @ Tue, 13 Aug 2019 00:27:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:27:08: #1 finished! INFO @ Tue, 13 Aug 2019 00:27:08: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:27:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:27:10: #2 number of paired peaks: 1148 INFO @ Tue, 13 Aug 2019 00:27:10: start model_add_line... INFO @ Tue, 13 Aug 2019 00:27:10: start X-correlation... INFO @ Tue, 13 Aug 2019 00:27:10: end of X-cor INFO @ Tue, 13 Aug 2019 00:27:10: #2 finished! INFO @ Tue, 13 Aug 2019 00:27:10: #2 predicted fragment length is 49 bps INFO @ Tue, 13 Aug 2019 00:27:10: #2 alternative fragment length(s) may be 3,49,596 bps INFO @ Tue, 13 Aug 2019 00:27:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.10_model.r WARNING @ Tue, 13 Aug 2019 00:27:10: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:27:10: #2 You may need to consider one of the other alternative d(s): 3,49,596 WARNING @ Tue, 13 Aug 2019 00:27:10: #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 00:27:10: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:27:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:27:15: 15000000 INFO @ Tue, 13 Aug 2019 00:27:15: 16000000 INFO @ Tue, 13 Aug 2019 00:27:23: 16000000 INFO @ Tue, 13 Aug 2019 00:27:24: 17000000 INFO @ Tue, 13 Aug 2019 00:27:31: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:27:31: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:27:31: #1 total tags in treatment: 17886971 INFO @ Tue, 13 Aug 2019 00:27:31: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:27:31: #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 00:27:31: #1 tags after filtering in treatment: 17886971 INFO @ Tue, 13 Aug 2019 00:27:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:27:31: #1 finished! INFO @ Tue, 13 Aug 2019 00:27:31: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:27:31: 17000000 INFO @ Tue, 13 Aug 2019 00:27:33: #2 number of paired peaks: 1148 INFO @ Tue, 13 Aug 2019 00:27:33: start model_add_line... INFO @ Tue, 13 Aug 2019 00:27:33: start X-correlation... INFO @ Tue, 13 Aug 2019 00:27:33: end of X-cor INFO @ Tue, 13 Aug 2019 00:27:33: #2 finished! INFO @ Tue, 13 Aug 2019 00:27:33: #2 predicted fragment length is 49 bps INFO @ Tue, 13 Aug 2019 00:27:33: #2 alternative fragment length(s) may be 3,49,596 bps INFO @ Tue, 13 Aug 2019 00:27:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.20_model.r WARNING @ Tue, 13 Aug 2019 00:27:33: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:27:33: #2 You may need to consider one of the other alternative d(s): 3,49,596 WARNING @ Tue, 13 Aug 2019 00:27:33: #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 00:27:33: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:27:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:27:39: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:27:39: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:27:39: #1 total tags in treatment: 17886971 INFO @ Tue, 13 Aug 2019 00:27:39: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:27:39: #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 00:27:39: #1 tags after filtering in treatment: 17886971 INFO @ Tue, 13 Aug 2019 00:27:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:27:39: #1 finished! INFO @ Tue, 13 Aug 2019 00:27:39: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:27:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:27:41: #2 number of paired peaks: 1148 INFO @ Tue, 13 Aug 2019 00:27:41: start model_add_line... INFO @ Tue, 13 Aug 2019 00:27:41: start X-correlation... INFO @ Tue, 13 Aug 2019 00:27:41: end of X-cor INFO @ Tue, 13 Aug 2019 00:27:41: #2 finished! INFO @ Tue, 13 Aug 2019 00:27:41: #2 predicted fragment length is 49 bps INFO @ Tue, 13 Aug 2019 00:27:41: #2 alternative fragment length(s) may be 3,49,596 bps INFO @ Tue, 13 Aug 2019 00:27:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.05_model.r WARNING @ Tue, 13 Aug 2019 00:27:41: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:27:41: #2 You may need to consider one of the other alternative d(s): 3,49,596 WARNING @ Tue, 13 Aug 2019 00:27:41: #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 00:27:41: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:27:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:27:56: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:28:19: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:28:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:28:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:28:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.10_summits.bed INFO @ Tue, 13 Aug 2019 00:28:21: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (5862 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:28:26: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:28:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:28:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:28:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.20_summits.bed INFO @ Tue, 13 Aug 2019 00:28:44: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1317 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:28:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:28:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:28:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661487/SRX5661487.05_summits.bed INFO @ Tue, 13 Aug 2019 00:28:51: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (14460 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。