Job ID = 2161381 sra ファイルのダウンロード中... Completed: 236313K bytes transferred in 5 seconds (362596K bits/sec), in 2 files, 3 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 108 1082 0 1082 0 0 1744 0 --:--:-- --:--:-- --:--:-- 2516 100 44529 0 44529 0 0 44553 0 --:--:-- --:--:-- --:--:-- 55042 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 6611077 spots for /home/okishinya/chipatlas/results/dm3/SRX025470/SRR063865.sra Written 6611077 spots total Written 8794379 spots for /home/okishinya/chipatlas/results/dm3/SRX025470/SRR063864.sra Written 8794379 spots total 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: 00:09:41 15405456 reads; of these: 15405456 (100.00%) were unpaired; of these: 1803896 (11.71%) aligned 0 times 5463177 (35.46%) aligned exactly 1 time 8138383 (52.83%) aligned >1 times 88.29% overall alignment rate Time searching: 00:09:41 Overall time: 00:09:41 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_rmdupse_core] 7210431 / 13601560 = 0.5301 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, 21 Apr 2015 12:41:42: # Command line: callpeak -t SRX025470.bam -f BAM -g dm -n SRX025470.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX025470.10 # format = BAM # ChIP-seq file = ['SRX025470.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 INFO @ Tue, 21 Apr 2015 12:41:42: # Command line: callpeak -t SRX025470.bam -f BAM -g dm -n SRX025470.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX025470.05 # format = BAM # ChIP-seq file = ['SRX025470.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 INFO @ Tue, 21 Apr 2015 12:41:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:41:42: # Command line: callpeak -t SRX025470.bam -f BAM -g dm -n SRX025470.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX025470.20 # format = BAM # ChIP-seq file = ['SRX025470.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 INFO @ Tue, 21 Apr 2015 12:41:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:41:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:41:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:41:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:41:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:41:47: 1000000 INFO @ Tue, 21 Apr 2015 12:41:47: 1000000 INFO @ Tue, 21 Apr 2015 12:41:47: 1000000 INFO @ Tue, 21 Apr 2015 12:41:52: 2000000 INFO @ Tue, 21 Apr 2015 12:41:52: 2000000 INFO @ Tue, 21 Apr 2015 12:41:52: 2000000 INFO @ Tue, 21 Apr 2015 12:41:57: 3000000 INFO @ Tue, 21 Apr 2015 12:41:57: 3000000 INFO @ Tue, 21 Apr 2015 12:41:57: 3000000 INFO @ Tue, 21 Apr 2015 12:42:02: 4000000 INFO @ Tue, 21 Apr 2015 12:42:02: 4000000 INFO @ Tue, 21 Apr 2015 12:42:03: 4000000 INFO @ Tue, 21 Apr 2015 12:42:07: 5000000 INFO @ Tue, 21 Apr 2015 12:42:07: 5000000 INFO @ Tue, 21 Apr 2015 12:42:08: 5000000 INFO @ Tue, 21 Apr 2015 12:42:12: 6000000 INFO @ Tue, 21 Apr 2015 12:42:12: 6000000 INFO @ Tue, 21 Apr 2015 12:42:13: 6000000 INFO @ Tue, 21 Apr 2015 12:42:14: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:42:14: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:42:14: #1 total tags in treatment: 6391129 INFO @ Tue, 21 Apr 2015 12:42:14: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:42:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:42:14: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:42:14: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:42:14: #1 total tags in treatment: 6391129 INFO @ Tue, 21 Apr 2015 12:42:14: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:42:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:42:15: #1 tags after filtering in treatment: 6390088 INFO @ Tue, 21 Apr 2015 12:42:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:42:15: #1 finished! INFO @ Tue, 21 Apr 2015 12:42:15: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:42:15: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:42:15: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:42:15: #1 total tags in treatment: 6391129 INFO @ Tue, 21 Apr 2015 12:42:15: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:42:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:42:15: #1 tags after filtering in treatment: 6390088 INFO @ Tue, 21 Apr 2015 12:42:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:42:15: #1 finished! INFO @ Tue, 21 Apr 2015 12:42:15: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:42:16: #1 tags after filtering in treatment: 6390088 INFO @ Tue, 21 Apr 2015 12:42:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:42:16: #1 finished! INFO @ Tue, 21 Apr 2015 12:42:16: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:42:17: #2 number of paired peaks: 4920 INFO @ Tue, 21 Apr 2015 12:42:17: start model_add_line... INFO @ Tue, 21 Apr 2015 12:42:17: #2 number of paired peaks: 4920 INFO @ Tue, 21 Apr 2015 12:42:17: start model_add_line... INFO @ Tue, 21 Apr 2015 12:42:18: #2 number of paired peaks: 4920 INFO @ Tue, 21 Apr 2015 12:42:18: start model_add_line... INFO @ Tue, 21 Apr 2015 12:42:36: start X-correlation... INFO @ Tue, 21 Apr 2015 12:42:36: end of X-cor INFO @ Tue, 21 Apr 2015 12:42:36: #2 finished! INFO @ Tue, 21 Apr 2015 12:42:36: #2 predicted fragment length is 35 bps INFO @ Tue, 21 Apr 2015 12:42:36: #2 alternative fragment length(s) may be 35 bps INFO @ Tue, 21 Apr 2015 12:42:36: #2.2 Generate R script for model : SRX025470.20_model.r WARNING @ Tue, 21 Apr 2015 12:42:36: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:42:36: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Tue, 21 Apr 2015 12:42:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:42:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:42:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:42:36: start X-correlation... INFO @ Tue, 21 Apr 2015 12:42:36: end of X-cor INFO @ Tue, 21 Apr 2015 12:42:36: #2 finished! INFO @ Tue, 21 Apr 2015 12:42:36: #2 predicted fragment length is 35 bps INFO @ Tue, 21 Apr 2015 12:42:36: #2 alternative fragment length(s) may be 35 bps INFO @ Tue, 21 Apr 2015 12:42:36: #2.2 Generate R script for model : SRX025470.05_model.r WARNING @ Tue, 21 Apr 2015 12:42:36: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:42:36: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Tue, 21 Apr 2015 12:42:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:42:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:42:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:42:36: start X-correlation... INFO @ Tue, 21 Apr 2015 12:42:36: end of X-cor INFO @ Tue, 21 Apr 2015 12:42:36: #2 finished! INFO @ Tue, 21 Apr 2015 12:42:36: #2 predicted fragment length is 35 bps INFO @ Tue, 21 Apr 2015 12:42:36: #2 alternative fragment length(s) may be 35 bps INFO @ Tue, 21 Apr 2015 12:42:36: #2.2 Generate R script for model : SRX025470.10_model.r WARNING @ Tue, 21 Apr 2015 12:42:36: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:42:36: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Tue, 21 Apr 2015 12:42:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:42:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:42:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:43:09: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:43:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:43:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:43:35: #4 Write output xls file... SRX025470.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:43:35: #4 Write peak in narrowPeak format file... SRX025470.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:43:35: #4 Write summits bed file... SRX025470.20_summits.bed INFO @ Tue, 21 Apr 2015 12:43:35: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1193 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:43:35: #4 Write output xls file... SRX025470.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:43:35: #4 Write peak in narrowPeak format file... SRX025470.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:43:35: #4 Write summits bed file... SRX025470.10_summits.bed INFO @ Tue, 21 Apr 2015 12:43:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2608 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:43:37: #4 Write output xls file... SRX025470.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:43:37: #4 Write peak in narrowPeak format file... SRX025470.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:43:38: #4 Write summits bed file... SRX025470.05_summits.bed INFO @ Tue, 21 Apr 2015 12:43:38: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10848 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。