Job ID = 2161562 sra ファイルのダウンロード中... Completed: 804657K bytes transferred in 9 seconds (679549K 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 --:--:-- --:--:-- --:--:-- 0 100 6920 0 6920 0 0 12208 0 --:--:-- --:--:-- --:--:-- 18404 100 44533 0 44533 0 0 47075 0 --:--:-- --:--:-- --:--:-- 58984 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 25148880 spots for /home/okishinya/chipatlas/results/dm3/SRX030151/SRR071266.sra Written 25148880 spots total Written 25182685 spots for /home/okishinya/chipatlas/results/dm3/SRX030151/SRR071267.sra Written 25182685 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: 00:17:57 50331565 reads; of these: 50331565 (100.00%) were unpaired; of these: 2892242 (5.75%) aligned 0 times 32961133 (65.49%) aligned exactly 1 time 14478190 (28.77%) aligned >1 times 94.25% overall alignment rate Time searching: 00:17:57 Overall time: 00:17:57 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] 38373960 / 47439323 = 0.8089 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 13:15:18: # Command line: callpeak -t SRX030151.bam -f BAM -g dm -n SRX030151.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX030151.20 # format = BAM # ChIP-seq file = ['SRX030151.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 13:15:18: # Command line: callpeak -t SRX030151.bam -f BAM -g dm -n SRX030151.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX030151.05 # format = BAM # ChIP-seq file = ['SRX030151.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 13:15:18: # Command line: callpeak -t SRX030151.bam -f BAM -g dm -n SRX030151.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX030151.10 # format = BAM # ChIP-seq file = ['SRX030151.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 13:15:18: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:15:18: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:15:18: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:15:18: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:15:18: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:15:18: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:15:23: 1000000 INFO @ Tue, 21 Apr 2015 13:15:24: 1000000 INFO @ Tue, 21 Apr 2015 13:15:24: 1000000 INFO @ Tue, 21 Apr 2015 13:15:29: 2000000 INFO @ Tue, 21 Apr 2015 13:15:30: 2000000 INFO @ Tue, 21 Apr 2015 13:15:30: 2000000 INFO @ Tue, 21 Apr 2015 13:15:35: 3000000 INFO @ Tue, 21 Apr 2015 13:15:35: 3000000 INFO @ Tue, 21 Apr 2015 13:15:36: 3000000 INFO @ Tue, 21 Apr 2015 13:15:41: 4000000 INFO @ Tue, 21 Apr 2015 13:15:41: 4000000 INFO @ Tue, 21 Apr 2015 13:15:42: 4000000 INFO @ Tue, 21 Apr 2015 13:15:47: 5000000 INFO @ Tue, 21 Apr 2015 13:15:47: 5000000 INFO @ Tue, 21 Apr 2015 13:15:48: 5000000 INFO @ Tue, 21 Apr 2015 13:15:53: 6000000 INFO @ Tue, 21 Apr 2015 13:15:53: 6000000 INFO @ Tue, 21 Apr 2015 13:15:54: 6000000 INFO @ Tue, 21 Apr 2015 13:15:58: 7000000 INFO @ Tue, 21 Apr 2015 13:15:59: 7000000 INFO @ Tue, 21 Apr 2015 13:16:00: 7000000 INFO @ Tue, 21 Apr 2015 13:16:04: 8000000 INFO @ Tue, 21 Apr 2015 13:16:05: 8000000 INFO @ Tue, 21 Apr 2015 13:16:06: 8000000 INFO @ Tue, 21 Apr 2015 13:16:09: 9000000 INFO @ Tue, 21 Apr 2015 13:16:10: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:16:10: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:16:10: #1 total tags in treatment: 9065363 INFO @ Tue, 21 Apr 2015 13:16:10: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:16:10: #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 13:16:11: 9000000 INFO @ Tue, 21 Apr 2015 13:16:11: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:16:11: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:16:11: #1 total tags in treatment: 9065363 INFO @ Tue, 21 Apr 2015 13:16:11: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:16:11: #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 13:16:12: #1 tags after filtering in treatment: 9064027 INFO @ Tue, 21 Apr 2015 13:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:16:12: #1 finished! INFO @ Tue, 21 Apr 2015 13:16:12: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:16:12: 9000000 INFO @ Tue, 21 Apr 2015 13:16:12: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:16:12: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:16:12: #1 total tags in treatment: 9065363 INFO @ Tue, 21 Apr 2015 13:16:12: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:16:12: #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 13:16:13: #1 tags after filtering in treatment: 9064027 INFO @ Tue, 21 Apr 2015 13:16:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:16:13: #1 finished! INFO @ Tue, 21 Apr 2015 13:16:13: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:16:14: #2 number of paired peaks: 1318 INFO @ Tue, 21 Apr 2015 13:16:14: start model_add_line... INFO @ Tue, 21 Apr 2015 13:16:14: #1 tags after filtering in treatment: 9064027 INFO @ Tue, 21 Apr 2015 13:16:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:16:14: #1 finished! INFO @ Tue, 21 Apr 2015 13:16:14: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:16:15: #2 number of paired peaks: 1318 INFO @ Tue, 21 Apr 2015 13:16:15: start model_add_line... INFO @ Tue, 21 Apr 2015 13:16:16: #2 number of paired peaks: 1318 INFO @ Tue, 21 Apr 2015 13:16:16: start model_add_line... INFO @ Tue, 21 Apr 2015 13:16:23: start X-correlation... INFO @ Tue, 21 Apr 2015 13:16:23: end of X-cor INFO @ Tue, 21 Apr 2015 13:16:23: #2 finished! INFO @ Tue, 21 Apr 2015 13:16:23: #2 predicted fragment length is 54 bps INFO @ Tue, 21 Apr 2015 13:16:23: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 21 Apr 2015 13:16:23: #2.2 Generate R script for model : SRX030151.10_model.r WARNING @ Tue, 21 Apr 2015 13:16:23: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:16:23: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 21 Apr 2015 13:16:23: #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 13:16:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:16:24: start X-correlation... INFO @ Tue, 21 Apr 2015 13:16:24: end of X-cor INFO @ Tue, 21 Apr 2015 13:16:24: #2 finished! INFO @ Tue, 21 Apr 2015 13:16:24: #2 predicted fragment length is 54 bps INFO @ Tue, 21 Apr 2015 13:16:24: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 21 Apr 2015 13:16:24: #2.2 Generate R script for model : SRX030151.05_model.r WARNING @ Tue, 21 Apr 2015 13:16:24: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:16:24: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 21 Apr 2015 13:16:24: #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 13:16:24: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:16:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:16:25: start X-correlation... INFO @ Tue, 21 Apr 2015 13:16:25: end of X-cor INFO @ Tue, 21 Apr 2015 13:16:25: #2 finished! INFO @ Tue, 21 Apr 2015 13:16:25: #2 predicted fragment length is 54 bps INFO @ Tue, 21 Apr 2015 13:16:25: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 21 Apr 2015 13:16:25: #2.2 Generate R script for model : SRX030151.20_model.r WARNING @ Tue, 21 Apr 2015 13:16:25: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:16:25: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 21 Apr 2015 13:16:25: #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 13:16:25: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:17:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:17:13: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:17:13: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:17:46: #4 Write output xls file... SRX030151.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:17:46: #4 Write peak in narrowPeak format file... SRX030151.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:17:46: #4 Write summits bed file... SRX030151.10_summits.bed INFO @ Tue, 21 Apr 2015 13:17:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2194 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:17:47: #4 Write output xls file... SRX030151.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:17:47: #4 Write peak in narrowPeak format file... SRX030151.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:17:47: #4 Write summits bed file... SRX030151.20_summits.bed INFO @ Tue, 21 Apr 2015 13:17:47: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1411 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:17:49: #4 Write output xls file... SRX030151.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:17:49: #4 Write peak in narrowPeak format file... SRX030151.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:17:49: #4 Write summits bed file... SRX030151.05_summits.bed INFO @ Tue, 21 Apr 2015 13:17:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3500 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。