Job ID = 2161828 sra ファイルのダウンロード中... Completed: 515588K bytes transferred in 7 seconds (582092K bits/sec), in 1 file, 2 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 17821 0 17821 0 0 24133 0 --:--:-- --:--:-- --:--:-- 32520 100 44908 0 44908 0 0 48393 0 --:--:-- --:--:-- --:--:-- 60933 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 24197156 spots for /home/okishinya/chipatlas/results/dm3/SRX033320/SRR080715.sra Written 24197156 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:09:10 24197156 reads; of these: 24197156 (100.00%) were unpaired; of these: 354694 (1.47%) aligned 0 times 17200278 (71.08%) aligned exactly 1 time 6642184 (27.45%) aligned >1 times 98.53% overall alignment rate Time searching: 00:09:10 Overall time: 00:09:10 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] 3310706 / 23842462 = 0.1389 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 13:20:20: # Command line: callpeak -t SRX033320.bam -f BAM -g dm -n SRX033320.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX033320.10 # format = BAM # ChIP-seq file = ['SRX033320.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 13:20:20: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:20:20: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:20:20: # Command line: callpeak -t SRX033320.bam -f BAM -g dm -n SRX033320.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX033320.05 # format = BAM # ChIP-seq file = ['SRX033320.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 13:20:20: # Command line: callpeak -t SRX033320.bam -f BAM -g dm -n SRX033320.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX033320.20 # format = BAM # ChIP-seq file = ['SRX033320.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 13:20:20: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:20:20: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:20:20: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:20:20: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:20:25: 1000000 INFO @ Tue, 21 Apr 2015 13:20:25: 1000000 INFO @ Tue, 21 Apr 2015 13:20:25: 1000000 INFO @ Tue, 21 Apr 2015 13:20:30: 2000000 INFO @ Tue, 21 Apr 2015 13:20:31: 2000000 INFO @ Tue, 21 Apr 2015 13:20:31: 2000000 INFO @ Tue, 21 Apr 2015 13:20:36: 3000000 INFO @ Tue, 21 Apr 2015 13:20:36: 3000000 INFO @ Tue, 21 Apr 2015 13:20:37: 3000000 INFO @ Tue, 21 Apr 2015 13:20:41: 4000000 INFO @ Tue, 21 Apr 2015 13:20:42: 4000000 INFO @ Tue, 21 Apr 2015 13:20:43: 4000000 INFO @ Tue, 21 Apr 2015 13:20:46: 5000000 INFO @ Tue, 21 Apr 2015 13:20:48: 5000000 INFO @ Tue, 21 Apr 2015 13:20:49: 5000000 INFO @ Tue, 21 Apr 2015 13:20:51: 6000000 INFO @ Tue, 21 Apr 2015 13:20:54: 6000000 INFO @ Tue, 21 Apr 2015 13:20:55: 6000000 INFO @ Tue, 21 Apr 2015 13:20:57: 7000000 INFO @ Tue, 21 Apr 2015 13:20:59: 7000000 INFO @ Tue, 21 Apr 2015 13:21:01: 7000000 INFO @ Tue, 21 Apr 2015 13:21:02: 8000000 INFO @ Tue, 21 Apr 2015 13:21:05: 8000000 INFO @ Tue, 21 Apr 2015 13:21:07: 8000000 INFO @ Tue, 21 Apr 2015 13:21:07: 9000000 INFO @ Tue, 21 Apr 2015 13:21:11: 9000000 INFO @ Tue, 21 Apr 2015 13:21:12: 10000000 INFO @ Tue, 21 Apr 2015 13:21:13: 9000000 INFO @ Tue, 21 Apr 2015 13:21:17: 10000000 INFO @ Tue, 21 Apr 2015 13:21:17: 11000000 INFO @ Tue, 21 Apr 2015 13:21:19: 10000000 INFO @ Tue, 21 Apr 2015 13:21:23: 12000000 INFO @ Tue, 21 Apr 2015 13:21:23: 11000000 INFO @ Tue, 21 Apr 2015 13:21:25: 11000000 INFO @ Tue, 21 Apr 2015 13:21:28: 13000000 INFO @ Tue, 21 Apr 2015 13:21:28: 12000000 INFO @ Tue, 21 Apr 2015 13:21:31: 12000000 INFO @ Tue, 21 Apr 2015 13:21:33: 14000000 INFO @ Tue, 21 Apr 2015 13:21:34: 13000000 INFO @ Tue, 21 Apr 2015 13:21:37: 13000000 INFO @ Tue, 21 Apr 2015 13:21:38: 15000000 INFO @ Tue, 21 Apr 2015 13:21:40: 14000000 INFO @ Tue, 21 Apr 2015 13:21:43: 14000000 INFO @ Tue, 21 Apr 2015 13:21:43: 16000000 INFO @ Tue, 21 Apr 2015 13:21:46: 15000000 INFO @ Tue, 21 Apr 2015 13:21:49: 17000000 INFO @ Tue, 21 Apr 2015 13:21:49: 15000000 INFO @ Tue, 21 Apr 2015 13:21:51: 16000000 INFO @ Tue, 21 Apr 2015 13:21:54: 18000000 INFO @ Tue, 21 Apr 2015 13:21:55: 16000000 INFO @ Tue, 21 Apr 2015 13:21:56: 17000000 INFO @ Tue, 21 Apr 2015 13:22:00: 19000000 INFO @ Tue, 21 Apr 2015 13:22:01: 18000000 INFO @ Tue, 21 Apr 2015 13:22:02: 17000000 INFO @ Tue, 21 Apr 2015 13:22:06: 20000000 INFO @ Tue, 21 Apr 2015 13:22:06: 19000000 INFO @ Tue, 21 Apr 2015 13:22:08: 18000000 INFO @ Tue, 21 Apr 2015 13:22:10: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:22:10: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:22:10: #1 total tags in treatment: 20531756 INFO @ Tue, 21 Apr 2015 13:22:10: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:22:10: #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 13:22:12: 20000000 INFO @ Tue, 21 Apr 2015 13:22:13: #1 tags after filtering in treatment: 20529397 INFO @ Tue, 21 Apr 2015 13:22:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:22:13: #1 finished! INFO @ Tue, 21 Apr 2015 13:22:13: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:22:14: 19000000 INFO @ Tue, 21 Apr 2015 13:22:15: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:22:15: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:22:15: #1 total tags in treatment: 20531756 INFO @ Tue, 21 Apr 2015 13:22:15: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:22:15: #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 13:22:17: #2 number of paired peaks: 220 WARNING @ Tue, 21 Apr 2015 13:22:17: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 21 Apr 2015 13:22:17: start model_add_line... INFO @ Tue, 21 Apr 2015 13:22:18: #1 tags after filtering in treatment: 20529397 INFO @ Tue, 21 Apr 2015 13:22:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:22:18: #1 finished! INFO @ Tue, 21 Apr 2015 13:22:18: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:22:19: 20000000 INFO @ Tue, 21 Apr 2015 13:22:20: start X-correlation... INFO @ Tue, 21 Apr 2015 13:22:20: end of X-cor INFO @ Tue, 21 Apr 2015 13:22:20: #2 finished! INFO @ Tue, 21 Apr 2015 13:22:20: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 13:22:20: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 13:22:20: #2.2 Generate R script for model : SRX033320.05_model.r WARNING @ Tue, 21 Apr 2015 13:22:20: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:22:20: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 13:22:20: #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 13:22:20: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:22:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:22:22: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:22:22: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:22:22: #1 total tags in treatment: 20531756 INFO @ Tue, 21 Apr 2015 13:22:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:22:22: #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 13:22:22: #2 number of paired peaks: 220 WARNING @ Tue, 21 Apr 2015 13:22:22: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 21 Apr 2015 13:22:22: start model_add_line... INFO @ Tue, 21 Apr 2015 13:22:25: start X-correlation... INFO @ Tue, 21 Apr 2015 13:22:25: end of X-cor INFO @ Tue, 21 Apr 2015 13:22:25: #2 finished! INFO @ Tue, 21 Apr 2015 13:22:25: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 13:22:25: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 13:22:25: #2.2 Generate R script for model : SRX033320.20_model.r WARNING @ Tue, 21 Apr 2015 13:22:25: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:22:25: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 13:22:25: #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 13:22:25: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:22:26: #1 tags after filtering in treatment: 20529397 INFO @ Tue, 21 Apr 2015 13:22:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:22:26: #1 finished! INFO @ Tue, 21 Apr 2015 13:22:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:22:29: #2 number of paired peaks: 220 WARNING @ Tue, 21 Apr 2015 13:22:29: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 21 Apr 2015 13:22:29: start model_add_line... INFO @ Tue, 21 Apr 2015 13:22:32: start X-correlation... INFO @ Tue, 21 Apr 2015 13:22:32: end of X-cor INFO @ Tue, 21 Apr 2015 13:22:32: #2 finished! INFO @ Tue, 21 Apr 2015 13:22:32: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 13:22:32: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 13:22:32: #2.2 Generate R script for model : SRX033320.10_model.r WARNING @ Tue, 21 Apr 2015 13:22:32: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:22:32: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 13:22:32: #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 13:22:32: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:22:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:23:55: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:24:02: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:24:12: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:25:09: #4 Write output xls file... SRX033320.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:25:09: #4 Write peak in narrowPeak format file... SRX033320.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:25:09: #4 Write summits bed file... SRX033320.05_summits.bed INFO @ Tue, 21 Apr 2015 13:25:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1967 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:25:14: #4 Write output xls file... SRX033320.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:25:14: #4 Write peak in narrowPeak format file... SRX033320.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:25:14: #4 Write summits bed file... SRX033320.20_summits.bed INFO @ Tue, 21 Apr 2015 13:25:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1144 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:25:26: #4 Write output xls file... SRX033320.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:25:26: #4 Write peak in narrowPeak format file... SRX033320.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:25:26: #4 Write summits bed file... SRX033320.10_summits.bed INFO @ Tue, 21 Apr 2015 13:25:26: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1693 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。