Job ID = 2161431 sra ファイルのダウンロード中... Completed: 905775K bytes transferred in 9 seconds (754278K 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 44918 0 44918 0 0 46351 0 --:--:-- --:--:-- --:--:-- 57809 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 21236027 spots for /home/okishinya/chipatlas/results/dm3/SRX026861/SRR065760.sra Written 21236027 spots total Written 22197905 spots for /home/okishinya/chipatlas/results/dm3/SRX026861/SRR065761.sra Written 22197905 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: 00:25:49 43433932 reads; of these: 43433932 (100.00%) were unpaired; of these: 1413777 (3.26%) aligned 0 times 21889784 (50.40%) aligned exactly 1 time 20130371 (46.35%) aligned >1 times 96.74% overall alignment rate Time searching: 00:25:49 Overall time: 00:25:49 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] 22136641 / 42020155 = 0.5268 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 13:14:30: # Command line: callpeak -t SRX026861.bam -f BAM -g dm -n SRX026861.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX026861.10 # format = BAM # ChIP-seq file = ['SRX026861.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 13:14:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:14:30: # Command line: callpeak -t SRX026861.bam -f BAM -g dm -n SRX026861.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX026861.05 # format = BAM # ChIP-seq file = ['SRX026861.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 13:14:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:14:30: # Command line: callpeak -t SRX026861.bam -f BAM -g dm -n SRX026861.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX026861.20 # format = BAM # ChIP-seq file = ['SRX026861.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 13:14:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:14:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:14:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:14:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:14:35: 1000000 INFO @ Tue, 21 Apr 2015 13:14:35: 1000000 INFO @ Tue, 21 Apr 2015 13:14:35: 1000000 INFO @ Tue, 21 Apr 2015 13:14:41: 2000000 INFO @ Tue, 21 Apr 2015 13:14:41: 2000000 INFO @ Tue, 21 Apr 2015 13:14:41: 2000000 INFO @ Tue, 21 Apr 2015 13:14:47: 3000000 INFO @ Tue, 21 Apr 2015 13:14:47: 3000000 INFO @ Tue, 21 Apr 2015 13:14:47: 3000000 INFO @ Tue, 21 Apr 2015 13:14:53: 4000000 INFO @ Tue, 21 Apr 2015 13:14:53: 4000000 INFO @ Tue, 21 Apr 2015 13:14:53: 4000000 INFO @ Tue, 21 Apr 2015 13:14:59: 5000000 INFO @ Tue, 21 Apr 2015 13:14:59: 5000000 INFO @ Tue, 21 Apr 2015 13:14:59: 5000000 INFO @ Tue, 21 Apr 2015 13:15:05: 6000000 INFO @ Tue, 21 Apr 2015 13:15:05: 6000000 INFO @ Tue, 21 Apr 2015 13:15:05: 6000000 INFO @ Tue, 21 Apr 2015 13:15:11: 7000000 INFO @ Tue, 21 Apr 2015 13:15:11: 7000000 INFO @ Tue, 21 Apr 2015 13:15:11: 7000000 INFO @ Tue, 21 Apr 2015 13:15:16: 8000000 INFO @ Tue, 21 Apr 2015 13:15:16: 8000000 INFO @ Tue, 21 Apr 2015 13:15:17: 8000000 INFO @ Tue, 21 Apr 2015 13:15:22: 9000000 INFO @ Tue, 21 Apr 2015 13:15:22: 9000000 INFO @ Tue, 21 Apr 2015 13:15:23: 9000000 INFO @ Tue, 21 Apr 2015 13:15:28: 10000000 INFO @ Tue, 21 Apr 2015 13:15:28: 10000000 INFO @ Tue, 21 Apr 2015 13:15:30: 10000000 INFO @ Tue, 21 Apr 2015 13:15:34: 11000000 INFO @ Tue, 21 Apr 2015 13:15:34: 11000000 INFO @ Tue, 21 Apr 2015 13:15:37: 11000000 INFO @ Tue, 21 Apr 2015 13:15:40: 12000000 INFO @ Tue, 21 Apr 2015 13:15:40: 12000000 INFO @ Tue, 21 Apr 2015 13:15:44: 12000000 INFO @ Tue, 21 Apr 2015 13:15:46: 13000000 INFO @ Tue, 21 Apr 2015 13:15:46: 13000000 INFO @ Tue, 21 Apr 2015 13:15:50: 13000000 INFO @ Tue, 21 Apr 2015 13:15:52: 14000000 INFO @ Tue, 21 Apr 2015 13:15:52: 14000000 INFO @ Tue, 21 Apr 2015 13:15:57: 14000000 INFO @ Tue, 21 Apr 2015 13:15:58: 15000000 INFO @ Tue, 21 Apr 2015 13:15:58: 15000000 INFO @ Tue, 21 Apr 2015 13:16:03: 15000000 INFO @ Tue, 21 Apr 2015 13:16:04: 16000000 INFO @ Tue, 21 Apr 2015 13:16:04: 16000000 INFO @ Tue, 21 Apr 2015 13:16:09: 16000000 INFO @ Tue, 21 Apr 2015 13:16:10: 17000000 INFO @ Tue, 21 Apr 2015 13:16:10: 17000000 INFO @ Tue, 21 Apr 2015 13:16:15: 18000000 INFO @ Tue, 21 Apr 2015 13:16:15: 18000000 INFO @ Tue, 21 Apr 2015 13:16:16: 17000000 INFO @ Tue, 21 Apr 2015 13:16:21: 19000000 INFO @ Tue, 21 Apr 2015 13:16:21: 19000000 INFO @ Tue, 21 Apr 2015 13:16:22: 18000000 INFO @ Tue, 21 Apr 2015 13:16:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:16:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:16:27: #1 total tags in treatment: 19883514 INFO @ Tue, 21 Apr 2015 13:16:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:16:27: #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 13:16:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:16:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:16:27: #1 total tags in treatment: 19883514 INFO @ Tue, 21 Apr 2015 13:16:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:16:27: #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 13:16:28: 19000000 INFO @ Tue, 21 Apr 2015 13:16:30: #1 tags after filtering in treatment: 19879089 INFO @ Tue, 21 Apr 2015 13:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:16:30: #1 finished! INFO @ Tue, 21 Apr 2015 13:16:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:16:30: #1 tags after filtering in treatment: 19879089 INFO @ Tue, 21 Apr 2015 13:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:16:30: #1 finished! INFO @ Tue, 21 Apr 2015 13:16:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:16:33: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:16:33: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:16:33: #1 total tags in treatment: 19883514 INFO @ Tue, 21 Apr 2015 13:16:33: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:16:33: #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 13:16:34: #2 number of paired peaks: 558 WARNING @ Tue, 21 Apr 2015 13:16:34: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 21 Apr 2015 13:16:34: start model_add_line... INFO @ Tue, 21 Apr 2015 13:16:34: #2 number of paired peaks: 558 WARNING @ Tue, 21 Apr 2015 13:16:34: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 21 Apr 2015 13:16:34: start model_add_line... INFO @ Tue, 21 Apr 2015 13:16:37: #1 tags after filtering in treatment: 19879089 INFO @ Tue, 21 Apr 2015 13:16:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:16:37: #1 finished! INFO @ Tue, 21 Apr 2015 13:16:37: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:16:40: start X-correlation... INFO @ Tue, 21 Apr 2015 13:16:40: end of X-cor INFO @ Tue, 21 Apr 2015 13:16:40: #2 finished! INFO @ Tue, 21 Apr 2015 13:16:40: #2 predicted fragment length is 32 bps INFO @ Tue, 21 Apr 2015 13:16:40: #2 alternative fragment length(s) may be 32 bps INFO @ Tue, 21 Apr 2015 13:16:40: #2.2 Generate R script for model : SRX026861.20_model.r WARNING @ Tue, 21 Apr 2015 13:16:40: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:16:40: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Tue, 21 Apr 2015 13:16:40: #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 13:16:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:16:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:16:40: #2 number of paired peaks: 558 WARNING @ Tue, 21 Apr 2015 13:16:40: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 21 Apr 2015 13:16:40: start model_add_line... INFO @ Tue, 21 Apr 2015 13:16:40: start X-correlation... INFO @ Tue, 21 Apr 2015 13:16:40: end of X-cor INFO @ Tue, 21 Apr 2015 13:16:40: #2 finished! INFO @ Tue, 21 Apr 2015 13:16:40: #2 predicted fragment length is 32 bps INFO @ Tue, 21 Apr 2015 13:16:40: #2 alternative fragment length(s) may be 32 bps INFO @ Tue, 21 Apr 2015 13:16:40: #2.2 Generate R script for model : SRX026861.10_model.r WARNING @ Tue, 21 Apr 2015 13:16:40: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:16:40: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Tue, 21 Apr 2015 13:16:40: #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 13:16:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:16:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:16:46: start X-correlation... INFO @ Tue, 21 Apr 2015 13:16:46: end of X-cor INFO @ Tue, 21 Apr 2015 13:16:46: #2 finished! INFO @ Tue, 21 Apr 2015 13:16:46: #2 predicted fragment length is 32 bps INFO @ Tue, 21 Apr 2015 13:16:46: #2 alternative fragment length(s) may be 32 bps INFO @ Tue, 21 Apr 2015 13:16:46: #2.2 Generate R script for model : SRX026861.05_model.r WARNING @ Tue, 21 Apr 2015 13:16:46: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:16:46: #2 You may need to consider one of the other alternative d(s): 32 WARNING @ Tue, 21 Apr 2015 13:16:46: #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 13:16:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:16:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:18:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:18:21: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:18:21: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:19:34: #4 Write output xls file... SRX026861.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:19:34: #4 Write peak in narrowPeak format file... SRX026861.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:19:34: #4 Write summits bed file... SRX026861.20_summits.bed INFO @ Tue, 21 Apr 2015 13:19:34: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1113 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:19:35: #4 Write output xls file... SRX026861.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:19:35: #4 Write peak in narrowPeak format file... SRX026861.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:19:35: #4 Write summits bed file... SRX026861.10_summits.bed INFO @ Tue, 21 Apr 2015 13:19:35: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6533 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:19:40: #4 Write output xls file... SRX026861.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:19:40: #4 Write peak in narrowPeak format file... SRX026861.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:19:40: #4 Write summits bed file... SRX026861.05_summits.bed INFO @ Tue, 21 Apr 2015 13:19:41: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (16390 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。