Job ID = 2162428 sra ファイルのダウンロード中... Completed: 987598K bytes transferred in 11 seconds (716822K 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 20753 0 20753 0 0 26881 0 --:--:-- --:--:-- --:--:-- 35719 100 36909 0 36909 0 0 47754 0 --:--:-- --:--:-- --:--:-- 63417 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 38502055 spots for /home/okishinya/chipatlas/results/dm3/SRX097620/SRR345571.sra Written 38502055 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: 00:09:29 38502055 reads; of these: 38502055 (100.00%) were unpaired; of these: 9651261 (25.07%) aligned 0 times 22142476 (57.51%) aligned exactly 1 time 6708318 (17.42%) aligned >1 times 74.93% overall alignment rate Time searching: 00:09:29 Overall time: 00:09:29 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] 11350117 / 28850794 = 0.3934 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 14:12:29: # Command line: callpeak -t SRX097620.bam -f BAM -g dm -n SRX097620.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX097620.05 # format = BAM # ChIP-seq file = ['SRX097620.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 14:12:29: # Command line: callpeak -t SRX097620.bam -f BAM -g dm -n SRX097620.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX097620.10 # format = BAM # ChIP-seq file = ['SRX097620.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 14:12:29: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:12:29: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:12:29: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:12:29: # Command line: callpeak -t SRX097620.bam -f BAM -g dm -n SRX097620.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX097620.20 # format = BAM # ChIP-seq file = ['SRX097620.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 14:12:29: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:12:29: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:12:29: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:12:33: 1000000 INFO @ Tue, 21 Apr 2015 14:12:34: 1000000 INFO @ Tue, 21 Apr 2015 14:12:34: 1000000 INFO @ Tue, 21 Apr 2015 14:12:38: 2000000 INFO @ Tue, 21 Apr 2015 14:12:39: 2000000 INFO @ Tue, 21 Apr 2015 14:12:39: 2000000 INFO @ Tue, 21 Apr 2015 14:12:43: 3000000 INFO @ Tue, 21 Apr 2015 14:12:44: 3000000 INFO @ Tue, 21 Apr 2015 14:12:45: 3000000 INFO @ Tue, 21 Apr 2015 14:12:47: 4000000 INFO @ Tue, 21 Apr 2015 14:12:49: 4000000 INFO @ Tue, 21 Apr 2015 14:12:50: 4000000 INFO @ Tue, 21 Apr 2015 14:12:52: 5000000 INFO @ Tue, 21 Apr 2015 14:12:54: 5000000 INFO @ Tue, 21 Apr 2015 14:12:56: 5000000 INFO @ Tue, 21 Apr 2015 14:12:57: 6000000 INFO @ Tue, 21 Apr 2015 14:12:59: 6000000 INFO @ Tue, 21 Apr 2015 14:13:01: 6000000 INFO @ Tue, 21 Apr 2015 14:13:01: 7000000 INFO @ Tue, 21 Apr 2015 14:13:04: 7000000 INFO @ Tue, 21 Apr 2015 14:13:06: 8000000 INFO @ Tue, 21 Apr 2015 14:13:06: 7000000 INFO @ Tue, 21 Apr 2015 14:13:09: 8000000 INFO @ Tue, 21 Apr 2015 14:13:10: 9000000 INFO @ Tue, 21 Apr 2015 14:13:12: 8000000 INFO @ Tue, 21 Apr 2015 14:13:15: 9000000 INFO @ Tue, 21 Apr 2015 14:13:15: 10000000 INFO @ Tue, 21 Apr 2015 14:13:17: 9000000 INFO @ Tue, 21 Apr 2015 14:13:20: 11000000 INFO @ Tue, 21 Apr 2015 14:13:20: 10000000 INFO @ Tue, 21 Apr 2015 14:13:23: 10000000 INFO @ Tue, 21 Apr 2015 14:13:24: 12000000 INFO @ Tue, 21 Apr 2015 14:13:25: 11000000 INFO @ Tue, 21 Apr 2015 14:13:28: 11000000 INFO @ Tue, 21 Apr 2015 14:13:29: 13000000 INFO @ Tue, 21 Apr 2015 14:13:30: 12000000 INFO @ Tue, 21 Apr 2015 14:13:33: 14000000 INFO @ Tue, 21 Apr 2015 14:13:34: 12000000 INFO @ Tue, 21 Apr 2015 14:13:35: 13000000 INFO @ Tue, 21 Apr 2015 14:13:38: 15000000 INFO @ Tue, 21 Apr 2015 14:13:39: 13000000 INFO @ Tue, 21 Apr 2015 14:13:40: 14000000 INFO @ Tue, 21 Apr 2015 14:13:43: 16000000 INFO @ Tue, 21 Apr 2015 14:13:44: 14000000 INFO @ Tue, 21 Apr 2015 14:13:45: 15000000 INFO @ Tue, 21 Apr 2015 14:13:47: 17000000 INFO @ Tue, 21 Apr 2015 14:13:50: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:13:50: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:13:50: #1 total tags in treatment: 17500677 INFO @ Tue, 21 Apr 2015 14:13:50: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:13:50: #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 14:13:50: 15000000 INFO @ Tue, 21 Apr 2015 14:13:50: 16000000 INFO @ Tue, 21 Apr 2015 14:13:53: #1 tags after filtering in treatment: 17498239 INFO @ Tue, 21 Apr 2015 14:13:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:13:53: #1 finished! INFO @ Tue, 21 Apr 2015 14:13:53: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:13:55: 16000000 INFO @ Tue, 21 Apr 2015 14:13:55: 17000000 INFO @ Tue, 21 Apr 2015 14:13:56: #2 number of paired peaks: 464 WARNING @ Tue, 21 Apr 2015 14:13:56: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 21 Apr 2015 14:13:56: start model_add_line... INFO @ Tue, 21 Apr 2015 14:13:58: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:13:58: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:13:58: #1 total tags in treatment: 17500677 INFO @ Tue, 21 Apr 2015 14:13:58: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:13:58: #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 14:14:01: 17000000 INFO @ Tue, 21 Apr 2015 14:14:02: #1 tags after filtering in treatment: 17498239 INFO @ Tue, 21 Apr 2015 14:14:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:14:02: #1 finished! INFO @ Tue, 21 Apr 2015 14:14:02: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:14:02: start X-correlation... INFO @ Tue, 21 Apr 2015 14:14:02: end of X-cor INFO @ Tue, 21 Apr 2015 14:14:02: #2 finished! INFO @ Tue, 21 Apr 2015 14:14:02: #2 predicted fragment length is 47 bps INFO @ Tue, 21 Apr 2015 14:14:02: #2 alternative fragment length(s) may be 47 bps INFO @ Tue, 21 Apr 2015 14:14:02: #2.2 Generate R script for model : SRX097620.20_model.r WARNING @ Tue, 21 Apr 2015 14:14:02: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:14:02: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Tue, 21 Apr 2015 14:14:02: #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 14:14:02: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:14:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:14:03: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 14:14:03: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 14:14:03: #1 total tags in treatment: 17500677 INFO @ Tue, 21 Apr 2015 14:14:03: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:14:03: #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 14:14:05: #2 number of paired peaks: 464 WARNING @ Tue, 21 Apr 2015 14:14:05: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 21 Apr 2015 14:14:05: start model_add_line... INFO @ Tue, 21 Apr 2015 14:14:06: #1 tags after filtering in treatment: 17498239 INFO @ Tue, 21 Apr 2015 14:14:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:14:06: #1 finished! INFO @ Tue, 21 Apr 2015 14:14:06: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:14:09: #2 number of paired peaks: 464 WARNING @ Tue, 21 Apr 2015 14:14:09: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 21 Apr 2015 14:14:09: start model_add_line... INFO @ Tue, 21 Apr 2015 14:14:11: start X-correlation... INFO @ Tue, 21 Apr 2015 14:14:11: end of X-cor INFO @ Tue, 21 Apr 2015 14:14:11: #2 finished! INFO @ Tue, 21 Apr 2015 14:14:11: #2 predicted fragment length is 47 bps INFO @ Tue, 21 Apr 2015 14:14:11: #2 alternative fragment length(s) may be 47 bps INFO @ Tue, 21 Apr 2015 14:14:11: #2.2 Generate R script for model : SRX097620.05_model.r WARNING @ Tue, 21 Apr 2015 14:14:11: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:14:11: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Tue, 21 Apr 2015 14:14:11: #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 14:14:11: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:14:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:14:15: start X-correlation... INFO @ Tue, 21 Apr 2015 14:14:15: end of X-cor INFO @ Tue, 21 Apr 2015 14:14:15: #2 finished! INFO @ Tue, 21 Apr 2015 14:14:15: #2 predicted fragment length is 47 bps INFO @ Tue, 21 Apr 2015 14:14:15: #2 alternative fragment length(s) may be 47 bps INFO @ Tue, 21 Apr 2015 14:14:15: #2.2 Generate R script for model : SRX097620.10_model.r WARNING @ Tue, 21 Apr 2015 14:14:15: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 14:14:15: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Tue, 21 Apr 2015 14:14:15: #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 14:14:15: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:14:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:15:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:15:37: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:15:46: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:16:40: #4 Write output xls file... SRX097620.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:16:40: #4 Write peak in narrowPeak format file... SRX097620.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:16:41: #4 Write summits bed file... SRX097620.05_summits.bed INFO @ Tue, 21 Apr 2015 14:16:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7559 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:16:44: #4 Write output xls file... SRX097620.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:16:45: #4 Write peak in narrowPeak format file... SRX097620.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:16:45: #4 Write summits bed file... SRX097620.20_summits.bed INFO @ Tue, 21 Apr 2015 14:16:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1880 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:16:53: #4 Write output xls file... SRX097620.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:16:53: #4 Write peak in narrowPeak format file... SRX097620.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:16:53: #4 Write summits bed file... SRX097620.10_summits.bed INFO @ Tue, 21 Apr 2015 14:16:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4270 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。