Job ID = 2163424 sra ファイルのダウンロード中... Completed: 441246K bytes transferred in 6 seconds (517319K 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 14921 0 14921 0 0 19597 0 --:--:-- --:--:-- --:--:-- 26177 100 37077 0 37077 0 0 48642 0 --:--:-- --:--:-- --:--:-- 64933 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 16118438 spots for /home/okishinya/chipatlas/results/dm3/SRX149194/SRR500154.sra Written 16118438 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: 00:07:13 16118438 reads; of these: 16118438 (100.00%) were unpaired; of these: 484844 (3.01%) aligned 0 times 9203826 (57.10%) aligned exactly 1 time 6429768 (39.89%) aligned >1 times 96.99% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 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] 2714359 / 15633594 = 0.1736 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 17:09:01: # Command line: callpeak -t SRX149194.bam -f BAM -g dm -n SRX149194.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX149194.20 # format = BAM # ChIP-seq file = ['SRX149194.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 17:09:01: # Command line: callpeak -t SRX149194.bam -f BAM -g dm -n SRX149194.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX149194.10 # format = BAM # ChIP-seq file = ['SRX149194.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 17:09:01: # Command line: callpeak -t SRX149194.bam -f BAM -g dm -n SRX149194.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX149194.05 # format = BAM # ChIP-seq file = ['SRX149194.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 17:09:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 17:09:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 17:09:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 17:09:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 17:09:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 17:09:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 17:09:07: 1000000 INFO @ Tue, 21 Apr 2015 17:09:07: 1000000 INFO @ Tue, 21 Apr 2015 17:09:07: 1000000 INFO @ Tue, 21 Apr 2015 17:09:12: 2000000 INFO @ Tue, 21 Apr 2015 17:09:12: 2000000 INFO @ Tue, 21 Apr 2015 17:09:13: 2000000 INFO @ Tue, 21 Apr 2015 17:09:18: 3000000 INFO @ Tue, 21 Apr 2015 17:09:18: 3000000 INFO @ Tue, 21 Apr 2015 17:09:19: 3000000 INFO @ Tue, 21 Apr 2015 17:09:23: 4000000 INFO @ Tue, 21 Apr 2015 17:09:24: 4000000 INFO @ Tue, 21 Apr 2015 17:09:25: 4000000 INFO @ Tue, 21 Apr 2015 17:09:29: 5000000 INFO @ Tue, 21 Apr 2015 17:09:30: 5000000 INFO @ Tue, 21 Apr 2015 17:09:31: 5000000 INFO @ Tue, 21 Apr 2015 17:09:34: 6000000 INFO @ Tue, 21 Apr 2015 17:09:36: 6000000 INFO @ Tue, 21 Apr 2015 17:09:37: 6000000 INFO @ Tue, 21 Apr 2015 17:09:39: 7000000 INFO @ Tue, 21 Apr 2015 17:09:41: 7000000 INFO @ Tue, 21 Apr 2015 17:09:43: 7000000 INFO @ Tue, 21 Apr 2015 17:09:45: 8000000 INFO @ Tue, 21 Apr 2015 17:09:47: 8000000 INFO @ Tue, 21 Apr 2015 17:09:49: 8000000 INFO @ Tue, 21 Apr 2015 17:09:50: 9000000 INFO @ Tue, 21 Apr 2015 17:09:53: 9000000 INFO @ Tue, 21 Apr 2015 17:09:56: 9000000 INFO @ Tue, 21 Apr 2015 17:09:56: 10000000 INFO @ Tue, 21 Apr 2015 17:09:59: 10000000 INFO @ Tue, 21 Apr 2015 17:10:01: 11000000 INFO @ Tue, 21 Apr 2015 17:10:02: 10000000 INFO @ Tue, 21 Apr 2015 17:10:05: 11000000 INFO @ Tue, 21 Apr 2015 17:10:07: 12000000 INFO @ Tue, 21 Apr 2015 17:10:08: 11000000 INFO @ Tue, 21 Apr 2015 17:10:11: 12000000 INFO @ Tue, 21 Apr 2015 17:10:12: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 17:10:12: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 17:10:12: #1 total tags in treatment: 12919235 INFO @ Tue, 21 Apr 2015 17:10:12: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 17:10:12: #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 17:10:14: 12000000 INFO @ Tue, 21 Apr 2015 17:10:14: #1 tags after filtering in treatment: 12917707 INFO @ Tue, 21 Apr 2015 17:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 17:10:14: #1 finished! INFO @ Tue, 21 Apr 2015 17:10:14: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 17:10:16: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 17:10:16: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 17:10:16: #1 total tags in treatment: 12919235 INFO @ Tue, 21 Apr 2015 17:10:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 17:10:16: #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 17:10:17: #2 number of paired peaks: 904 WARNING @ Tue, 21 Apr 2015 17:10:17: Fewer paired peaks (904) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 904 pairs to build model! INFO @ Tue, 21 Apr 2015 17:10:17: start model_add_line... INFO @ Tue, 21 Apr 2015 17:10:19: #1 tags after filtering in treatment: 12917707 INFO @ Tue, 21 Apr 2015 17:10:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 17:10:19: #1 finished! INFO @ Tue, 21 Apr 2015 17:10:19: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 17:10:19: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 17:10:19: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 17:10:19: #1 total tags in treatment: 12919235 INFO @ Tue, 21 Apr 2015 17:10:19: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 17:10:19: #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 17:10:21: #2 number of paired peaks: 904 WARNING @ Tue, 21 Apr 2015 17:10:21: Fewer paired peaks (904) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 904 pairs to build model! INFO @ Tue, 21 Apr 2015 17:10:21: start model_add_line... INFO @ Tue, 21 Apr 2015 17:10:22: #1 tags after filtering in treatment: 12917707 INFO @ Tue, 21 Apr 2015 17:10:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 17:10:22: #1 finished! INFO @ Tue, 21 Apr 2015 17:10:22: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 17:10:24: #2 number of paired peaks: 904 WARNING @ Tue, 21 Apr 2015 17:10:24: Fewer paired peaks (904) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 904 pairs to build model! INFO @ Tue, 21 Apr 2015 17:10:24: start model_add_line... INFO @ Tue, 21 Apr 2015 17:10:24: start X-correlation... INFO @ Tue, 21 Apr 2015 17:10:24: end of X-cor INFO @ Tue, 21 Apr 2015 17:10:24: #2 finished! INFO @ Tue, 21 Apr 2015 17:10:24: #2 predicted fragment length is 39 bps INFO @ Tue, 21 Apr 2015 17:10:24: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 21 Apr 2015 17:10:24: #2.2 Generate R script for model : SRX149194.05_model.r WARNING @ Tue, 21 Apr 2015 17:10:24: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 17:10:24: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 21 Apr 2015 17:10:24: #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 17:10:24: #3 Call peaks... INFO @ Tue, 21 Apr 2015 17:10:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 17:10:28: start X-correlation... INFO @ Tue, 21 Apr 2015 17:10:28: end of X-cor INFO @ Tue, 21 Apr 2015 17:10:28: #2 finished! INFO @ Tue, 21 Apr 2015 17:10:28: #2 predicted fragment length is 39 bps INFO @ Tue, 21 Apr 2015 17:10:28: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 21 Apr 2015 17:10:28: #2.2 Generate R script for model : SRX149194.10_model.r WARNING @ Tue, 21 Apr 2015 17:10:28: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 17:10:28: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 21 Apr 2015 17:10:28: #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 17:10:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 17:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 17:10:32: start X-correlation... INFO @ Tue, 21 Apr 2015 17:10:32: end of X-cor INFO @ Tue, 21 Apr 2015 17:10:32: #2 finished! INFO @ Tue, 21 Apr 2015 17:10:32: #2 predicted fragment length is 39 bps INFO @ Tue, 21 Apr 2015 17:10:32: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 21 Apr 2015 17:10:32: #2.2 Generate R script for model : SRX149194.20_model.r WARNING @ Tue, 21 Apr 2015 17:10:32: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 17:10:32: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 21 Apr 2015 17:10:32: #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 17:10:32: #3 Call peaks... INFO @ Tue, 21 Apr 2015 17:10:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 17:11:31: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 17:11:37: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 17:11:39: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 17:12:20: #4 Write output xls file... SRX149194.05_peaks.xls INFO @ Tue, 21 Apr 2015 17:12:20: #4 Write peak in narrowPeak format file... SRX149194.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 17:12:21: #4 Write summits bed file... SRX149194.05_summits.bed INFO @ Tue, 21 Apr 2015 17:12:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3612 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 17:12:26: #4 Write output xls file... SRX149194.10_peaks.xls INFO @ Tue, 21 Apr 2015 17:12:26: #4 Write peak in narrowPeak format file... SRX149194.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 17:12:26: #4 Write summits bed file... SRX149194.10_summits.bed INFO @ Tue, 21 Apr 2015 17:12:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2164 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 17:12:27: #4 Write output xls file... SRX149194.20_peaks.xls INFO @ Tue, 21 Apr 2015 17:12:27: #4 Write peak in narrowPeak format file... SRX149194.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 17:12:27: #4 Write summits bed file... SRX149194.20_summits.bed INFO @ Tue, 21 Apr 2015 17:12:27: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1024 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。