Job ID = 2161438 sra ファイルのダウンロード中... Completed: 848409K bytes transferred in 9 seconds (711379K 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 --:--:-- --:--:-- --:--:-- 0 101 2547 0 2547 0 0 4901 0 --:--:-- --:--:-- --:--:-- 7741 100 45021 0 45021 0 0 50105 0 --:--:-- --:--:-- --:--:-- 63588 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 25496800 spots for /home/okishinya/chipatlas/results/dm3/SRX026867/SRR065769.sra Written 25496800 spots total Written 26764718 spots for /home/okishinya/chipatlas/results/dm3/SRX026867/SRR065768.sra Written 26764718 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: 00:20:16 52261518 reads; of these: 52261518 (100.00%) were unpaired; of these: 859046 (1.64%) aligned 0 times 35495991 (67.92%) aligned exactly 1 time 15906481 (30.44%) aligned >1 times 98.36% overall alignment rate Time searching: 00:20:16 Overall time: 00:20:16 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 16 files... [bam_rmdupse_core] 31314833 / 51402472 = 0.6092 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 13:12:26: # Command line: callpeak -t SRX026867.bam -f BAM -g dm -n SRX026867.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX026867.20 # format = BAM # ChIP-seq file = ['SRX026867.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 13:12:26: # Command line: callpeak -t SRX026867.bam -f BAM -g dm -n SRX026867.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX026867.10 # format = BAM # ChIP-seq file = ['SRX026867.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 13:12:26: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:12:26: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:12:26: # Command line: callpeak -t SRX026867.bam -f BAM -g dm -n SRX026867.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX026867.05 # format = BAM # ChIP-seq file = ['SRX026867.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 13:12:26: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:12:26: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:12:26: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:12:26: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:12:33: 1000000 INFO @ Tue, 21 Apr 2015 13:12:33: 1000000 INFO @ Tue, 21 Apr 2015 13:12:33: 1000000 INFO @ Tue, 21 Apr 2015 13:12:39: 2000000 INFO @ Tue, 21 Apr 2015 13:12:39: 2000000 INFO @ Tue, 21 Apr 2015 13:12:39: 2000000 INFO @ Tue, 21 Apr 2015 13:12:46: 3000000 INFO @ Tue, 21 Apr 2015 13:12:46: 3000000 INFO @ Tue, 21 Apr 2015 13:12:46: 3000000 INFO @ Tue, 21 Apr 2015 13:12:52: 4000000 INFO @ Tue, 21 Apr 2015 13:12:52: 4000000 INFO @ Tue, 21 Apr 2015 13:12:52: 4000000 INFO @ Tue, 21 Apr 2015 13:12:58: 5000000 INFO @ Tue, 21 Apr 2015 13:12:58: 5000000 INFO @ Tue, 21 Apr 2015 13:12:58: 5000000 INFO @ Tue, 21 Apr 2015 13:13:04: 6000000 INFO @ Tue, 21 Apr 2015 13:13:04: 6000000 INFO @ Tue, 21 Apr 2015 13:13:04: 6000000 INFO @ Tue, 21 Apr 2015 13:13:10: 7000000 INFO @ Tue, 21 Apr 2015 13:13:10: 7000000 INFO @ Tue, 21 Apr 2015 13:13:10: 7000000 INFO @ Tue, 21 Apr 2015 13:13:16: 8000000 INFO @ Tue, 21 Apr 2015 13:13:16: 8000000 INFO @ Tue, 21 Apr 2015 13:13:16: 8000000 INFO @ Tue, 21 Apr 2015 13:13:22: 9000000 INFO @ Tue, 21 Apr 2015 13:13:22: 9000000 INFO @ Tue, 21 Apr 2015 13:13:22: 9000000 INFO @ Tue, 21 Apr 2015 13:13:28: 10000000 INFO @ Tue, 21 Apr 2015 13:13:28: 10000000 INFO @ Tue, 21 Apr 2015 13:13:29: 10000000 INFO @ Tue, 21 Apr 2015 13:13:34: 11000000 INFO @ Tue, 21 Apr 2015 13:13:34: 11000000 INFO @ Tue, 21 Apr 2015 13:13:35: 11000000 INFO @ Tue, 21 Apr 2015 13:13:40: 12000000 INFO @ Tue, 21 Apr 2015 13:13:41: 12000000 INFO @ Tue, 21 Apr 2015 13:13:41: 12000000 INFO @ Tue, 21 Apr 2015 13:13:47: 13000000 INFO @ Tue, 21 Apr 2015 13:13:47: 13000000 INFO @ Tue, 21 Apr 2015 13:13:48: 13000000 INFO @ Tue, 21 Apr 2015 13:13:53: 14000000 INFO @ Tue, 21 Apr 2015 13:13:53: 14000000 INFO @ Tue, 21 Apr 2015 13:13:54: 14000000 INFO @ Tue, 21 Apr 2015 13:13:59: 15000000 INFO @ Tue, 21 Apr 2015 13:14:00: 15000000 INFO @ Tue, 21 Apr 2015 13:14:01: 15000000 INFO @ Tue, 21 Apr 2015 13:14:05: 16000000 INFO @ Tue, 21 Apr 2015 13:14:06: 16000000 INFO @ Tue, 21 Apr 2015 13:14:07: 16000000 INFO @ Tue, 21 Apr 2015 13:14:11: 17000000 INFO @ Tue, 21 Apr 2015 13:14:12: 17000000 INFO @ Tue, 21 Apr 2015 13:14:13: 17000000 INFO @ Tue, 21 Apr 2015 13:14:17: 18000000 INFO @ Tue, 21 Apr 2015 13:14:18: 18000000 INFO @ Tue, 21 Apr 2015 13:14:19: 18000000 INFO @ Tue, 21 Apr 2015 13:14:23: 19000000 INFO @ Tue, 21 Apr 2015 13:14:24: 19000000 INFO @ Tue, 21 Apr 2015 13:14:25: 19000000 INFO @ Tue, 21 Apr 2015 13:14:29: 20000000 INFO @ Tue, 21 Apr 2015 13:14:30: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:14:30: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:14:30: #1 total tags in treatment: 20087639 INFO @ Tue, 21 Apr 2015 13:14:30: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:14:30: #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 13:14:30: 20000000 INFO @ Tue, 21 Apr 2015 13:14:31: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:14:31: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:14:31: #1 total tags in treatment: 20087639 INFO @ Tue, 21 Apr 2015 13:14:31: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:14:31: #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 13:14:31: 20000000 INFO @ Tue, 21 Apr 2015 13:14:32: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:14:32: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:14:32: #1 total tags in treatment: 20087639 INFO @ Tue, 21 Apr 2015 13:14:32: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:14:32: #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 13:14:33: #1 tags after filtering in treatment: 20086504 INFO @ Tue, 21 Apr 2015 13:14:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:14:33: #1 finished! INFO @ Tue, 21 Apr 2015 13:14:33: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:14:35: #1 tags after filtering in treatment: 20086504 INFO @ Tue, 21 Apr 2015 13:14:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:14:35: #1 finished! INFO @ Tue, 21 Apr 2015 13:14:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:14:35: #1 tags after filtering in treatment: 20086504 INFO @ Tue, 21 Apr 2015 13:14:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:14:35: #1 finished! INFO @ Tue, 21 Apr 2015 13:14:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:14:37: #2 number of paired peaks: 375 WARNING @ Tue, 21 Apr 2015 13:14:37: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 21 Apr 2015 13:14:37: start model_add_line... INFO @ Tue, 21 Apr 2015 13:14:39: #2 number of paired peaks: 375 WARNING @ Tue, 21 Apr 2015 13:14:39: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 21 Apr 2015 13:14:39: start model_add_line... INFO @ Tue, 21 Apr 2015 13:14:39: #2 number of paired peaks: 375 WARNING @ Tue, 21 Apr 2015 13:14:39: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 21 Apr 2015 13:14:39: start model_add_line... INFO @ Tue, 21 Apr 2015 13:14:42: start X-correlation... INFO @ Tue, 21 Apr 2015 13:14:42: end of X-cor INFO @ Tue, 21 Apr 2015 13:14:42: #2 finished! INFO @ Tue, 21 Apr 2015 13:14:42: #2 predicted fragment length is 45 bps INFO @ Tue, 21 Apr 2015 13:14:42: #2 alternative fragment length(s) may be 45 bps INFO @ Tue, 21 Apr 2015 13:14:42: #2.2 Generate R script for model : SRX026867.10_model.r WARNING @ Tue, 21 Apr 2015 13:14:42: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:14:42: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Tue, 21 Apr 2015 13:14:42: #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 13:14:42: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:14:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:14:43: start X-correlation... INFO @ Tue, 21 Apr 2015 13:14:43: end of X-cor INFO @ Tue, 21 Apr 2015 13:14:43: #2 finished! INFO @ Tue, 21 Apr 2015 13:14:43: #2 predicted fragment length is 45 bps INFO @ Tue, 21 Apr 2015 13:14:43: #2 alternative fragment length(s) may be 45 bps INFO @ Tue, 21 Apr 2015 13:14:43: #2.2 Generate R script for model : SRX026867.05_model.r WARNING @ Tue, 21 Apr 2015 13:14:43: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:14:43: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Tue, 21 Apr 2015 13:14:43: #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 13:14:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:14:44: start X-correlation... INFO @ Tue, 21 Apr 2015 13:14:44: end of X-cor INFO @ Tue, 21 Apr 2015 13:14:44: #2 finished! INFO @ Tue, 21 Apr 2015 13:14:44: #2 predicted fragment length is 45 bps INFO @ Tue, 21 Apr 2015 13:14:44: #2 alternative fragment length(s) may be 45 bps INFO @ Tue, 21 Apr 2015 13:14:44: #2.2 Generate R script for model : SRX026867.20_model.r WARNING @ Tue, 21 Apr 2015 13:14:44: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:14:44: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Tue, 21 Apr 2015 13:14:44: #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 13:14:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:14:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:16:19: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:16:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:16:22: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:17:34: #4 Write output xls file... SRX026867.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:17:34: #4 Write peak in narrowPeak format file... SRX026867.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:17:34: #4 Write summits bed file... SRX026867.10_summits.bed INFO @ Tue, 21 Apr 2015 13:17:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2060 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:17:34: #4 Write output xls file... SRX026867.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:17:34: #4 Write peak in narrowPeak format file... SRX026867.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:17:34: #4 Write summits bed file... SRX026867.05_summits.bed INFO @ Tue, 21 Apr 2015 13:17:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4734 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:17:34: #4 Write output xls file... SRX026867.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:17:35: #4 Write peak in narrowPeak format file... SRX026867.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:17:35: #4 Write summits bed file... SRX026867.20_summits.bed INFO @ Tue, 21 Apr 2015 13:17:35: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1280 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。