Job ID = 2161917 sra ファイルのダウンロード中... Completed: 928999K bytes transferred in 10 seconds (723920K 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 9088 0 9088 0 0 16301 0 --:--:-- --:--:-- --:--:-- 24762 100 45157 0 45157 0 0 48209 0 --:--:-- --:--:-- --:--:-- 60532 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 24847144 spots for /home/okishinya/chipatlas/results/dm3/SRX041381/SRR099108.sra Written 24847144 spots total Written 28483105 spots for /home/okishinya/chipatlas/results/dm3/SRX041381/SRR099109.sra Written 28483105 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: 00:12:22 53330249 reads; of these: 53330249 (100.00%) were unpaired; of these: 3289514 (6.17%) aligned 0 times 43599280 (81.75%) aligned exactly 1 time 6441455 (12.08%) aligned >1 times 93.83% overall alignment rate Time searching: 00:12:22 Overall time: 00:12:22 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] 23119267 / 50040735 = 0.4620 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 13:34:59: # Command line: callpeak -t SRX041381.bam -f BAM -g dm -n SRX041381.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX041381.05 # format = BAM # ChIP-seq file = ['SRX041381.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 13:34:59: # Command line: callpeak -t SRX041381.bam -f BAM -g dm -n SRX041381.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX041381.10 # format = BAM # ChIP-seq file = ['SRX041381.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 13:34:59: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:34:59: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:34:59: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:34:59: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:34:59: # Command line: callpeak -t SRX041381.bam -f BAM -g dm -n SRX041381.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX041381.20 # format = BAM # ChIP-seq file = ['SRX041381.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 13:34:59: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:34:59: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:35:03: 1000000 INFO @ Tue, 21 Apr 2015 13:35:03: 1000000 INFO @ Tue, 21 Apr 2015 13:35:03: 1000000 INFO @ Tue, 21 Apr 2015 13:35:08: 2000000 INFO @ Tue, 21 Apr 2015 13:35:08: 2000000 INFO @ Tue, 21 Apr 2015 13:35:08: 2000000 INFO @ Tue, 21 Apr 2015 13:35:12: 3000000 INFO @ Tue, 21 Apr 2015 13:35:12: 3000000 INFO @ Tue, 21 Apr 2015 13:35:13: 3000000 INFO @ Tue, 21 Apr 2015 13:35:17: 4000000 INFO @ Tue, 21 Apr 2015 13:35:17: 4000000 INFO @ Tue, 21 Apr 2015 13:35:18: 4000000 INFO @ Tue, 21 Apr 2015 13:35:21: 5000000 INFO @ Tue, 21 Apr 2015 13:35:22: 5000000 INFO @ Tue, 21 Apr 2015 13:35:22: 5000000 INFO @ Tue, 21 Apr 2015 13:35:26: 6000000 INFO @ Tue, 21 Apr 2015 13:35:27: 6000000 INFO @ Tue, 21 Apr 2015 13:35:27: 6000000 INFO @ Tue, 21 Apr 2015 13:35:30: 7000000 INFO @ Tue, 21 Apr 2015 13:35:31: 7000000 INFO @ Tue, 21 Apr 2015 13:35:32: 7000000 INFO @ Tue, 21 Apr 2015 13:35:35: 8000000 INFO @ Tue, 21 Apr 2015 13:35:36: 8000000 INFO @ Tue, 21 Apr 2015 13:35:36: 8000000 INFO @ Tue, 21 Apr 2015 13:35:40: 9000000 INFO @ Tue, 21 Apr 2015 13:35:41: 9000000 INFO @ Tue, 21 Apr 2015 13:35:41: 9000000 INFO @ Tue, 21 Apr 2015 13:35:44: 10000000 INFO @ Tue, 21 Apr 2015 13:35:46: 10000000 INFO @ Tue, 21 Apr 2015 13:35:46: 10000000 INFO @ Tue, 21 Apr 2015 13:35:49: 11000000 INFO @ Tue, 21 Apr 2015 13:35:50: 11000000 INFO @ Tue, 21 Apr 2015 13:35:51: 11000000 INFO @ Tue, 21 Apr 2015 13:35:53: 12000000 INFO @ Tue, 21 Apr 2015 13:35:55: 12000000 INFO @ Tue, 21 Apr 2015 13:35:55: 12000000 INFO @ Tue, 21 Apr 2015 13:35:58: 13000000 INFO @ Tue, 21 Apr 2015 13:36:00: 13000000 INFO @ Tue, 21 Apr 2015 13:36:00: 13000000 INFO @ Tue, 21 Apr 2015 13:36:03: 14000000 INFO @ Tue, 21 Apr 2015 13:36:05: 14000000 INFO @ Tue, 21 Apr 2015 13:36:05: 14000000 INFO @ Tue, 21 Apr 2015 13:36:07: 15000000 INFO @ Tue, 21 Apr 2015 13:36:09: 15000000 INFO @ Tue, 21 Apr 2015 13:36:09: 15000000 INFO @ Tue, 21 Apr 2015 13:36:12: 16000000 INFO @ Tue, 21 Apr 2015 13:36:14: 16000000 INFO @ Tue, 21 Apr 2015 13:36:14: 16000000 INFO @ Tue, 21 Apr 2015 13:36:16: 17000000 INFO @ Tue, 21 Apr 2015 13:36:19: 17000000 INFO @ Tue, 21 Apr 2015 13:36:19: 17000000 INFO @ Tue, 21 Apr 2015 13:36:21: 18000000 INFO @ Tue, 21 Apr 2015 13:36:23: 18000000 INFO @ Tue, 21 Apr 2015 13:36:23: 18000000 INFO @ Tue, 21 Apr 2015 13:36:25: 19000000 INFO @ Tue, 21 Apr 2015 13:36:28: 19000000 INFO @ Tue, 21 Apr 2015 13:36:28: 19000000 INFO @ Tue, 21 Apr 2015 13:36:30: 20000000 INFO @ Tue, 21 Apr 2015 13:36:33: 20000000 INFO @ Tue, 21 Apr 2015 13:36:33: 20000000 INFO @ Tue, 21 Apr 2015 13:36:34: 21000000 INFO @ Tue, 21 Apr 2015 13:36:38: 21000000 INFO @ Tue, 21 Apr 2015 13:36:38: 21000000 INFO @ Tue, 21 Apr 2015 13:36:39: 22000000 INFO @ Tue, 21 Apr 2015 13:36:42: 22000000 INFO @ Tue, 21 Apr 2015 13:36:42: 22000000 INFO @ Tue, 21 Apr 2015 13:36:44: 23000000 INFO @ Tue, 21 Apr 2015 13:36:47: 23000000 INFO @ Tue, 21 Apr 2015 13:36:47: 23000000 INFO @ Tue, 21 Apr 2015 13:36:48: 24000000 INFO @ Tue, 21 Apr 2015 13:36:52: 24000000 INFO @ Tue, 21 Apr 2015 13:36:52: 24000000 INFO @ Tue, 21 Apr 2015 13:36:53: 25000000 INFO @ Tue, 21 Apr 2015 13:36:57: 25000000 INFO @ Tue, 21 Apr 2015 13:36:57: 25000000 INFO @ Tue, 21 Apr 2015 13:36:57: 26000000 INFO @ Tue, 21 Apr 2015 13:37:01: 26000000 INFO @ Tue, 21 Apr 2015 13:37:01: 26000000 INFO @ Tue, 21 Apr 2015 13:37:02: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:37:02: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:37:02: #1 total tags in treatment: 26921468 INFO @ Tue, 21 Apr 2015 13:37:02: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:37:02: #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 13:37:06: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:37:06: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:37:06: #1 total tags in treatment: 26921468 INFO @ Tue, 21 Apr 2015 13:37:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:37:06: #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 13:37:06: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:37:06: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:37:06: #1 total tags in treatment: 26921468 INFO @ Tue, 21 Apr 2015 13:37:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:37:06: #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 13:37:07: #1 tags after filtering in treatment: 26916498 INFO @ Tue, 21 Apr 2015 13:37:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:37:07: #1 finished! INFO @ Tue, 21 Apr 2015 13:37:07: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:37:11: #1 tags after filtering in treatment: 26916498 INFO @ Tue, 21 Apr 2015 13:37:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:37:11: #1 finished! INFO @ Tue, 21 Apr 2015 13:37:11: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:37:11: #1 tags after filtering in treatment: 26916498 INFO @ Tue, 21 Apr 2015 13:37:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:37:11: #1 finished! INFO @ Tue, 21 Apr 2015 13:37:11: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:37:12: #2 number of paired peaks: 117 WARNING @ Tue, 21 Apr 2015 13:37:12: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 21 Apr 2015 13:37:12: start model_add_line... INFO @ Tue, 21 Apr 2015 13:37:15: #2 number of paired peaks: 117 WARNING @ Tue, 21 Apr 2015 13:37:15: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 21 Apr 2015 13:37:15: start model_add_line... INFO @ Tue, 21 Apr 2015 13:37:15: start X-correlation... INFO @ Tue, 21 Apr 2015 13:37:15: end of X-cor INFO @ Tue, 21 Apr 2015 13:37:15: #2 finished! INFO @ Tue, 21 Apr 2015 13:37:15: #2 predicted fragment length is 186 bps INFO @ Tue, 21 Apr 2015 13:37:15: #2 alternative fragment length(s) may be 186 bps INFO @ Tue, 21 Apr 2015 13:37:15: #2.2 Generate R script for model : SRX041381.10_model.r INFO @ Tue, 21 Apr 2015 13:37:15: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:37:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:37:15: #2 number of paired peaks: 117 WARNING @ Tue, 21 Apr 2015 13:37:15: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 21 Apr 2015 13:37:15: start model_add_line... INFO @ Tue, 21 Apr 2015 13:37:18: start X-correlation... INFO @ Tue, 21 Apr 2015 13:37:18: end of X-cor INFO @ Tue, 21 Apr 2015 13:37:18: #2 finished! INFO @ Tue, 21 Apr 2015 13:37:18: #2 predicted fragment length is 186 bps INFO @ Tue, 21 Apr 2015 13:37:18: #2 alternative fragment length(s) may be 186 bps INFO @ Tue, 21 Apr 2015 13:37:18: #2.2 Generate R script for model : SRX041381.05_model.r INFO @ Tue, 21 Apr 2015 13:37:18: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:37:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:37:19: start X-correlation... INFO @ Tue, 21 Apr 2015 13:37:19: end of X-cor INFO @ Tue, 21 Apr 2015 13:37:19: #2 finished! INFO @ Tue, 21 Apr 2015 13:37:19: #2 predicted fragment length is 186 bps INFO @ Tue, 21 Apr 2015 13:37:19: #2 alternative fragment length(s) may be 186 bps INFO @ Tue, 21 Apr 2015 13:37:19: #2.2 Generate R script for model : SRX041381.20_model.r INFO @ Tue, 21 Apr 2015 13:37:19: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:37:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:39:25: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:39:31: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:39:31: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:41:01: #4 Write output xls file... SRX041381.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:41:01: #4 Write peak in narrowPeak format file... SRX041381.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:41:01: #4 Write summits bed file... SRX041381.20_summits.bed INFO @ Tue, 21 Apr 2015 13:41:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1129 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:41:05: #4 Write output xls file... SRX041381.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:41:05: #4 Write peak in narrowPeak format file... SRX041381.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:41:05: #4 Write summits bed file... SRX041381.10_summits.bed INFO @ Tue, 21 Apr 2015 13:41:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2874 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:41:16: #4 Write output xls file... SRX041381.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:41:16: #4 Write peak in narrowPeak format file... SRX041381.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:41:16: #4 Write summits bed file... SRX041381.05_summits.bed INFO @ Tue, 21 Apr 2015 13:41:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6221 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。