Job ID = 2162049 sra ファイルのダウンロード中... Completed: 3545068K bytes transferred in 30 seconds (958091K bits/sec), in 7 files, 8 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 34838 0 34838 0 0 49791 0 --:--:-- --:--:-- --:--:-- 68578 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 22788769 spots for /home/okishinya/chipatlas/results/dm3/SRX046654/SRR121534.sra Written 22788769 spots total Written 23391502 spots for /home/okishinya/chipatlas/results/dm3/SRX046654/SRR121533.sra Written 23391502 spots total Written 23877320 spots for /home/okishinya/chipatlas/results/dm3/SRX046654/SRR121535.sra Written 23877320 spots total Written 27506417 spots for /home/okishinya/chipatlas/results/dm3/SRX046654/SRR121536.sra Written 27506417 spots total Written 27762915 spots for /home/okishinya/chipatlas/results/dm3/SRX046654/SRR121537.sra Written 27762915 spots total Written 27571437 spots for /home/okishinya/chipatlas/results/dm3/SRX046654/SRR121539.sra Written 27571437 spots total Written 27590931 spots for /home/okishinya/chipatlas/results/dm3/SRX046654/SRR121538.sra Written 27590931 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: 00:39:08 180489291 reads; of these: 180489291 (100.00%) were unpaired; of these: 32955194 (18.26%) aligned 0 times 113963613 (63.14%) aligned exactly 1 time 33570484 (18.60%) aligned >1 times 81.74% overall alignment rate Time searching: 00:39:08 Overall time: 00:39:08 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 40 files... [bam_rmdupse_core] 101904094 / 147534097 = 0.6907 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 14:29:06: # Command line: callpeak -t SRX046654.bam -f BAM -g dm -n SRX046654.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX046654.05 # format = BAM # ChIP-seq file = ['SRX046654.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 14:29:06: # Command line: callpeak -t SRX046654.bam -f BAM -g dm -n SRX046654.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX046654.10 # format = BAM # ChIP-seq file = ['SRX046654.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 14:29:06: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:29:06: # Command line: callpeak -t SRX046654.bam -f BAM -g dm -n SRX046654.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX046654.20 # format = BAM # ChIP-seq file = ['SRX046654.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 14:29:06: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:29:06: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:29:06: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:29:06: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:29:06: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:29:12: 1000000 INFO @ Tue, 21 Apr 2015 14:29:12: 1000000 INFO @ Tue, 21 Apr 2015 14:29:12: 1000000 INFO @ Tue, 21 Apr 2015 14:29:17: 2000000 INFO @ Tue, 21 Apr 2015 14:29:17: 2000000 INFO @ Tue, 21 Apr 2015 14:29:17: 2000000 INFO @ Tue, 21 Apr 2015 14:29:22: 3000000 INFO @ Tue, 21 Apr 2015 14:29:22: 3000000 INFO @ Tue, 21 Apr 2015 14:29:22: 3000000 INFO @ Tue, 21 Apr 2015 14:29:27: 4000000 INFO @ Tue, 21 Apr 2015 14:29:27: 4000000 INFO @ Tue, 21 Apr 2015 14:29:27: 4000000 INFO @ Tue, 21 Apr 2015 14:29:32: 5000000 INFO @ Tue, 21 Apr 2015 14:29:32: 5000000 INFO @ Tue, 21 Apr 2015 14:29:32: 5000000 INFO @ Tue, 21 Apr 2015 14:29:37: 6000000 INFO @ Tue, 21 Apr 2015 14:29:37: 6000000 INFO @ Tue, 21 Apr 2015 14:29:37: 6000000 INFO @ Tue, 21 Apr 2015 14:29:42: 7000000 INFO @ Tue, 21 Apr 2015 14:29:42: 7000000 INFO @ Tue, 21 Apr 2015 14:29:42: 7000000 INFO @ Tue, 21 Apr 2015 14:29:47: 8000000 INFO @ Tue, 21 Apr 2015 14:29:48: 8000000 INFO @ Tue, 21 Apr 2015 14:29:48: 8000000 INFO @ Tue, 21 Apr 2015 14:29:52: 9000000 INFO @ Tue, 21 Apr 2015 14:29:53: 9000000 INFO @ Tue, 21 Apr 2015 14:29:53: 9000000 INFO @ Tue, 21 Apr 2015 14:29:58: 10000000 INFO @ Tue, 21 Apr 2015 14:29:58: 10000000 INFO @ Tue, 21 Apr 2015 14:29:58: 10000000 INFO @ Tue, 21 Apr 2015 14:30:03: 11000000 INFO @ Tue, 21 Apr 2015 14:30:03: 11000000 INFO @ Tue, 21 Apr 2015 14:30:03: 11000000 INFO @ Tue, 21 Apr 2015 14:30:08: 12000000 INFO @ Tue, 21 Apr 2015 14:30:08: 12000000 INFO @ Tue, 21 Apr 2015 14:30:08: 12000000 INFO @ Tue, 21 Apr 2015 14:30:13: 13000000 INFO @ Tue, 21 Apr 2015 14:30:13: 13000000 INFO @ Tue, 21 Apr 2015 14:30:13: 13000000 INFO @ Tue, 21 Apr 2015 14:30:18: 14000000 INFO @ Tue, 21 Apr 2015 14:30:18: 14000000 INFO @ Tue, 21 Apr 2015 14:30:18: 14000000 INFO @ Tue, 21 Apr 2015 14:30:23: 15000000 INFO @ Tue, 21 Apr 2015 14:30:23: 15000000 INFO @ Tue, 21 Apr 2015 14:30:23: 15000000 INFO @ Tue, 21 Apr 2015 14:30:28: 16000000 INFO @ Tue, 21 Apr 2015 14:30:28: 16000000 INFO @ Tue, 21 Apr 2015 14:30:28: 16000000 INFO @ Tue, 21 Apr 2015 14:30:33: 17000000 INFO @ Tue, 21 Apr 2015 14:30:33: 17000000 INFO @ Tue, 21 Apr 2015 14:30:33: 17000000 INFO @ Tue, 21 Apr 2015 14:30:38: 18000000 INFO @ Tue, 21 Apr 2015 14:30:38: 18000000 INFO @ Tue, 21 Apr 2015 14:30:38: 18000000 INFO @ Tue, 21 Apr 2015 14:30:43: 19000000 INFO @ Tue, 21 Apr 2015 14:30:43: 19000000 INFO @ Tue, 21 Apr 2015 14:30:43: 19000000 INFO @ Tue, 21 Apr 2015 14:30:48: 20000000 INFO @ Tue, 21 Apr 2015 14:30:48: 20000000 INFO @ Tue, 21 Apr 2015 14:30:48: 20000000 INFO @ Tue, 21 Apr 2015 14:30:53: 21000000 INFO @ Tue, 21 Apr 2015 14:30:53: 21000000 INFO @ Tue, 21 Apr 2015 14:30:53: 21000000 INFO @ Tue, 21 Apr 2015 14:30:58: 22000000 INFO @ Tue, 21 Apr 2015 14:30:58: 22000000 INFO @ Tue, 21 Apr 2015 14:30:58: 22000000 INFO @ Tue, 21 Apr 2015 14:31:03: 23000000 INFO @ Tue, 21 Apr 2015 14:31:03: 23000000 INFO @ Tue, 21 Apr 2015 14:31:03: 23000000 INFO @ Tue, 21 Apr 2015 14:31:08: 24000000 INFO @ Tue, 21 Apr 2015 14:31:08: 24000000 INFO @ Tue, 21 Apr 2015 14:31:08: 24000000 INFO @ Tue, 21 Apr 2015 14:31:13: 25000000 INFO @ Tue, 21 Apr 2015 14:31:13: 25000000 INFO @ Tue, 21 Apr 2015 14:31:14: 25000000 INFO @ Tue, 21 Apr 2015 14:31:18: 26000000 INFO @ Tue, 21 Apr 2015 14:31:18: 26000000 INFO @ Tue, 21 Apr 2015 14:31:19: 26000000 INFO @ Tue, 21 Apr 2015 14:31:23: 27000000 INFO @ Tue, 21 Apr 2015 14:31:23: 27000000 INFO @ Tue, 21 Apr 2015 14:31:24: 27000000 INFO @ Tue, 21 Apr 2015 14:31:28: 28000000 INFO @ Tue, 21 Apr 2015 14:31:28: 28000000 INFO @ Tue, 21 Apr 2015 14:31:29: 28000000 INFO @ Tue, 21 Apr 2015 14:31:33: 29000000 INFO @ Tue, 21 Apr 2015 14:31:33: 29000000 INFO @ Tue, 21 Apr 2015 14:31:34: 29000000 INFO @ Tue, 21 Apr 2015 14:31:38: 30000000 INFO @ Tue, 21 Apr 2015 14:31:38: 30000000 INFO @ Tue, 21 Apr 2015 14:31:39: 30000000 INFO @ Tue, 21 Apr 2015 14:31:43: 31000000 INFO @ Tue, 21 Apr 2015 14:31:43: 31000000 INFO @ Tue, 21 Apr 2015 14:31:44: 31000000 INFO @ Tue, 21 Apr 2015 14:31:48: 32000000 INFO @ Tue, 21 Apr 2015 14:31:48: 32000000 INFO @ Tue, 21 Apr 2015 14:31:49: 32000000 INFO @ Tue, 21 Apr 2015 14:31:53: 33000000 INFO @ Tue, 21 Apr 2015 14:31:53: 33000000 INFO @ Tue, 21 Apr 2015 14:31:54: 33000000 INFO @ Tue, 21 Apr 2015 14:31:58: 34000000 INFO @ Tue, 21 Apr 2015 14:31:58: 34000000 INFO @ Tue, 21 Apr 2015 14:31:59: 34000000 INFO @ Tue, 21 Apr 2015 14:32:03: 35000000 INFO @ Tue, 21 Apr 2015 14:32:03: 35000000 INFO @ Tue, 21 Apr 2015 14:32:04: 35000000 INFO @ Tue, 21 Apr 2015 14:32:08: 36000000 INFO @ Tue, 21 Apr 2015 14:32:09: 36000000 INFO @ Tue, 21 Apr 2015 14:32:09: 36000000 INFO @ Tue, 21 Apr 2015 14:32:14: 37000000 INFO @ Tue, 21 Apr 2015 14:32:14: 37000000 INFO @ Tue, 21 Apr 2015 14:32:14: 37000000 INFO @ Tue, 21 Apr 2015 14:32:19: 38000000 INFO @ Tue, 21 Apr 2015 14:32:19: 38000000 INFO @ Tue, 21 Apr 2015 14:32:19: 38000000 INFO @ Tue, 21 Apr 2015 14:32:24: 39000000 INFO @ Tue, 21 Apr 2015 14:32:24: 39000000 INFO @ Tue, 21 Apr 2015 14:32:25: 39000000 INFO @ Tue, 21 Apr 2015 14:32:29: 40000000 INFO @ Tue, 21 Apr 2015 14:32:29: 40000000 INFO @ Tue, 21 Apr 2015 14:32:30: 40000000 INFO @ Tue, 21 Apr 2015 14:32:34: 41000000 INFO @ Tue, 21 Apr 2015 14:32:34: 41000000 INFO @ Tue, 21 Apr 2015 14:32:35: 41000000 INFO @ Tue, 21 Apr 2015 14:32:39: 42000000 INFO @ Tue, 21 Apr 2015 14:32:40: 42000000 INFO @ Tue, 21 Apr 2015 14:32:40: 42000000 INFO @ Tue, 21 Apr 2015 14:32:45: 43000000 INFO @ Tue, 21 Apr 2015 14:32:45: 43000000 INFO @ Tue, 21 Apr 2015 14:32:45: 43000000 INFO @ Tue, 21 Apr 2015 14:32:50: 44000000 INFO @ Tue, 21 Apr 2015 14:32:50: 44000000 INFO @ Tue, 21 Apr 2015 14:32:51: 44000000 INFO @ Tue, 21 Apr 2015 14:32:56: 45000000 INFO @ Tue, 21 Apr 2015 14:32:56: 45000000 INFO @ Tue, 21 Apr 2015 14:32:58: 45000000 INFO @ Tue, 21 Apr 2015 14:33:00: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:33:00: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:33:00: #1 total tags in treatment: 45630003 INFO @ Tue, 21 Apr 2015 14:33:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:33:00: #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 14:33:01: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:33:01: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:33:01: #1 total tags in treatment: 45630003 INFO @ Tue, 21 Apr 2015 14:33:01: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:33:01: #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 14:33:02: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:33:02: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:33:02: #1 total tags in treatment: 45630003 INFO @ Tue, 21 Apr 2015 14:33:02: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:33:02: #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 14:33:09: #1 tags after filtering in treatment: 45609262 INFO @ Tue, 21 Apr 2015 14:33:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:33:09: #1 finished! INFO @ Tue, 21 Apr 2015 14:33:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:33:09: #1 tags after filtering in treatment: 45609262 INFO @ Tue, 21 Apr 2015 14:33:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:33:09: #1 finished! INFO @ Tue, 21 Apr 2015 14:33:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:33:10: #1 tags after filtering in treatment: 45609262 INFO @ Tue, 21 Apr 2015 14:33:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:33:10: #1 finished! INFO @ Tue, 21 Apr 2015 14:33:10: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:33:17: #2 number of paired peaks: 314 WARNING @ Tue, 21 Apr 2015 14:33:17: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Tue, 21 Apr 2015 14:33:17: start model_add_line... INFO @ Tue, 21 Apr 2015 14:33:17: #2 number of paired peaks: 314 WARNING @ Tue, 21 Apr 2015 14:33:17: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Tue, 21 Apr 2015 14:33:17: start model_add_line... INFO @ Tue, 21 Apr 2015 14:33:18: #2 number of paired peaks: 314 WARNING @ Tue, 21 Apr 2015 14:33:18: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Tue, 21 Apr 2015 14:33:18: start model_add_line... INFO @ Tue, 21 Apr 2015 14:33:28: start X-correlation... INFO @ Tue, 21 Apr 2015 14:33:28: end of X-cor INFO @ Tue, 21 Apr 2015 14:33:28: #2 finished! INFO @ Tue, 21 Apr 2015 14:33:28: #2 predicted fragment length is 98 bps INFO @ Tue, 21 Apr 2015 14:33:28: #2 alternative fragment length(s) may be 2,57,98 bps INFO @ Tue, 21 Apr 2015 14:33:28: #2.2 Generate R script for model : SRX046654.20_model.r INFO @ Tue, 21 Apr 2015 14:33:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:33:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:33:29: start X-correlation... INFO @ Tue, 21 Apr 2015 14:33:29: end of X-cor INFO @ Tue, 21 Apr 2015 14:33:29: #2 finished! INFO @ Tue, 21 Apr 2015 14:33:29: #2 predicted fragment length is 98 bps INFO @ Tue, 21 Apr 2015 14:33:29: #2 alternative fragment length(s) may be 2,57,98 bps INFO @ Tue, 21 Apr 2015 14:33:29: #2.2 Generate R script for model : SRX046654.10_model.r INFO @ Tue, 21 Apr 2015 14:33:29: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:33:30: start X-correlation... INFO @ Tue, 21 Apr 2015 14:33:30: end of X-cor INFO @ Tue, 21 Apr 2015 14:33:30: #2 finished! INFO @ Tue, 21 Apr 2015 14:33:30: #2 predicted fragment length is 98 bps INFO @ Tue, 21 Apr 2015 14:33:30: #2 alternative fragment length(s) may be 2,57,98 bps INFO @ Tue, 21 Apr 2015 14:33:30: #2.2 Generate R script for model : SRX046654.05_model.r INFO @ Tue, 21 Apr 2015 14:33:30: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:36:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:36:40: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:36:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:38:31: #4 Write output xls file... SRX046654.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:38:31: #4 Write peak in narrowPeak format file... SRX046654.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:38:31: #4 Write summits bed file... SRX046654.20_summits.bed INFO @ Tue, 21 Apr 2015 14:38:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7197 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:39:07: #4 Write output xls file... SRX046654.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:39:07: #4 Write peak in narrowPeak format file... SRX046654.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:39:07: #4 Write summits bed file... SRX046654.10_summits.bed INFO @ Tue, 21 Apr 2015 14:39:07: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13590 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:39:25: #4 Write output xls file... SRX046654.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:39:25: #4 Write peak in narrowPeak format file... SRX046654.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:39:25: #4 Write summits bed file... SRX046654.05_summits.bed INFO @ Tue, 21 Apr 2015 14:39:26: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (18634 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。