Job ID = 2236869 sra ファイルのダウンロード中... Completed: 439989K bytes transferred in 9 seconds (387857K 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 --:--:-- --:--:-- --:--:-- 0 101 2540 0 2540 0 0 4811 0 --:--:-- --:--:-- --:--:-- 7537 100 34748 0 34748 0 0 48398 0 --:--:-- --:--:-- --:--:-- 65935 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 25360297 spots for /home/okishinya/chipatlas/results/ce10/SRX059245/SRR190685.sra Written 25360297 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: 00:04:43 25360297 reads; of these: 25360297 (100.00%) were unpaired; of these: 2318142 (9.14%) aligned 0 times 20433943 (80.57%) aligned exactly 1 time 2608212 (10.28%) aligned >1 times 90.86% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 7840504 / 23042155 = 0.3403 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 @ Thu, 30 Apr 2015 11:20:38: # Command line: callpeak -t SRX059245.bam -f BAM -g ce -n SRX059245.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059245.05 # format = BAM # ChIP-seq file = ['SRX059245.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:20:38: # Command line: callpeak -t SRX059245.bam -f BAM -g ce -n SRX059245.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059245.10 # format = BAM # ChIP-seq file = ['SRX059245.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:20:38: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:20:38: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:20:38: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:20:38: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:20:38: # Command line: callpeak -t SRX059245.bam -f BAM -g ce -n SRX059245.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059245.20 # format = BAM # ChIP-seq file = ['SRX059245.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:20:38: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:20:38: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:20:43: 1000000 INFO @ Thu, 30 Apr 2015 11:20:43: 1000000 INFO @ Thu, 30 Apr 2015 11:20:44: 1000000 INFO @ Thu, 30 Apr 2015 11:20:48: 2000000 INFO @ Thu, 30 Apr 2015 11:20:49: 2000000 INFO @ Thu, 30 Apr 2015 11:20:50: 2000000 INFO @ Thu, 30 Apr 2015 11:20:54: 3000000 INFO @ Thu, 30 Apr 2015 11:20:55: 3000000 INFO @ Thu, 30 Apr 2015 11:20:56: 3000000 INFO @ Thu, 30 Apr 2015 11:20:59: 4000000 INFO @ Thu, 30 Apr 2015 11:21:01: 4000000 INFO @ Thu, 30 Apr 2015 11:21:03: 4000000 INFO @ Thu, 30 Apr 2015 11:21:05: 5000000 INFO @ Thu, 30 Apr 2015 11:21:08: 5000000 INFO @ Thu, 30 Apr 2015 11:21:10: 5000000 INFO @ Thu, 30 Apr 2015 11:21:12: 6000000 INFO @ Thu, 30 Apr 2015 11:21:14: 6000000 INFO @ Thu, 30 Apr 2015 11:21:18: 7000000 INFO @ Thu, 30 Apr 2015 11:21:18: 6000000 INFO @ Thu, 30 Apr 2015 11:21:21: 7000000 INFO @ Thu, 30 Apr 2015 11:21:23: 8000000 INFO @ Thu, 30 Apr 2015 11:21:25: 7000000 INFO @ Thu, 30 Apr 2015 11:21:26: 8000000 INFO @ Thu, 30 Apr 2015 11:21:28: 9000000 INFO @ Thu, 30 Apr 2015 11:21:31: 8000000 INFO @ Thu, 30 Apr 2015 11:21:32: 9000000 INFO @ Thu, 30 Apr 2015 11:21:33: 10000000 INFO @ Thu, 30 Apr 2015 11:21:37: 9000000 INFO @ Thu, 30 Apr 2015 11:21:38: 10000000 INFO @ Thu, 30 Apr 2015 11:21:39: 11000000 INFO @ Thu, 30 Apr 2015 11:21:43: 10000000 INFO @ Thu, 30 Apr 2015 11:21:43: 11000000 INFO @ Thu, 30 Apr 2015 11:21:44: 12000000 INFO @ Thu, 30 Apr 2015 11:21:49: 13000000 INFO @ Thu, 30 Apr 2015 11:21:49: 12000000 INFO @ Thu, 30 Apr 2015 11:21:49: 11000000 INFO @ Thu, 30 Apr 2015 11:21:54: 14000000 INFO @ Thu, 30 Apr 2015 11:21:55: 13000000 INFO @ Thu, 30 Apr 2015 11:21:56: 12000000 INFO @ Thu, 30 Apr 2015 11:21:59: 15000000 INFO @ Thu, 30 Apr 2015 11:22:00: 14000000 INFO @ Thu, 30 Apr 2015 11:22:01: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:22:01: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:22:01: #1 total tags in treatment: 15201651 INFO @ Thu, 30 Apr 2015 11:22:01: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:22:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:22:01: 13000000 INFO @ Thu, 30 Apr 2015 11:22:04: #1 tags after filtering in treatment: 15198009 INFO @ Thu, 30 Apr 2015 11:22:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:22:04: #1 finished! INFO @ Thu, 30 Apr 2015 11:22:04: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:22:05: 15000000 INFO @ Thu, 30 Apr 2015 11:22:06: #2 number of paired peaks: 208 WARNING @ Thu, 30 Apr 2015 11:22:06: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Thu, 30 Apr 2015 11:22:06: start model_add_line... INFO @ Thu, 30 Apr 2015 11:22:06: 14000000 INFO @ Thu, 30 Apr 2015 11:22:07: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:22:07: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:22:07: #1 total tags in treatment: 15201651 INFO @ Thu, 30 Apr 2015 11:22:07: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:22:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:22:10: start X-correlation... INFO @ Thu, 30 Apr 2015 11:22:10: end of X-cor INFO @ Thu, 30 Apr 2015 11:22:10: #2 finished! INFO @ Thu, 30 Apr 2015 11:22:10: #2 predicted fragment length is 122 bps INFO @ Thu, 30 Apr 2015 11:22:10: #2 alternative fragment length(s) may be 4,122,565 bps INFO @ Thu, 30 Apr 2015 11:22:10: #2.2 Generate R script for model : SRX059245.05_model.r INFO @ Thu, 30 Apr 2015 11:22:10: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:22:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:22:10: #1 tags after filtering in treatment: 15198009 INFO @ Thu, 30 Apr 2015 11:22:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:22:10: #1 finished! INFO @ Thu, 30 Apr 2015 11:22:10: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:22:11: 15000000 INFO @ Thu, 30 Apr 2015 11:22:13: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:22:13: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:22:13: #1 total tags in treatment: 15201651 INFO @ Thu, 30 Apr 2015 11:22:13: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:22:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:22:13: #2 number of paired peaks: 208 WARNING @ Thu, 30 Apr 2015 11:22:13: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Thu, 30 Apr 2015 11:22:13: start model_add_line... INFO @ Thu, 30 Apr 2015 11:22:15: #1 tags after filtering in treatment: 15198009 INFO @ Thu, 30 Apr 2015 11:22:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:22:15: #1 finished! INFO @ Thu, 30 Apr 2015 11:22:15: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:22:17: start X-correlation... INFO @ Thu, 30 Apr 2015 11:22:17: end of X-cor INFO @ Thu, 30 Apr 2015 11:22:17: #2 finished! INFO @ Thu, 30 Apr 2015 11:22:17: #2 predicted fragment length is 122 bps INFO @ Thu, 30 Apr 2015 11:22:17: #2 alternative fragment length(s) may be 4,122,565 bps INFO @ Thu, 30 Apr 2015 11:22:17: #2.2 Generate R script for model : SRX059245.20_model.r INFO @ Thu, 30 Apr 2015 11:22:17: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:22:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:22:18: #2 number of paired peaks: 208 WARNING @ Thu, 30 Apr 2015 11:22:18: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Thu, 30 Apr 2015 11:22:18: start model_add_line... INFO @ Thu, 30 Apr 2015 11:22:21: start X-correlation... INFO @ Thu, 30 Apr 2015 11:22:21: end of X-cor INFO @ Thu, 30 Apr 2015 11:22:21: #2 finished! INFO @ Thu, 30 Apr 2015 11:22:21: #2 predicted fragment length is 122 bps INFO @ Thu, 30 Apr 2015 11:22:21: #2 alternative fragment length(s) may be 4,122,565 bps INFO @ Thu, 30 Apr 2015 11:22:21: #2.2 Generate R script for model : SRX059245.10_model.r INFO @ Thu, 30 Apr 2015 11:22:21: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:22:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:25: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:36: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:38: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:24:25: #4 Write output xls file... SRX059245.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:24:25: #4 Write peak in narrowPeak format file... SRX059245.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:24:25: #4 Write summits bed file... SRX059245.05_summits.bed INFO @ Thu, 30 Apr 2015 11:24:25: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7564 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:24:34: #4 Write output xls file... SRX059245.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:24:34: #4 Write peak in narrowPeak format file... SRX059245.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:24:34: #4 Write summits bed file... SRX059245.20_summits.bed INFO @ Thu, 30 Apr 2015 11:24:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1121 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:24:37: #4 Write output xls file... SRX059245.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:24:37: #4 Write peak in narrowPeak format file... SRX059245.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:24:37: #4 Write summits bed file... SRX059245.10_summits.bed INFO @ Thu, 30 Apr 2015 11:24:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3576 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。