Job ID = 2236868 sra ファイルのダウンロード中... Completed: 283791K bytes transferred in 7 seconds (294224K 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 34733 0 34733 0 0 48572 0 --:--:-- --:--:-- --:--:-- 66411 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 16597845 spots for /home/okishinya/chipatlas/results/ce10/SRX059244/SRR190684.sra Written 16597845 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: 00:03:20 16597845 reads; of these: 16597845 (100.00%) were unpaired; of these: 324462 (1.95%) aligned 0 times 13613058 (82.02%) aligned exactly 1 time 2660325 (16.03%) aligned >1 times 98.05% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 1938892 / 16273383 = 0.1191 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 11:17:52: # Command line: callpeak -t SRX059244.bam -f BAM -g ce -n SRX059244.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059244.20 # format = BAM # ChIP-seq file = ['SRX059244.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 11:17:52: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:17:52: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:17:52: # Command line: callpeak -t SRX059244.bam -f BAM -g ce -n SRX059244.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059244.05 # format = BAM # ChIP-seq file = ['SRX059244.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 11:17:52: # Command line: callpeak -t SRX059244.bam -f BAM -g ce -n SRX059244.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059244.10 # format = BAM # ChIP-seq file = ['SRX059244.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 11:17:52: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:17:52: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:17:52: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:17:52: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:17:58: 1000000 INFO @ Thu, 30 Apr 2015 11:17:58: 1000000 INFO @ Thu, 30 Apr 2015 11:17:58: 1000000 INFO @ Thu, 30 Apr 2015 11:18:03: 2000000 INFO @ Thu, 30 Apr 2015 11:18:03: 2000000 INFO @ Thu, 30 Apr 2015 11:18:03: 2000000 INFO @ Thu, 30 Apr 2015 11:18:08: 3000000 INFO @ Thu, 30 Apr 2015 11:18:08: 3000000 INFO @ Thu, 30 Apr 2015 11:18:09: 3000000 INFO @ Thu, 30 Apr 2015 11:18:14: 4000000 INFO @ Thu, 30 Apr 2015 11:18:14: 4000000 INFO @ Thu, 30 Apr 2015 11:18:15: 4000000 INFO @ Thu, 30 Apr 2015 11:18:19: 5000000 INFO @ Thu, 30 Apr 2015 11:18:19: 5000000 INFO @ Thu, 30 Apr 2015 11:18:20: 5000000 INFO @ Thu, 30 Apr 2015 11:18:24: 6000000 INFO @ Thu, 30 Apr 2015 11:18:24: 6000000 INFO @ Thu, 30 Apr 2015 11:18:26: 6000000 INFO @ Thu, 30 Apr 2015 11:18:29: 7000000 INFO @ Thu, 30 Apr 2015 11:18:29: 7000000 INFO @ Thu, 30 Apr 2015 11:18:32: 7000000 INFO @ Thu, 30 Apr 2015 11:18:35: 8000000 INFO @ Thu, 30 Apr 2015 11:18:36: 8000000 INFO @ Thu, 30 Apr 2015 11:18:38: 8000000 INFO @ Thu, 30 Apr 2015 11:18:41: 9000000 INFO @ Thu, 30 Apr 2015 11:18:42: 9000000 INFO @ Thu, 30 Apr 2015 11:18:44: 9000000 INFO @ Thu, 30 Apr 2015 11:18:46: 10000000 INFO @ Thu, 30 Apr 2015 11:18:47: 10000000 INFO @ Thu, 30 Apr 2015 11:18:50: 10000000 INFO @ Thu, 30 Apr 2015 11:18:51: 11000000 INFO @ Thu, 30 Apr 2015 11:18:52: 11000000 INFO @ Thu, 30 Apr 2015 11:18:56: 11000000 INFO @ Thu, 30 Apr 2015 11:18:56: 12000000 INFO @ Thu, 30 Apr 2015 11:18:58: 12000000 INFO @ Thu, 30 Apr 2015 11:19:01: 12000000 INFO @ Thu, 30 Apr 2015 11:19:02: 13000000 INFO @ Thu, 30 Apr 2015 11:19:03: 13000000 INFO @ Thu, 30 Apr 2015 11:19:07: 13000000 INFO @ Thu, 30 Apr 2015 11:19:07: 14000000 INFO @ Thu, 30 Apr 2015 11:19:08: 14000000 INFO @ Thu, 30 Apr 2015 11:19:09: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:19:09: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:19:09: #1 total tags in treatment: 14334491 INFO @ Thu, 30 Apr 2015 11:19:09: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:19:09: #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 11:19:10: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:19:10: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:19:10: #1 total tags in treatment: 14334491 INFO @ Thu, 30 Apr 2015 11:19:10: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:19:10: #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 11:19:11: #1 tags after filtering in treatment: 14333157 INFO @ Thu, 30 Apr 2015 11:19:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:19:11: #1 finished! INFO @ Thu, 30 Apr 2015 11:19:11: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:19:12: 14000000 INFO @ Thu, 30 Apr 2015 11:19:12: #1 tags after filtering in treatment: 14333157 INFO @ Thu, 30 Apr 2015 11:19:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:19:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:19:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:19:14: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:19:14: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:19:14: #1 total tags in treatment: 14334491 INFO @ Thu, 30 Apr 2015 11:19:14: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:19:14: #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 11:19:14: #2 number of paired peaks: 596 WARNING @ Thu, 30 Apr 2015 11:19:14: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Thu, 30 Apr 2015 11:19:14: start model_add_line... INFO @ Thu, 30 Apr 2015 11:19:15: #2 number of paired peaks: 596 WARNING @ Thu, 30 Apr 2015 11:19:15: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Thu, 30 Apr 2015 11:19:15: start model_add_line... INFO @ Thu, 30 Apr 2015 11:19:17: #1 tags after filtering in treatment: 14333157 INFO @ Thu, 30 Apr 2015 11:19:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:19:17: #1 finished! INFO @ Thu, 30 Apr 2015 11:19:17: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:19:19: #2 number of paired peaks: 596 WARNING @ Thu, 30 Apr 2015 11:19:19: Fewer paired peaks (596) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 596 pairs to build model! INFO @ Thu, 30 Apr 2015 11:19:19: start model_add_line... INFO @ Thu, 30 Apr 2015 11:19:22: start X-correlation... INFO @ Thu, 30 Apr 2015 11:19:22: end of X-cor INFO @ Thu, 30 Apr 2015 11:19:22: #2 finished! INFO @ Thu, 30 Apr 2015 11:19:22: #2 predicted fragment length is 112 bps INFO @ Thu, 30 Apr 2015 11:19:22: #2 alternative fragment length(s) may be 112 bps INFO @ Thu, 30 Apr 2015 11:19:22: #2.2 Generate R script for model : SRX059244.05_model.r INFO @ Thu, 30 Apr 2015 11:19:22: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:19:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:19:23: start X-correlation... INFO @ Thu, 30 Apr 2015 11:19:23: end of X-cor INFO @ Thu, 30 Apr 2015 11:19:23: #2 finished! INFO @ Thu, 30 Apr 2015 11:19:23: #2 predicted fragment length is 112 bps INFO @ Thu, 30 Apr 2015 11:19:23: #2 alternative fragment length(s) may be 112 bps INFO @ Thu, 30 Apr 2015 11:19:23: #2.2 Generate R script for model : SRX059244.20_model.r INFO @ Thu, 30 Apr 2015 11:19:23: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:19:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:19:27: start X-correlation... INFO @ Thu, 30 Apr 2015 11:19:27: end of X-cor INFO @ Thu, 30 Apr 2015 11:19:27: #2 finished! INFO @ Thu, 30 Apr 2015 11:19:27: #2 predicted fragment length is 112 bps INFO @ Thu, 30 Apr 2015 11:19:27: #2 alternative fragment length(s) may be 112 bps INFO @ Thu, 30 Apr 2015 11:19:27: #2.2 Generate R script for model : SRX059244.10_model.r INFO @ Thu, 30 Apr 2015 11:19:27: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:19:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:20:34: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:20:37: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:20:40: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:21:29: #4 Write output xls file... SRX059244.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:21:29: #4 Write peak in narrowPeak format file... SRX059244.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:21:29: #4 Write summits bed file... SRX059244.20_summits.bed INFO @ Thu, 30 Apr 2015 11:21:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1678 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:21:34: #4 Write output xls file... SRX059244.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:21:34: #4 Write peak in narrowPeak format file... SRX059244.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:21:34: #4 Write summits bed file... SRX059244.05_summits.bed INFO @ Thu, 30 Apr 2015 11:21:34: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9199 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:21:36: #4 Write output xls file... SRX059244.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:21:36: #4 Write peak in narrowPeak format file... SRX059244.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:21:36: #4 Write summits bed file... SRX059244.10_summits.bed INFO @ Thu, 30 Apr 2015 11:21:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4344 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。