Job ID = 2236888 sra ファイルのダウンロード中... Completed: 188291K bytes transferred in 14 seconds (102867K 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 20748 0 20748 0 0 26478 0 --:--:-- --:--:-- --:--:-- 34988 100 35120 0 35120 0 0 44763 0 --:--:-- --:--:-- --:--:-- 59124 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 10785689 spots for /home/okishinya/chipatlas/results/ce10/SRX059270/SRR190710.sra Written 10785689 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: 00:01:06 10785689 reads; of these: 10785689 (100.00%) were unpaired; of these: 7039678 (65.27%) aligned 0 times 3043983 (28.22%) aligned exactly 1 time 702028 (6.51%) aligned >1 times 34.73% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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_rmdupse_core] 801502 / 3746011 = 0.2140 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 11:13:22: # Command line: callpeak -t SRX059270.bam -f BAM -g ce -n SRX059270.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059270.10 # format = BAM # ChIP-seq file = ['SRX059270.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 11:13:22: # Command line: callpeak -t SRX059270.bam -f BAM -g ce -n SRX059270.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059270.05 # format = BAM # ChIP-seq file = ['SRX059270.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 11:13:22: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:13:22: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:13:22: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:13:22: # Command line: callpeak -t SRX059270.bam -f BAM -g ce -n SRX059270.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059270.20 # format = BAM # ChIP-seq file = ['SRX059270.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 11:13:22: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:13:22: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:13:22: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:13:27: 1000000 INFO @ Thu, 30 Apr 2015 11:13:28: 1000000 INFO @ Thu, 30 Apr 2015 11:13:28: 1000000 INFO @ Thu, 30 Apr 2015 11:13:33: 2000000 INFO @ Thu, 30 Apr 2015 11:13:33: 2000000 INFO @ Thu, 30 Apr 2015 11:13:33: 2000000 INFO @ Thu, 30 Apr 2015 11:13:38: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:13:38: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:13:38: #1 total tags in treatment: 2944509 INFO @ Thu, 30 Apr 2015 11:13:38: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:13:38: #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 11:13:38: #1 tags after filtering in treatment: 2944487 INFO @ Thu, 30 Apr 2015 11:13:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:13:38: #1 finished! INFO @ Thu, 30 Apr 2015 11:13:38: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:13:39: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:13:39: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:13:39: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:13:39: #1 total tags in treatment: 2944509 INFO @ Thu, 30 Apr 2015 11:13:39: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:13:39: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:13:39: #1 total tags in treatment: 2944509 INFO @ Thu, 30 Apr 2015 11:13:39: #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 11:13:39: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:13:39: #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 11:13:39: #2 number of paired peaks: 749 WARNING @ Thu, 30 Apr 2015 11:13:39: Fewer paired peaks (749) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 749 pairs to build model! INFO @ Thu, 30 Apr 2015 11:13:39: start model_add_line... INFO @ Thu, 30 Apr 2015 11:13:39: #1 tags after filtering in treatment: 2944487 INFO @ Thu, 30 Apr 2015 11:13:39: #1 tags after filtering in treatment: 2944487 INFO @ Thu, 30 Apr 2015 11:13:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:13:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:13:39: #1 finished! INFO @ Thu, 30 Apr 2015 11:13:39: #1 finished! INFO @ Thu, 30 Apr 2015 11:13:39: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:13:39: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:13:40: #2 number of paired peaks: 749 WARNING @ Thu, 30 Apr 2015 11:13:40: Fewer paired peaks (749) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 749 pairs to build model! INFO @ Thu, 30 Apr 2015 11:13:40: start model_add_line... INFO @ Thu, 30 Apr 2015 11:13:40: #2 number of paired peaks: 749 WARNING @ Thu, 30 Apr 2015 11:13:40: Fewer paired peaks (749) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 749 pairs to build model! INFO @ Thu, 30 Apr 2015 11:13:40: start model_add_line... INFO @ Thu, 30 Apr 2015 11:13:42: start X-correlation... INFO @ Thu, 30 Apr 2015 11:13:42: end of X-cor INFO @ Thu, 30 Apr 2015 11:13:42: #2 finished! INFO @ Thu, 30 Apr 2015 11:13:42: #2 predicted fragment length is 143 bps INFO @ Thu, 30 Apr 2015 11:13:42: #2 alternative fragment length(s) may be 143 bps INFO @ Thu, 30 Apr 2015 11:13:42: #2.2 Generate R script for model : SRX059270.20_model.r INFO @ Thu, 30 Apr 2015 11:13:42: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:13:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:13:43: start X-correlation... INFO @ Thu, 30 Apr 2015 11:13:43: end of X-cor INFO @ Thu, 30 Apr 2015 11:13:43: #2 finished! INFO @ Thu, 30 Apr 2015 11:13:43: #2 predicted fragment length is 143 bps INFO @ Thu, 30 Apr 2015 11:13:43: #2 alternative fragment length(s) may be 143 bps INFO @ Thu, 30 Apr 2015 11:13:43: #2.2 Generate R script for model : SRX059270.05_model.r INFO @ Thu, 30 Apr 2015 11:13:43: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:13:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:13:43: start X-correlation... INFO @ Thu, 30 Apr 2015 11:13:43: end of X-cor INFO @ Thu, 30 Apr 2015 11:13:43: #2 finished! INFO @ Thu, 30 Apr 2015 11:13:43: #2 predicted fragment length is 143 bps INFO @ Thu, 30 Apr 2015 11:13:43: #2 alternative fragment length(s) may be 143 bps INFO @ Thu, 30 Apr 2015 11:13:43: #2.2 Generate R script for model : SRX059270.10_model.r INFO @ Thu, 30 Apr 2015 11:13:43: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:13:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:14:00: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:14:01: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:14:01: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:14:13: #4 Write output xls file... SRX059270.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:14:13: #4 Write peak in narrowPeak format file... SRX059270.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:14:13: #4 Write summits bed file... SRX059270.20_summits.bed INFO @ Thu, 30 Apr 2015 11:14:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (409 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:14:14: #4 Write output xls file... SRX059270.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:14:14: #4 Write peak in narrowPeak format file... SRX059270.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:14:14: #4 Write summits bed file... SRX059270.05_summits.bed INFO @ Thu, 30 Apr 2015 11:14:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1064 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:14:15: #4 Write output xls file... SRX059270.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:14:15: #4 Write peak in narrowPeak format file... SRX059270.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:14:15: #4 Write summits bed file... SRX059270.10_summits.bed INFO @ Thu, 30 Apr 2015 11:14:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (711 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。