Job ID = 2236676 sra ファイルのダウンロード中... Completed: 3494720K bytes transferred in 38 seconds (749019K 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 21498 0 21498 0 0 30283 0 --:--:-- --:--:-- --:--:-- 41421 100 37811 0 37811 0 0 53198 0 --:--:-- --:--:-- --:--:-- 72713 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 8379722 spots for /home/okishinya/chipatlas/results/ce10/SRX012297/SRR029216.sra Written 8379722 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: 00:01:24 8379722 reads; of these: 8379722 (100.00%) were unpaired; of these: 2528434 (30.17%) aligned 0 times 5085947 (60.69%) aligned exactly 1 time 765341 (9.13%) aligned >1 times 69.83% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 4462304 / 5851288 = 0.7626 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 10:56:20: # Command line: callpeak -t SRX012297.bam -f BAM -g ce -n SRX012297.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX012297.05 # format = BAM # ChIP-seq file = ['SRX012297.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 10:56:20: # Command line: callpeak -t SRX012297.bam -f BAM -g ce -n SRX012297.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX012297.10 # format = BAM # ChIP-seq file = ['SRX012297.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 10:56:20: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:56:20: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:56:20: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:56:20: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:56:20: # Command line: callpeak -t SRX012297.bam -f BAM -g ce -n SRX012297.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX012297.20 # format = BAM # ChIP-seq file = ['SRX012297.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 10:56:20: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:56:20: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:56:25: 1000000 INFO @ Thu, 30 Apr 2015 10:56:25: 1000000 INFO @ Thu, 30 Apr 2015 10:56:25: 1000000 INFO @ Thu, 30 Apr 2015 10:56:27: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 10:56:27: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 10:56:27: #1 total tags in treatment: 1388984 INFO @ Thu, 30 Apr 2015 10:56:27: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:56:27: #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 10:56:27: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 10:56:27: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 10:56:27: #1 total tags in treatment: 1388984 INFO @ Thu, 30 Apr 2015 10:56:27: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:56:27: #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 10:56:27: #1 tags after filtering in treatment: 1388830 INFO @ Thu, 30 Apr 2015 10:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:56:27: #1 finished! INFO @ Thu, 30 Apr 2015 10:56:27: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:56:28: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 10:56:28: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 10:56:28: #1 total tags in treatment: 1388984 INFO @ Thu, 30 Apr 2015 10:56:28: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:56:28: #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 10:56:28: #1 tags after filtering in treatment: 1388830 INFO @ Thu, 30 Apr 2015 10:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:56:28: #1 finished! INFO @ Thu, 30 Apr 2015 10:56:28: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:56:28: #2 number of paired peaks: 641 WARNING @ Thu, 30 Apr 2015 10:56:28: Fewer paired peaks (641) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 641 pairs to build model! INFO @ Thu, 30 Apr 2015 10:56:28: start model_add_line... INFO @ Thu, 30 Apr 2015 10:56:28: #1 tags after filtering in treatment: 1388830 INFO @ Thu, 30 Apr 2015 10:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:56:28: #1 finished! INFO @ Thu, 30 Apr 2015 10:56:28: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:56:28: #2 number of paired peaks: 641 WARNING @ Thu, 30 Apr 2015 10:56:28: Fewer paired peaks (641) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 641 pairs to build model! INFO @ Thu, 30 Apr 2015 10:56:28: start model_add_line... INFO @ Thu, 30 Apr 2015 10:56:28: #2 number of paired peaks: 641 WARNING @ Thu, 30 Apr 2015 10:56:28: Fewer paired peaks (641) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 641 pairs to build model! INFO @ Thu, 30 Apr 2015 10:56:28: start model_add_line... INFO @ Thu, 30 Apr 2015 10:56:29: start X-correlation... INFO @ Thu, 30 Apr 2015 10:56:29: end of X-cor INFO @ Thu, 30 Apr 2015 10:56:29: #2 finished! INFO @ Thu, 30 Apr 2015 10:56:29: #2 predicted fragment length is 128 bps INFO @ Thu, 30 Apr 2015 10:56:29: #2 alternative fragment length(s) may be 0,40,89,128,527,579 bps INFO @ Thu, 30 Apr 2015 10:56:29: #2.2 Generate R script for model : SRX012297.05_model.r INFO @ Thu, 30 Apr 2015 10:56:29: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:56:29: start X-correlation... INFO @ Thu, 30 Apr 2015 10:56:29: end of X-cor INFO @ Thu, 30 Apr 2015 10:56:29: #2 finished! INFO @ Thu, 30 Apr 2015 10:56:29: #2 predicted fragment length is 128 bps INFO @ Thu, 30 Apr 2015 10:56:29: #2 alternative fragment length(s) may be 0,40,89,128,527,579 bps INFO @ Thu, 30 Apr 2015 10:56:29: #2.2 Generate R script for model : SRX012297.20_model.r INFO @ Thu, 30 Apr 2015 10:56:29: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:56:29: start X-correlation... INFO @ Thu, 30 Apr 2015 10:56:29: end of X-cor INFO @ Thu, 30 Apr 2015 10:56:29: #2 finished! INFO @ Thu, 30 Apr 2015 10:56:29: #2 predicted fragment length is 128 bps INFO @ Thu, 30 Apr 2015 10:56:29: #2 alternative fragment length(s) may be 0,40,89,128,527,579 bps INFO @ Thu, 30 Apr 2015 10:56:29: #2.2 Generate R script for model : SRX012297.10_model.r INFO @ Thu, 30 Apr 2015 10:56:29: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:56:37: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:56:38: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:56:38: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:56:43: #4 Write output xls file... SRX012297.05_peaks.xls INFO @ Thu, 30 Apr 2015 10:56:43: #4 Write peak in narrowPeak format file... SRX012297.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:56:43: #4 Write summits bed file... SRX012297.05_summits.bed INFO @ Thu, 30 Apr 2015 10:56:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (321 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 10:56:43: #4 Write output xls file... SRX012297.10_peaks.xls INFO @ Thu, 30 Apr 2015 10:56:43: #4 Write peak in narrowPeak format file... SRX012297.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:56:43: #4 Write summits bed file... SRX012297.10_summits.bed INFO @ Thu, 30 Apr 2015 10:56:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (106 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 10:56:44: #4 Write output xls file... SRX012297.20_peaks.xls INFO @ Thu, 30 Apr 2015 10:56:44: #4 Write peak in narrowPeak format file... SRX012297.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:56:44: #4 Write summits bed file... SRX012297.20_summits.bed INFO @ Thu, 30 Apr 2015 10:56:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (32 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。