Job ID = 2236854 sra ファイルのダウンロード中... Completed: 104596K bytes transferred in 5 seconds (163702K 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 14909 0 14909 0 0 19516 0 --:--:-- --:--:-- --:--:-- 26019 100 34618 0 34618 0 0 45258 0 --:--:-- --:--:-- --:--:-- 60310 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 4429111 spots for /home/okishinya/chipatlas/results/ce10/SRX059230/SRR190670.sra Written 4429111 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: 00:00:49 4429111 reads; of these: 4429111 (100.00%) were unpaired; of these: 1143795 (25.82%) aligned 0 times 2626152 (59.29%) aligned exactly 1 time 659164 (14.88%) aligned >1 times 74.18% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 336588 / 3285316 = 0.1025 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 11:11:40: # Command line: callpeak -t SRX059230.bam -f BAM -g ce -n SRX059230.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059230.05 # format = BAM # ChIP-seq file = ['SRX059230.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 11:11:40: # Command line: callpeak -t SRX059230.bam -f BAM -g ce -n SRX059230.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059230.10 # format = BAM # ChIP-seq file = ['SRX059230.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 11:11:40: # Command line: callpeak -t SRX059230.bam -f BAM -g ce -n SRX059230.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059230.20 # format = BAM # ChIP-seq file = ['SRX059230.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 11:11:40: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:11:40: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:11:40: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:11:40: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:11:40: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:11:40: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:11:47: 1000000 INFO @ Thu, 30 Apr 2015 11:11:47: 1000000 INFO @ Thu, 30 Apr 2015 11:11:47: 1000000 INFO @ Thu, 30 Apr 2015 11:11:54: 2000000 INFO @ Thu, 30 Apr 2015 11:11:54: 2000000 INFO @ Thu, 30 Apr 2015 11:11:54: 2000000 INFO @ Thu, 30 Apr 2015 11:12:00: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:12:00: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:12:00: #1 total tags in treatment: 2948728 INFO @ Thu, 30 Apr 2015 11:12:00: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:12:00: #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 11:12:00: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:12:00: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:12:00: #1 total tags in treatment: 2948728 INFO @ Thu, 30 Apr 2015 11:12:00: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:12:00: #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 11:12:00: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:12:00: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:12:00: #1 total tags in treatment: 2948728 INFO @ Thu, 30 Apr 2015 11:12:00: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:12:00: #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 11:12:01: #1 tags after filtering in treatment: 2948460 INFO @ Thu, 30 Apr 2015 11:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:12:01: #1 finished! INFO @ Thu, 30 Apr 2015 11:12:01: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:12:01: #1 tags after filtering in treatment: 2948460 INFO @ Thu, 30 Apr 2015 11:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:12:01: #1 finished! INFO @ Thu, 30 Apr 2015 11:12:01: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:12:01: #1 tags after filtering in treatment: 2948460 INFO @ Thu, 30 Apr 2015 11:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:12:01: #1 finished! INFO @ Thu, 30 Apr 2015 11:12:01: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:12:01: #2 number of paired peaks: 852 WARNING @ Thu, 30 Apr 2015 11:12:01: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Thu, 30 Apr 2015 11:12:01: start model_add_line... INFO @ Thu, 30 Apr 2015 11:12:01: #2 number of paired peaks: 852 WARNING @ Thu, 30 Apr 2015 11:12:01: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Thu, 30 Apr 2015 11:12:01: start model_add_line... INFO @ Thu, 30 Apr 2015 11:12:01: #2 number of paired peaks: 852 WARNING @ Thu, 30 Apr 2015 11:12:01: Fewer paired peaks (852) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 852 pairs to build model! INFO @ Thu, 30 Apr 2015 11:12:01: start model_add_line... INFO @ Thu, 30 Apr 2015 11:12:04: start X-correlation... INFO @ Thu, 30 Apr 2015 11:12:04: end of X-cor INFO @ Thu, 30 Apr 2015 11:12:04: #2 finished! INFO @ Thu, 30 Apr 2015 11:12:04: #2 predicted fragment length is 95 bps INFO @ Thu, 30 Apr 2015 11:12:04: #2 alternative fragment length(s) may be 95 bps INFO @ Thu, 30 Apr 2015 11:12:04: #2.2 Generate R script for model : SRX059230.05_model.r INFO @ Thu, 30 Apr 2015 11:12:04: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:12:04: start X-correlation... INFO @ Thu, 30 Apr 2015 11:12:04: start X-correlation... INFO @ Thu, 30 Apr 2015 11:12:04: end of X-cor INFO @ Thu, 30 Apr 2015 11:12:04: #2 finished! INFO @ Thu, 30 Apr 2015 11:12:04: #2 predicted fragment length is 95 bps INFO @ Thu, 30 Apr 2015 11:12:04: #2 alternative fragment length(s) may be 95 bps INFO @ Thu, 30 Apr 2015 11:12:04: #2.2 Generate R script for model : SRX059230.10_model.r INFO @ Thu, 30 Apr 2015 11:12:04: end of X-cor INFO @ Thu, 30 Apr 2015 11:12:04: #2 finished! INFO @ Thu, 30 Apr 2015 11:12:04: #2 predicted fragment length is 95 bps INFO @ Thu, 30 Apr 2015 11:12:04: #2 alternative fragment length(s) may be 95 bps INFO @ Thu, 30 Apr 2015 11:12:04: #2.2 Generate R script for model : SRX059230.20_model.r INFO @ Thu, 30 Apr 2015 11:12:04: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:12:04: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:12:21: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:12:22: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:12:22: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:12:34: #4 Write output xls file... SRX059230.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:12:34: #4 Write peak in narrowPeak format file... SRX059230.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:12:34: #4 Write summits bed file... SRX059230.10_summits.bed INFO @ Thu, 30 Apr 2015 11:12:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1127 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:12:35: #4 Write output xls file... SRX059230.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:12:35: #4 Write peak in narrowPeak format file... SRX059230.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:12:35: #4 Write summits bed file... SRX059230.05_summits.bed INFO @ Thu, 30 Apr 2015 11:12:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2019 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:12:35: #4 Write output xls file... SRX059230.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:12:35: #4 Write peak in narrowPeak format file... SRX059230.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:12:35: #4 Write summits bed file... SRX059230.20_summits.bed INFO @ Thu, 30 Apr 2015 11:12:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (712 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。