Job ID = 9033171 sra ファイルのダウンロード中... Completed: 283567K bytes transferred in 6 seconds (381725K 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 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 22317 0 22317 0 0 2823 0 --:--:-- 0:00:07 --:--:-- 14454 100 67893 0 67893 0 0 7628 0 --:--:-- 0:00:08 --:--:-- 26729 100 93859 0 93859 0 0 10167 0 --:--:-- 0:00:09 --:--:-- 32692 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 8519226 spots for /home/okishinya/chipatlas/results/dm3/SRX914964/SRR1873274.sra Written 8519226 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: 00:02:07 8519226 reads; of these: 8519226 (100.00%) were unpaired; of these: 5184881 (60.86%) aligned 0 times 2826610 (33.18%) aligned exactly 1 time 507735 (5.96%) aligned >1 times 39.14% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2376946 / 3334345 = 0.7129 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 @ Sun, 04 Jun 2017 00:09:07: # Command line: callpeak -t SRX914964.bam -f BAM -g dm -n SRX914964.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX914964.10 # format = BAM # ChIP-seq file = ['SRX914964.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 04 Jun 2017 00:09:07: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:09:07: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:09:07: # Command line: callpeak -t SRX914964.bam -f BAM -g dm -n SRX914964.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX914964.20 # format = BAM # ChIP-seq file = ['SRX914964.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 04 Jun 2017 00:09:07: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:09:07: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:09:07: # Command line: callpeak -t SRX914964.bam -f BAM -g dm -n SRX914964.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX914964.05 # format = BAM # ChIP-seq file = ['SRX914964.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 04 Jun 2017 00:09:07: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:09:07: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:09:13: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:09:13: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:09:13: #1 total tags in treatment: 957399 INFO @ Sun, 04 Jun 2017 00:09:13: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:09:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:09:13: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:09:13: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:09:13: #1 total tags in treatment: 957399 INFO @ Sun, 04 Jun 2017 00:09:13: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:09:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:09:13: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:09:13: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:09:13: #1 total tags in treatment: 957399 INFO @ Sun, 04 Jun 2017 00:09:13: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:09:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:09:13: #1 tags after filtering in treatment: 956979 INFO @ Sun, 04 Jun 2017 00:09:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:09:13: #1 finished! INFO @ Sun, 04 Jun 2017 00:09:13: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:09:13: #1 tags after filtering in treatment: 956979 INFO @ Sun, 04 Jun 2017 00:09:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:09:13: #1 finished! INFO @ Sun, 04 Jun 2017 00:09:13: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:09:13: #1 tags after filtering in treatment: 956979 INFO @ Sun, 04 Jun 2017 00:09:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:09:13: #1 finished! INFO @ Sun, 04 Jun 2017 00:09:13: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:09:14: #2 number of paired peaks: 723 WARNING @ Sun, 04 Jun 2017 00:09:14: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Sun, 04 Jun 2017 00:09:14: start model_add_line... INFO @ Sun, 04 Jun 2017 00:09:14: #2 number of paired peaks: 723 WARNING @ Sun, 04 Jun 2017 00:09:14: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Sun, 04 Jun 2017 00:09:14: start model_add_line... INFO @ Sun, 04 Jun 2017 00:09:14: #2 number of paired peaks: 723 WARNING @ Sun, 04 Jun 2017 00:09:14: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Sun, 04 Jun 2017 00:09:14: start model_add_line... INFO @ Sun, 04 Jun 2017 00:09:14: start X-correlation... INFO @ Sun, 04 Jun 2017 00:09:14: end of X-cor INFO @ Sun, 04 Jun 2017 00:09:14: #2 finished! INFO @ Sun, 04 Jun 2017 00:09:14: #2 predicted fragment length is 120 bps INFO @ Sun, 04 Jun 2017 00:09:14: #2 alternative fragment length(s) may be 54,120,185 bps INFO @ Sun, 04 Jun 2017 00:09:14: #2.2 Generate R script for model : SRX914964.20_model.r INFO @ Sun, 04 Jun 2017 00:09:14: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:09:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:09:14: start X-correlation... INFO @ Sun, 04 Jun 2017 00:09:14: end of X-cor INFO @ Sun, 04 Jun 2017 00:09:14: #2 finished! INFO @ Sun, 04 Jun 2017 00:09:14: #2 predicted fragment length is 120 bps INFO @ Sun, 04 Jun 2017 00:09:14: #2 alternative fragment length(s) may be 54,120,185 bps INFO @ Sun, 04 Jun 2017 00:09:14: #2.2 Generate R script for model : SRX914964.05_model.r INFO @ Sun, 04 Jun 2017 00:09:14: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:09:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:09:14: start X-correlation... INFO @ Sun, 04 Jun 2017 00:09:14: end of X-cor INFO @ Sun, 04 Jun 2017 00:09:14: #2 finished! INFO @ Sun, 04 Jun 2017 00:09:14: #2 predicted fragment length is 120 bps INFO @ Sun, 04 Jun 2017 00:09:14: #2 alternative fragment length(s) may be 54,120,185 bps INFO @ Sun, 04 Jun 2017 00:09:14: #2.2 Generate R script for model : SRX914964.10_model.r INFO @ Sun, 04 Jun 2017 00:09:14: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:09:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:09:21: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:09:21: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:09:21: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:09:25: #4 Write output xls file... SRX914964.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:09:25: #4 Write peak in narrowPeak format file... SRX914964.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:09:25: #4 Write summits bed file... SRX914964.05_summits.bed INFO @ Sun, 04 Jun 2017 00:09:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:09:25: #4 Write output xls file... SRX914964.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:09:25: #4 Write peak in narrowPeak format file... SRX914964.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:09:25: #4 Write summits bed file... SRX914964.20_summits.bed INFO @ Sun, 04 Jun 2017 00:09:25: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (17 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:09:25: #4 Write output xls file... SRX914964.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:09:25: #4 Write peak in narrowPeak format file... SRX914964.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:09:25: #4 Write summits bed file... SRX914964.10_summits.bed INFO @ Sun, 04 Jun 2017 00:09:25: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (47 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。