Job ID = 2161260 sra ファイルのダウンロード中... Completed: 146807K bytes transferred in 5 seconds (239001K 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 34440 0 34440 0 0 43698 0 --:--:-- --:--:-- --:--:-- 57688 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 6705808 spots for /home/okishinya/chipatlas/results/dm3/SRX013104/SRR030370.sra Written 6705808 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: 00:01:23 6705808 reads; of these: 6705808 (100.00%) were unpaired; of these: 746190 (11.13%) aligned 0 times 5355150 (79.86%) aligned exactly 1 time 604468 (9.01%) aligned >1 times 88.87% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 1157476 / 5959618 = 0.1942 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 @ Tue, 21 Apr 2015 12:11:55: # Command line: callpeak -t SRX013104.bam -f BAM -g dm -n SRX013104.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013104.05 # format = BAM # ChIP-seq file = ['SRX013104.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 @ Tue, 21 Apr 2015 12:11:55: # Command line: callpeak -t SRX013104.bam -f BAM -g dm -n SRX013104.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013104.10 # format = BAM # ChIP-seq file = ['SRX013104.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 @ Tue, 21 Apr 2015 12:11:55: # Command line: callpeak -t SRX013104.bam -f BAM -g dm -n SRX013104.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013104.20 # format = BAM # ChIP-seq file = ['SRX013104.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 @ Tue, 21 Apr 2015 12:11:55: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:11:55: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:11:55: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:11:55: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:11:55: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:11:55: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:12:01: 1000000 INFO @ Tue, 21 Apr 2015 12:12:01: 1000000 INFO @ Tue, 21 Apr 2015 12:12:01: 1000000 INFO @ Tue, 21 Apr 2015 12:12:07: 2000000 INFO @ Tue, 21 Apr 2015 12:12:07: 2000000 INFO @ Tue, 21 Apr 2015 12:12:07: 2000000 INFO @ Tue, 21 Apr 2015 12:12:14: 3000000 INFO @ Tue, 21 Apr 2015 12:12:14: 3000000 INFO @ Tue, 21 Apr 2015 12:12:14: 3000000 INFO @ Tue, 21 Apr 2015 12:12:20: 4000000 INFO @ Tue, 21 Apr 2015 12:12:20: 4000000 INFO @ Tue, 21 Apr 2015 12:12:20: 4000000 INFO @ Tue, 21 Apr 2015 12:12:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:12:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:12:25: #1 total tags in treatment: 4802142 INFO @ Tue, 21 Apr 2015 12:12:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:12:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:12:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:12:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:12:25: #1 total tags in treatment: 4802142 INFO @ Tue, 21 Apr 2015 12:12:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:12:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:12:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:12:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:12:25: #1 total tags in treatment: 4802142 INFO @ Tue, 21 Apr 2015 12:12:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:12:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:12:26: #1 tags after filtering in treatment: 4801962 INFO @ Tue, 21 Apr 2015 12:12:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:12:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:12:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:12:26: #1 tags after filtering in treatment: 4801962 INFO @ Tue, 21 Apr 2015 12:12:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:12:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:12:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:12:26: #1 tags after filtering in treatment: 4801962 INFO @ Tue, 21 Apr 2015 12:12:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:12:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:12:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:12:27: #2 number of paired peaks: 3763 INFO @ Tue, 21 Apr 2015 12:12:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:12:27: #2 number of paired peaks: 3763 INFO @ Tue, 21 Apr 2015 12:12:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:12:27: #2 number of paired peaks: 3763 INFO @ Tue, 21 Apr 2015 12:12:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:12:38: start X-correlation... INFO @ Tue, 21 Apr 2015 12:12:38: end of X-cor INFO @ Tue, 21 Apr 2015 12:12:38: #2 finished! INFO @ Tue, 21 Apr 2015 12:12:38: #2 predicted fragment length is 184 bps INFO @ Tue, 21 Apr 2015 12:12:38: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 21 Apr 2015 12:12:38: #2.2 Generate R script for model : SRX013104.10_model.r INFO @ Tue, 21 Apr 2015 12:12:38: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:12:38: start X-correlation... INFO @ Tue, 21 Apr 2015 12:12:38: end of X-cor INFO @ Tue, 21 Apr 2015 12:12:38: #2 finished! INFO @ Tue, 21 Apr 2015 12:12:38: #2 predicted fragment length is 184 bps INFO @ Tue, 21 Apr 2015 12:12:38: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 21 Apr 2015 12:12:38: #2.2 Generate R script for model : SRX013104.20_model.r INFO @ Tue, 21 Apr 2015 12:12:38: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:12:38: start X-correlation... INFO @ Tue, 21 Apr 2015 12:12:38: end of X-cor INFO @ Tue, 21 Apr 2015 12:12:38: #2 finished! INFO @ Tue, 21 Apr 2015 12:12:38: #2 predicted fragment length is 184 bps INFO @ Tue, 21 Apr 2015 12:12:38: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 21 Apr 2015 12:12:38: #2.2 Generate R script for model : SRX013104.05_model.r INFO @ Tue, 21 Apr 2015 12:12:38: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:13:05: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:13:06: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:13:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:13:28: #4 Write output xls file... SRX013104.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:13:28: #4 Write peak in narrowPeak format file... SRX013104.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:13:28: #4 Write summits bed file... SRX013104.20_summits.bed INFO @ Tue, 21 Apr 2015 12:13:28: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2765 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:13:30: #4 Write output xls file... SRX013104.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:13:30: #4 Write peak in narrowPeak format file... SRX013104.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:13:30: #4 Write summits bed file... SRX013104.10_summits.bed INFO @ Tue, 21 Apr 2015 12:13:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4596 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:13:37: #4 Write output xls file... SRX013104.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:13:37: #4 Write peak in narrowPeak format file... SRX013104.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:13:37: #4 Write summits bed file... SRX013104.05_summits.bed INFO @ Tue, 21 Apr 2015 12:13:37: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (6390 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。