Job ID = 2162412 sra ファイルのダウンロード中... Completed: 1307675K bytes transferred in 13 seconds (767800K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0 100 36156 0 36156 0 0 25640 0 --:--:-- 0:00:01 --:--:-- 29660 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 32428673 spots for /home/okishinya/chipatlas/results/dm3/SRX085407/SRR317185.sra Written 32428673 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: 00:09:35 32428673 reads; of these: 32428673 (100.00%) were unpaired; of these: 7709612 (23.77%) aligned 0 times 18892352 (58.26%) aligned exactly 1 time 5826709 (17.97%) aligned >1 times 76.23% overall alignment rate Time searching: 00:09:35 Overall time: 00:09:35 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_sort_core] merging from 8 files... [bam_rmdupse_core] 21942858 / 24719061 = 0.8877 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 14:07:11: # Command line: callpeak -t SRX085407.bam -f BAM -g dm -n SRX085407.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX085407.10 # format = BAM # ChIP-seq file = ['SRX085407.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 14:07:11: # Command line: callpeak -t SRX085407.bam -f BAM -g dm -n SRX085407.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX085407.05 # format = BAM # ChIP-seq file = ['SRX085407.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 14:07:11: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:07:11: # Command line: callpeak -t SRX085407.bam -f BAM -g dm -n SRX085407.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX085407.20 # format = BAM # ChIP-seq file = ['SRX085407.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 14:07:11: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:07:11: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:07:11: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:07:11: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:07:11: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:07:17: 1000000 INFO @ Tue, 21 Apr 2015 14:07:18: 1000000 INFO @ Tue, 21 Apr 2015 14:07:18: 1000000 INFO @ Tue, 21 Apr 2015 14:07:23: 2000000 INFO @ Tue, 21 Apr 2015 14:07:24: 2000000 INFO @ Tue, 21 Apr 2015 14:07:24: 2000000 INFO @ Tue, 21 Apr 2015 14:07:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:07:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:07:27: #1 total tags in treatment: 2776203 INFO @ Tue, 21 Apr 2015 14:07:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:07:27: #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 14:07:28: #1 tags after filtering in treatment: 2774138 INFO @ Tue, 21 Apr 2015 14:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:07:28: #1 finished! INFO @ Tue, 21 Apr 2015 14:07:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:07:28: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:07:28: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:07:28: #1 total tags in treatment: 2776203 INFO @ Tue, 21 Apr 2015 14:07:28: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:07:28: #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 14:07:28: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:07:28: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:07:28: #1 total tags in treatment: 2776203 INFO @ Tue, 21 Apr 2015 14:07:28: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:07:28: #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 14:07:29: #1 tags after filtering in treatment: 2774138 INFO @ Tue, 21 Apr 2015 14:07:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:07:29: #1 finished! INFO @ Tue, 21 Apr 2015 14:07:29: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:07:29: #1 tags after filtering in treatment: 2774138 INFO @ Tue, 21 Apr 2015 14:07:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:07:29: #1 finished! INFO @ Tue, 21 Apr 2015 14:07:29: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:07:29: #2 number of paired peaks: 4580 INFO @ Tue, 21 Apr 2015 14:07:29: start model_add_line... INFO @ Tue, 21 Apr 2015 14:07:30: #2 number of paired peaks: 4580 INFO @ Tue, 21 Apr 2015 14:07:30: start model_add_line... INFO @ Tue, 21 Apr 2015 14:07:30: #2 number of paired peaks: 4580 INFO @ Tue, 21 Apr 2015 14:07:30: start model_add_line... INFO @ Tue, 21 Apr 2015 14:07:40: start X-correlation... INFO @ Tue, 21 Apr 2015 14:07:40: end of X-cor INFO @ Tue, 21 Apr 2015 14:07:40: #2 finished! INFO @ Tue, 21 Apr 2015 14:07:40: #2 predicted fragment length is 106 bps INFO @ Tue, 21 Apr 2015 14:07:40: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 21 Apr 2015 14:07:40: #2.2 Generate R script for model : SRX085407.10_model.r INFO @ Tue, 21 Apr 2015 14:07:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:07:41: start X-correlation... INFO @ Tue, 21 Apr 2015 14:07:41: end of X-cor INFO @ Tue, 21 Apr 2015 14:07:41: #2 finished! INFO @ Tue, 21 Apr 2015 14:07:41: #2 predicted fragment length is 106 bps INFO @ Tue, 21 Apr 2015 14:07:41: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 21 Apr 2015 14:07:41: #2.2 Generate R script for model : SRX085407.20_model.r INFO @ Tue, 21 Apr 2015 14:07:41: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:07:41: start X-correlation... INFO @ Tue, 21 Apr 2015 14:07:41: end of X-cor INFO @ Tue, 21 Apr 2015 14:07:41: #2 finished! INFO @ Tue, 21 Apr 2015 14:07:41: #2 predicted fragment length is 106 bps INFO @ Tue, 21 Apr 2015 14:07:41: #2 alternative fragment length(s) may be 106 bps INFO @ Tue, 21 Apr 2015 14:07:41: #2.2 Generate R script for model : SRX085407.05_model.r INFO @ Tue, 21 Apr 2015 14:07:41: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:07:57: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:07:58: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:07:58: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:08:12: #4 Write output xls file... SRX085407.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:08:12: #4 Write peak in narrowPeak format file... SRX085407.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:08:12: #4 Write summits bed file... SRX085407.20_summits.bed INFO @ Tue, 21 Apr 2015 14:08:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3413 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:08:13: #4 Write output xls file... SRX085407.10_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 21 Apr 2015 14:08:13: #4 Write peak in narrowPeak format file... SRX085407.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:08:13: #4 Write summits bed file... SRX085407.10_summits.bed INFO @ Tue, 21 Apr 2015 14:08:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4693 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:08:15: #4 Write output xls file... SRX085407.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:08:15: #4 Write peak in narrowPeak format file... SRX085407.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:08:15: #4 Write summits bed file... SRX085407.05_summits.bed INFO @ Tue, 21 Apr 2015 14:08:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6495 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。