Job ID = 2162453 sra ファイルのダウンロード中... Completed: 551751K bytes transferred in 7 seconds (598416K 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 13468 0 13468 0 0 21092 0 --:--:-- --:--:-- --:--:-- 30129 100 36298 0 36298 0 0 43803 0 --:--:-- --:--:-- --:--:-- 56982 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 24729310 spots for /home/okishinya/chipatlas/results/dm3/SRX101813/SRR360699.sra Written 24729310 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: 00:18:55 24729310 reads; of these: 24729310 (100.00%) were unpaired; of these: 3454071 (13.97%) aligned 0 times 9724654 (39.32%) aligned exactly 1 time 11550585 (46.71%) aligned >1 times 86.03% overall alignment rate Time searching: 00:18:55 Overall time: 00:18:55 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] 17208047 / 21275239 = 0.8088 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 14:27:55: # Command line: callpeak -t SRX101813.bam -f BAM -g dm -n SRX101813.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX101813.05 # format = BAM # ChIP-seq file = ['SRX101813.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 14:27:55: # Command line: callpeak -t SRX101813.bam -f BAM -g dm -n SRX101813.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX101813.20 # format = BAM # ChIP-seq file = ['SRX101813.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 14:27:55: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:27:55: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:27:55: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:27:55: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:27:55: # Command line: callpeak -t SRX101813.bam -f BAM -g dm -n SRX101813.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX101813.10 # format = BAM # ChIP-seq file = ['SRX101813.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 14:27:55: #1 read tag files... INFO @ Tue, 21 Apr 2015 14:27:55: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 14:28:02: 1000000 INFO @ Tue, 21 Apr 2015 14:28:02: 1000000 INFO @ Tue, 21 Apr 2015 14:28:02: 1000000 INFO @ Tue, 21 Apr 2015 14:28:08: 2000000 INFO @ Tue, 21 Apr 2015 14:28:08: 2000000 INFO @ Tue, 21 Apr 2015 14:28:09: 2000000 INFO @ Tue, 21 Apr 2015 14:28:15: 3000000 INFO @ Tue, 21 Apr 2015 14:28:15: 3000000 INFO @ Tue, 21 Apr 2015 14:28:15: 3000000 INFO @ Tue, 21 Apr 2015 14:28:21: 4000000 INFO @ Tue, 21 Apr 2015 14:28:21: 4000000 INFO @ Tue, 21 Apr 2015 14:28:22: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:28:22: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:28:22: #1 total tags in treatment: 4067192 INFO @ Tue, 21 Apr 2015 14:28:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:28:22: #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 14:28:22: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:28:22: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:28:22: #1 total tags in treatment: 4067192 INFO @ Tue, 21 Apr 2015 14:28:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:28:22: #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 14:28:22: 4000000 INFO @ Tue, 21 Apr 2015 14:28:22: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 14:28:22: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 14:28:22: #1 total tags in treatment: 4067192 INFO @ Tue, 21 Apr 2015 14:28:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 14:28:22: #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 14:28:23: #1 tags after filtering in treatment: 4064775 INFO @ Tue, 21 Apr 2015 14:28:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:28:23: #1 finished! INFO @ Tue, 21 Apr 2015 14:28:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:28:23: #1 tags after filtering in treatment: 4064775 INFO @ Tue, 21 Apr 2015 14:28:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:28:23: #1 finished! INFO @ Tue, 21 Apr 2015 14:28:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:28:23: #1 tags after filtering in treatment: 4064775 INFO @ Tue, 21 Apr 2015 14:28:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 14:28:23: #1 finished! INFO @ Tue, 21 Apr 2015 14:28:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 14:28:24: #2 number of paired peaks: 4822 INFO @ Tue, 21 Apr 2015 14:28:24: start model_add_line... INFO @ Tue, 21 Apr 2015 14:28:24: #2 number of paired peaks: 4822 INFO @ Tue, 21 Apr 2015 14:28:24: start model_add_line... INFO @ Tue, 21 Apr 2015 14:28:24: #2 number of paired peaks: 4822 INFO @ Tue, 21 Apr 2015 14:28:24: start model_add_line... INFO @ Tue, 21 Apr 2015 14:28:41: start X-correlation... INFO @ Tue, 21 Apr 2015 14:28:41: end of X-cor INFO @ Tue, 21 Apr 2015 14:28:41: #2 finished! INFO @ Tue, 21 Apr 2015 14:28:41: #2 predicted fragment length is 198 bps INFO @ Tue, 21 Apr 2015 14:28:41: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 21 Apr 2015 14:28:41: #2.2 Generate R script for model : SRX101813.20_model.r INFO @ Tue, 21 Apr 2015 14:28:41: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:28:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:28:42: start X-correlation... INFO @ Tue, 21 Apr 2015 14:28:42: end of X-cor INFO @ Tue, 21 Apr 2015 14:28:42: #2 finished! INFO @ Tue, 21 Apr 2015 14:28:42: #2 predicted fragment length is 198 bps INFO @ Tue, 21 Apr 2015 14:28:42: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 21 Apr 2015 14:28:42: #2.2 Generate R script for model : SRX101813.05_model.r INFO @ Tue, 21 Apr 2015 14:28:42: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:28:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:28:42: start X-correlation... INFO @ Tue, 21 Apr 2015 14:28:42: end of X-cor INFO @ Tue, 21 Apr 2015 14:28:42: #2 finished! INFO @ Tue, 21 Apr 2015 14:28:42: #2 predicted fragment length is 198 bps INFO @ Tue, 21 Apr 2015 14:28:42: #2 alternative fragment length(s) may be 198 bps INFO @ Tue, 21 Apr 2015 14:28:42: #2.2 Generate R script for model : SRX101813.10_model.r INFO @ Tue, 21 Apr 2015 14:28:42: #3 Call peaks... INFO @ Tue, 21 Apr 2015 14:28:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 14:29:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:29:09: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 14:29:12: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 21 Apr 2015 14:29:32: #4 Write output xls file... SRX101813.20_peaks.xls INFO @ Tue, 21 Apr 2015 14:29:32: #4 Write peak in narrowPeak format file... SRX101813.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:29:32: #4 Write summits bed file... SRX101813.20_summits.bed INFO @ Tue, 21 Apr 2015 14:29:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6046 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:29:39: #4 Write output xls file... SRX101813.05_peaks.xls INFO @ Tue, 21 Apr 2015 14:29:39: #4 Write peak in narrowPeak format file... SRX101813.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:29:39: #4 Write summits bed file... SRX101813.05_summits.bed INFO @ Tue, 21 Apr 2015 14:29:39: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10853 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 14:29:39: #4 Write output xls file... SRX101813.10_peaks.xls INFO @ Tue, 21 Apr 2015 14:29:39: #4 Write peak in narrowPeak format file... SRX101813.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 14:29:40: #4 Write summits bed file... SRX101813.10_summits.bed INFO @ Tue, 21 Apr 2015 14:29:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8501 records, 4 fields): 11 millis CompletedMACS2peakCalling