Job ID = 2161915 sra ファイルのダウンロード中... Completed: 281134K bytes transferred in 5 seconds (407482K 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 35578 0 35578 0 0 49652 0 --:--:-- --:--:-- --:--:-- 67767 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 10600299 spots for /home/okishinya/chipatlas/results/dm3/SRX040618/SRR097987.sra Written 10600299 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: 00:02:32 10600299 reads; of these: 10600299 (100.00%) were unpaired; of these: 761656 (7.19%) aligned 0 times 8579130 (80.93%) aligned exactly 1 time 1259513 (11.88%) aligned >1 times 92.81% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 5155533 / 9838643 = 0.5240 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 13:16:51: # Command line: callpeak -t SRX040618.bam -f BAM -g dm -n SRX040618.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX040618.05 # format = BAM # ChIP-seq file = ['SRX040618.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 13:16:51: # Command line: callpeak -t SRX040618.bam -f BAM -g dm -n SRX040618.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX040618.10 # format = BAM # ChIP-seq file = ['SRX040618.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 13:16:51: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:16:51: # Command line: callpeak -t SRX040618.bam -f BAM -g dm -n SRX040618.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX040618.20 # format = BAM # ChIP-seq file = ['SRX040618.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 13:16:51: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:16:51: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:16:51: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:16:51: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:16:51: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:16:56: 1000000 INFO @ Tue, 21 Apr 2015 13:16:56: 1000000 INFO @ Tue, 21 Apr 2015 13:16:56: 1000000 INFO @ Tue, 21 Apr 2015 13:17:01: 2000000 INFO @ Tue, 21 Apr 2015 13:17:01: 2000000 INFO @ Tue, 21 Apr 2015 13:17:02: 2000000 INFO @ Tue, 21 Apr 2015 13:17:06: 3000000 INFO @ Tue, 21 Apr 2015 13:17:07: 3000000 INFO @ Tue, 21 Apr 2015 13:17:09: 3000000 INFO @ Tue, 21 Apr 2015 13:17:11: 4000000 INFO @ Tue, 21 Apr 2015 13:17:12: 4000000 INFO @ Tue, 21 Apr 2015 13:17:15: 4000000 INFO @ Tue, 21 Apr 2015 13:17:15: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:17:15: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:17:15: #1 total tags in treatment: 4683110 INFO @ Tue, 21 Apr 2015 13:17:15: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:17:15: #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 13:17:16: #1 tags after filtering in treatment: 4682439 INFO @ Tue, 21 Apr 2015 13:17:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:17:16: #1 finished! INFO @ Tue, 21 Apr 2015 13:17:16: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:17:16: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:17:16: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:17:16: #1 total tags in treatment: 4683110 INFO @ Tue, 21 Apr 2015 13:17:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:17:16: #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 13:17:17: #2 number of paired peaks: 1287 INFO @ Tue, 21 Apr 2015 13:17:17: start model_add_line... INFO @ Tue, 21 Apr 2015 13:17:17: #1 tags after filtering in treatment: 4682439 INFO @ Tue, 21 Apr 2015 13:17:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:17:17: #1 finished! INFO @ Tue, 21 Apr 2015 13:17:17: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:17:18: #2 number of paired peaks: 1287 INFO @ Tue, 21 Apr 2015 13:17:18: start model_add_line... INFO @ Tue, 21 Apr 2015 13:17:18: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:17:18: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:17:18: #1 total tags in treatment: 4683110 INFO @ Tue, 21 Apr 2015 13:17:18: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:17:18: #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 13:17:19: #1 tags after filtering in treatment: 4682439 INFO @ Tue, 21 Apr 2015 13:17:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:17:19: #1 finished! INFO @ Tue, 21 Apr 2015 13:17:19: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:17:20: start X-correlation... INFO @ Tue, 21 Apr 2015 13:17:20: end of X-cor INFO @ Tue, 21 Apr 2015 13:17:20: #2 finished! INFO @ Tue, 21 Apr 2015 13:17:20: #2 predicted fragment length is 98 bps INFO @ Tue, 21 Apr 2015 13:17:20: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 21 Apr 2015 13:17:20: #2.2 Generate R script for model : SRX040618.05_model.r INFO @ Tue, 21 Apr 2015 13:17:20: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:17:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:17:20: #2 number of paired peaks: 1287 INFO @ Tue, 21 Apr 2015 13:17:20: start model_add_line... INFO @ Tue, 21 Apr 2015 13:17:21: start X-correlation... INFO @ Tue, 21 Apr 2015 13:17:21: end of X-cor INFO @ Tue, 21 Apr 2015 13:17:21: #2 finished! INFO @ Tue, 21 Apr 2015 13:17:21: #2 predicted fragment length is 98 bps INFO @ Tue, 21 Apr 2015 13:17:21: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 21 Apr 2015 13:17:21: #2.2 Generate R script for model : SRX040618.20_model.r INFO @ Tue, 21 Apr 2015 13:17:21: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:17:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:17:23: start X-correlation... INFO @ Tue, 21 Apr 2015 13:17:23: end of X-cor INFO @ Tue, 21 Apr 2015 13:17:23: #2 finished! INFO @ Tue, 21 Apr 2015 13:17:23: #2 predicted fragment length is 98 bps INFO @ Tue, 21 Apr 2015 13:17:23: #2 alternative fragment length(s) may be 98 bps INFO @ Tue, 21 Apr 2015 13:17:23: #2.2 Generate R script for model : SRX040618.10_model.r INFO @ Tue, 21 Apr 2015 13:17:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:17:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:17:47: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:17:47: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:17:51: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:18:07: #4 Write output xls file... SRX040618.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:18:07: #4 Write peak in narrowPeak format file... SRX040618.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:18:07: #4 Write summits bed file... SRX040618.20_summits.bed INFO @ Tue, 21 Apr 2015 13:18:07: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (1110 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:18:11: #4 Write output xls file... SRX040618.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:18:11: #4 Write peak in narrowPeak format file... SRX040618.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:18:11: #4 Write summits bed file... SRX040618.10_summits.bed INFO @ Tue, 21 Apr 2015 13:18:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3680 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:18:12: #4 Write output xls file... SRX040618.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:18:12: #4 Write peak in narrowPeak format file... SRX040618.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:18:12: #4 Write summits bed file... SRX040618.05_summits.bed INFO @ Tue, 21 Apr 2015 13:18:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8399 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。