Job ID = 2161420 sra ファイルのダウンロード中... Completed: 372639K bytes transferred in 6 seconds (490231K 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 35833 0 35833 0 0 42749 0 --:--:-- --:--:-- --:--:-- 55383 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 13982411 spots for /home/okishinya/chipatlas/results/dm3/SRX026738/SRR065624.sra Written 13982411 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: 00:02:31 13982411 reads; of these: 13982411 (100.00%) were unpaired; of these: 7588385 (54.27%) aligned 0 times 5075710 (36.30%) aligned exactly 1 time 1318316 (9.43%) aligned >1 times 45.73% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 905967 / 6394026 = 0.1417 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 12:40:54: # Command line: callpeak -t SRX026738.bam -f BAM -g dm -n SRX026738.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX026738.10 # format = BAM # ChIP-seq file = ['SRX026738.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 12:40:54: # Command line: callpeak -t SRX026738.bam -f BAM -g dm -n SRX026738.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX026738.05 # format = BAM # ChIP-seq file = ['SRX026738.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 12:40:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:40:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:40:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:40:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:40:54: # Command line: callpeak -t SRX026738.bam -f BAM -g dm -n SRX026738.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX026738.20 # format = BAM # ChIP-seq file = ['SRX026738.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 12:40:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:40:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:41:01: 1000000 INFO @ Tue, 21 Apr 2015 12:41:01: 1000000 INFO @ Tue, 21 Apr 2015 12:41:01: 1000000 INFO @ Tue, 21 Apr 2015 12:41:06: 2000000 INFO @ Tue, 21 Apr 2015 12:41:07: 2000000 INFO @ Tue, 21 Apr 2015 12:41:07: 2000000 INFO @ Tue, 21 Apr 2015 12:41:12: 3000000 INFO @ Tue, 21 Apr 2015 12:41:12: 3000000 INFO @ Tue, 21 Apr 2015 12:41:12: 3000000 INFO @ Tue, 21 Apr 2015 12:41:17: 4000000 INFO @ Tue, 21 Apr 2015 12:41:18: 4000000 INFO @ Tue, 21 Apr 2015 12:41:18: 4000000 INFO @ Tue, 21 Apr 2015 12:41:23: 5000000 INFO @ Tue, 21 Apr 2015 12:41:24: 5000000 INFO @ Tue, 21 Apr 2015 12:41:24: 5000000 INFO @ Tue, 21 Apr 2015 12:41:25: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 12:41:25: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 12:41:25: #1 total tags in treatment: 5488059 INFO @ Tue, 21 Apr 2015 12:41:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:41:25: #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 12:41:26: #1 tags after filtering in treatment: 5487591 INFO @ Tue, 21 Apr 2015 12:41:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:41:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:41:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:41:27: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 12:41:27: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 12:41:27: #1 total tags in treatment: 5488059 INFO @ Tue, 21 Apr 2015 12:41:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:41:27: #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 12:41:27: #1 tag size is determined as 40 bps INFO @ Tue, 21 Apr 2015 12:41:27: #1 tag size = 40 INFO @ Tue, 21 Apr 2015 12:41:27: #1 total tags in treatment: 5488059 INFO @ Tue, 21 Apr 2015 12:41:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:41:27: #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 12:41:28: #2 number of paired peaks: 329 WARNING @ Tue, 21 Apr 2015 12:41:28: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 21 Apr 2015 12:41:28: start model_add_line... INFO @ Tue, 21 Apr 2015 12:41:28: #1 tags after filtering in treatment: 5487591 INFO @ Tue, 21 Apr 2015 12:41:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:41:28: #1 finished! INFO @ Tue, 21 Apr 2015 12:41:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:41:28: #1 tags after filtering in treatment: 5487591 INFO @ Tue, 21 Apr 2015 12:41:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:41:28: #1 finished! INFO @ Tue, 21 Apr 2015 12:41:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:41:29: #2 number of paired peaks: 329 WARNING @ Tue, 21 Apr 2015 12:41:29: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 21 Apr 2015 12:41:29: start model_add_line... INFO @ Tue, 21 Apr 2015 12:41:29: start X-correlation... INFO @ Tue, 21 Apr 2015 12:41:29: end of X-cor INFO @ Tue, 21 Apr 2015 12:41:29: #2 finished! INFO @ Tue, 21 Apr 2015 12:41:29: #2 predicted fragment length is 104 bps INFO @ Tue, 21 Apr 2015 12:41:29: #2 alternative fragment length(s) may be 104 bps INFO @ Tue, 21 Apr 2015 12:41:29: #2.2 Generate R script for model : SRX026738.20_model.r INFO @ Tue, 21 Apr 2015 12:41:29: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:41:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:41:29: #2 number of paired peaks: 329 WARNING @ Tue, 21 Apr 2015 12:41:29: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Tue, 21 Apr 2015 12:41:29: start model_add_line... INFO @ Tue, 21 Apr 2015 12:41:31: start X-correlation... INFO @ Tue, 21 Apr 2015 12:41:31: end of X-cor INFO @ Tue, 21 Apr 2015 12:41:31: #2 finished! INFO @ Tue, 21 Apr 2015 12:41:31: #2 predicted fragment length is 104 bps INFO @ Tue, 21 Apr 2015 12:41:31: #2 alternative fragment length(s) may be 104 bps INFO @ Tue, 21 Apr 2015 12:41:31: #2.2 Generate R script for model : SRX026738.05_model.r INFO @ Tue, 21 Apr 2015 12:41:31: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:41:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:41:31: start X-correlation... INFO @ Tue, 21 Apr 2015 12:41:31: end of X-cor INFO @ Tue, 21 Apr 2015 12:41:31: #2 finished! INFO @ Tue, 21 Apr 2015 12:41:31: #2 predicted fragment length is 104 bps INFO @ Tue, 21 Apr 2015 12:41:31: #2 alternative fragment length(s) may be 104 bps INFO @ Tue, 21 Apr 2015 12:41:31: #2.2 Generate R script for model : SRX026738.10_model.r INFO @ Tue, 21 Apr 2015 12:41:31: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:41:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:42:00: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:42:01: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:42:02: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:42:22: #4 Write output xls file... SRX026738.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:42:22: #4 Write peak in narrowPeak format file... SRX026738.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:42:22: #4 Write summits bed file... SRX026738.20_summits.bed INFO @ Tue, 21 Apr 2015 12:42:22: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:42:24: #4 Write output xls file... SRX026738.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:42:24: #4 Write peak in narrowPeak format file... SRX026738.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:42:24: #4 Write summits bed file... SRX026738.10_summits.bed INFO @ Tue, 21 Apr 2015 12:42:24: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (710 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:42:25: #4 Write output xls file... SRX026738.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:42:25: #4 Write peak in narrowPeak format file... SRX026738.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:42:25: #4 Write summits bed file... SRX026738.05_summits.bed INFO @ Tue, 21 Apr 2015 12:42:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1326 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。