Job ID = 2161216 sra ファイルのダウンロード中... Completed: 89438K bytes transferred in 4 seconds (175433K 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 35214 0 35214 0 0 49858 0 --:--:-- --:--:-- --:--:-- 68509 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 3500257 spots for /home/okishinya/chipatlas/results/dm3/SRX013064/SRR030330.sra Written 3500257 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: 00:00:45 3500257 reads; of these: 3500257 (100.00%) were unpaired; of these: 489014 (13.97%) aligned 0 times 2662938 (76.08%) aligned exactly 1 time 348305 (9.95%) aligned >1 times 86.03% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 85620 / 3011243 = 0.0284 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 12:04:47: # Command line: callpeak -t SRX013064.bam -f BAM -g dm -n SRX013064.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013064.20 # format = BAM # ChIP-seq file = ['SRX013064.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 12:04:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:04:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:04:47: # Command line: callpeak -t SRX013064.bam -f BAM -g dm -n SRX013064.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013064.05 # format = BAM # ChIP-seq file = ['SRX013064.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 12:04:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:04:47: # Command line: callpeak -t SRX013064.bam -f BAM -g dm -n SRX013064.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013064.10 # format = BAM # ChIP-seq file = ['SRX013064.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 12:04:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:04:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:04:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:04:53: 1000000 INFO @ Tue, 21 Apr 2015 12:04:53: 1000000 INFO @ Tue, 21 Apr 2015 12:04:53: 1000000 INFO @ Tue, 21 Apr 2015 12:04:58: 2000000 INFO @ Tue, 21 Apr 2015 12:04:59: 2000000 INFO @ Tue, 21 Apr 2015 12:04:59: 2000000 INFO @ Tue, 21 Apr 2015 12:05:03: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:05:03: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:05:03: #1 total tags in treatment: 2925623 INFO @ Tue, 21 Apr 2015 12:05:03: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:05:03: #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 12:05:04: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:05:04: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:05:04: #1 total tags in treatment: 2925623 INFO @ Tue, 21 Apr 2015 12:05:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:05:04: #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 12:05:04: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:05:04: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:05:04: #1 total tags in treatment: 2925623 INFO @ Tue, 21 Apr 2015 12:05:04: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:05:04: #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 12:05:04: #1 tags after filtering in treatment: 2925547 INFO @ Tue, 21 Apr 2015 12:05:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:05:04: #1 finished! INFO @ Tue, 21 Apr 2015 12:05:04: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:05:04: #1 tags after filtering in treatment: 2925547 INFO @ Tue, 21 Apr 2015 12:05:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:05:04: #1 finished! INFO @ Tue, 21 Apr 2015 12:05:04: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:05:04: #1 tags after filtering in treatment: 2925547 INFO @ Tue, 21 Apr 2015 12:05:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:05:04: #1 finished! INFO @ Tue, 21 Apr 2015 12:05:04: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:05:04: #2 number of paired peaks: 281 WARNING @ Tue, 21 Apr 2015 12:05:04: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Tue, 21 Apr 2015 12:05:04: start model_add_line... INFO @ Tue, 21 Apr 2015 12:05:05: #2 number of paired peaks: 281 WARNING @ Tue, 21 Apr 2015 12:05:05: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Tue, 21 Apr 2015 12:05:05: start model_add_line... INFO @ Tue, 21 Apr 2015 12:05:05: #2 number of paired peaks: 281 WARNING @ Tue, 21 Apr 2015 12:05:05: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Tue, 21 Apr 2015 12:05:05: start model_add_line... INFO @ Tue, 21 Apr 2015 12:05:05: start X-correlation... INFO @ Tue, 21 Apr 2015 12:05:05: end of X-cor INFO @ Tue, 21 Apr 2015 12:05:05: #2 finished! INFO @ Tue, 21 Apr 2015 12:05:05: #2 predicted fragment length is 144 bps INFO @ Tue, 21 Apr 2015 12:05:05: #2 alternative fragment length(s) may be 144,593 bps INFO @ Tue, 21 Apr 2015 12:05:05: #2.2 Generate R script for model : SRX013064.10_model.r INFO @ Tue, 21 Apr 2015 12:05:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:05:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:05:06: start X-correlation... INFO @ Tue, 21 Apr 2015 12:05:06: end of X-cor INFO @ Tue, 21 Apr 2015 12:05:06: #2 finished! INFO @ Tue, 21 Apr 2015 12:05:06: #2 predicted fragment length is 144 bps INFO @ Tue, 21 Apr 2015 12:05:06: #2 alternative fragment length(s) may be 144,593 bps INFO @ Tue, 21 Apr 2015 12:05:06: #2.2 Generate R script for model : SRX013064.20_model.r INFO @ Tue, 21 Apr 2015 12:05:06: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:05:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:05:06: start X-correlation... INFO @ Tue, 21 Apr 2015 12:05:06: end of X-cor INFO @ Tue, 21 Apr 2015 12:05:06: #2 finished! INFO @ Tue, 21 Apr 2015 12:05:06: #2 predicted fragment length is 144 bps INFO @ Tue, 21 Apr 2015 12:05:06: #2 alternative fragment length(s) may be 144,593 bps INFO @ Tue, 21 Apr 2015 12:05:06: #2.2 Generate R script for model : SRX013064.05_model.r INFO @ Tue, 21 Apr 2015 12:05:06: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:05:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:05:23: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:05:23: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:05:23: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:05:35: #4 Write output xls file... SRX013064.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:05:35: #4 Write peak in narrowPeak format file... SRX013064.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:05:35: #4 Write summits bed file... SRX013064.10_summits.bed INFO @ Tue, 21 Apr 2015 12:05:35: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:05:35: #4 Write output xls file... SRX013064.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:05:35: #4 Write peak in narrowPeak format file... SRX013064.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:05:35: #4 Write summits bed file... SRX013064.20_summits.bed INFO @ Tue, 21 Apr 2015 12:05:35: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (15 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:05:36: #4 Write output xls file... SRX013064.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:05:36: #4 Write peak in narrowPeak format file... SRX013064.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:05:36: #4 Write summits bed file... SRX013064.05_summits.bed INFO @ Tue, 21 Apr 2015 12:05:36: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (837 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。