Job ID = 2161196 sra ファイルのダウンロード中... Completed: 122397K bytes transferred in 4 seconds (208395K 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 --:--:-- --:--:-- --:--:-- 0 108 1088 0 1088 0 0 1747 0 --:--:-- --:--:-- --:--:-- 2518 100 35024 0 35024 0 0 43115 0 --:--:-- --:--:-- --:--:-- 56308 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 5034276 spots for /home/okishinya/chipatlas/results/dm3/SRX013044/SRR030310.sra Written 5034276 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: 00:01:09 5034276 reads; of these: 5034276 (100.00%) were unpaired; of these: 466996 (9.28%) aligned 0 times 3903234 (77.53%) aligned exactly 1 time 664046 (13.19%) aligned >1 times 90.72% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 198290 / 4567280 = 0.0434 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 12:02:54: # Command line: callpeak -t SRX013044.bam -f BAM -g dm -n SRX013044.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013044.20 # format = BAM # ChIP-seq file = ['SRX013044.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 12:02:54: # Command line: callpeak -t SRX013044.bam -f BAM -g dm -n SRX013044.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013044.10 # format = BAM # ChIP-seq file = ['SRX013044.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 12:02:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:02:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:02:54: # Command line: callpeak -t SRX013044.bam -f BAM -g dm -n SRX013044.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013044.05 # format = BAM # ChIP-seq file = ['SRX013044.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 12:02:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:02:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:02:54: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:02:54: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:02:59: 1000000 INFO @ Tue, 21 Apr 2015 12:02:59: 1000000 INFO @ Tue, 21 Apr 2015 12:02:59: 1000000 INFO @ Tue, 21 Apr 2015 12:03:04: 2000000 INFO @ Tue, 21 Apr 2015 12:03:04: 2000000 INFO @ Tue, 21 Apr 2015 12:03:04: 2000000 INFO @ Tue, 21 Apr 2015 12:03:09: 3000000 INFO @ Tue, 21 Apr 2015 12:03:09: 3000000 INFO @ Tue, 21 Apr 2015 12:03:10: 3000000 INFO @ Tue, 21 Apr 2015 12:03:14: 4000000 INFO @ Tue, 21 Apr 2015 12:03:14: 4000000 INFO @ Tue, 21 Apr 2015 12:03:15: 4000000 INFO @ Tue, 21 Apr 2015 12:03:16: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:03:16: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:03:16: #1 total tags in treatment: 4368990 INFO @ Tue, 21 Apr 2015 12:03:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:03:16: #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 12:03:16: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:03:16: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:03:16: #1 total tags in treatment: 4368990 INFO @ Tue, 21 Apr 2015 12:03:16: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:03:16: #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 12:03:17: #1 tags after filtering in treatment: 4368859 INFO @ Tue, 21 Apr 2015 12:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:03:17: #1 finished! INFO @ Tue, 21 Apr 2015 12:03:17: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:03:17: #1 tags after filtering in treatment: 4368859 INFO @ Tue, 21 Apr 2015 12:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:03:17: #1 finished! INFO @ Tue, 21 Apr 2015 12:03:17: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:03:17: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:03:17: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:03:17: #1 total tags in treatment: 4368990 INFO @ Tue, 21 Apr 2015 12:03:17: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:03:17: #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 12:03:18: #2 number of paired peaks: 104 WARNING @ Tue, 21 Apr 2015 12:03:18: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 21 Apr 2015 12:03:18: start model_add_line... INFO @ Tue, 21 Apr 2015 12:03:18: #2 number of paired peaks: 104 WARNING @ Tue, 21 Apr 2015 12:03:18: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 21 Apr 2015 12:03:18: start model_add_line... INFO @ Tue, 21 Apr 2015 12:03:18: #1 tags after filtering in treatment: 4368859 INFO @ Tue, 21 Apr 2015 12:03:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:03:18: #1 finished! INFO @ Tue, 21 Apr 2015 12:03:18: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:03:18: start X-correlation... INFO @ Tue, 21 Apr 2015 12:03:18: end of X-cor INFO @ Tue, 21 Apr 2015 12:03:18: #2 finished! INFO @ Tue, 21 Apr 2015 12:03:18: #2 predicted fragment length is 154 bps INFO @ Tue, 21 Apr 2015 12:03:18: #2 alternative fragment length(s) may be 154,562 bps INFO @ Tue, 21 Apr 2015 12:03:18: #2.2 Generate R script for model : SRX013044.10_model.r INFO @ Tue, 21 Apr 2015 12:03:18: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:03:18: start X-correlation... INFO @ Tue, 21 Apr 2015 12:03:18: end of X-cor INFO @ Tue, 21 Apr 2015 12:03:18: #2 finished! INFO @ Tue, 21 Apr 2015 12:03:18: #2 predicted fragment length is 154 bps INFO @ Tue, 21 Apr 2015 12:03:18: #2 alternative fragment length(s) may be 154,562 bps INFO @ Tue, 21 Apr 2015 12:03:18: #2.2 Generate R script for model : SRX013044.05_model.r INFO @ Tue, 21 Apr 2015 12:03:18: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:03:19: #2 number of paired peaks: 104 WARNING @ Tue, 21 Apr 2015 12:03:19: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 21 Apr 2015 12:03:19: start model_add_line... INFO @ Tue, 21 Apr 2015 12:03:20: start X-correlation... INFO @ Tue, 21 Apr 2015 12:03:20: end of X-cor INFO @ Tue, 21 Apr 2015 12:03:20: #2 finished! INFO @ Tue, 21 Apr 2015 12:03:20: #2 predicted fragment length is 154 bps INFO @ Tue, 21 Apr 2015 12:03:20: #2 alternative fragment length(s) may be 154,562 bps INFO @ Tue, 21 Apr 2015 12:03:20: #2.2 Generate R script for model : SRX013044.20_model.r INFO @ Tue, 21 Apr 2015 12:03:20: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:03:44: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:03:44: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:03:46: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:04:02: #4 Write output xls file... SRX013044.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:04:02: #4 Write peak in narrowPeak format file... SRX013044.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:04:02: #4 Write summits bed file... SRX013044.05_summits.bed INFO @ Tue, 21 Apr 2015 12:04:02: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1433 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:04:02: #4 Write output xls file... SRX013044.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:04:02: #4 Write peak in narrowPeak format file... SRX013044.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:04:03: #4 Write summits bed file... SRX013044.10_summits.bed INFO @ Tue, 21 Apr 2015 12:04:03: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (399 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:04:06: #4 Write output xls file... SRX013044.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:04:06: #4 Write peak in narrowPeak format file... SRX013044.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:04:06: #4 Write summits bed file... SRX013044.20_summits.bed INFO @ Tue, 21 Apr 2015 12:04:06: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (84 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。