Job ID = 2161232 sra ファイルのダウンロード中... Completed: 157486K bytes transferred in 5 seconds (252395K 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 34450 0 34450 0 0 49152 0 --:--:-- --:--:-- --:--:-- 67681 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 5744566 spots for /home/okishinya/chipatlas/results/dm3/SRX013080/SRR030346.sra Written 5744566 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: 00:01:43 5744566 reads; of these: 5744566 (100.00%) were unpaired; of these: 380551 (6.62%) aligned 0 times 4084515 (71.10%) aligned exactly 1 time 1279500 (22.27%) aligned >1 times 93.38% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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] 183634 / 5364015 = 0.0342 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 12:07:55: # Command line: callpeak -t SRX013080.bam -f BAM -g dm -n SRX013080.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013080.05 # format = BAM # ChIP-seq file = ['SRX013080.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 12:07:55: # Command line: callpeak -t SRX013080.bam -f BAM -g dm -n SRX013080.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013080.10 # format = BAM # ChIP-seq file = ['SRX013080.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 12:07:55: # Command line: callpeak -t SRX013080.bam -f BAM -g dm -n SRX013080.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013080.20 # format = BAM # ChIP-seq file = ['SRX013080.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 12:07:55: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:07:55: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:07:55: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:07:55: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:07:55: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:07:55: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:08:00: 1000000 INFO @ Tue, 21 Apr 2015 12:08:00: 1000000 INFO @ Tue, 21 Apr 2015 12:08:00: 1000000 INFO @ Tue, 21 Apr 2015 12:08:05: 2000000 INFO @ Tue, 21 Apr 2015 12:08:06: 2000000 INFO @ Tue, 21 Apr 2015 12:08:06: 2000000 INFO @ Tue, 21 Apr 2015 12:08:10: 3000000 INFO @ Tue, 21 Apr 2015 12:08:11: 3000000 INFO @ Tue, 21 Apr 2015 12:08:11: 3000000 INFO @ Tue, 21 Apr 2015 12:08:15: 4000000 INFO @ Tue, 21 Apr 2015 12:08:16: 4000000 INFO @ Tue, 21 Apr 2015 12:08:16: 4000000 INFO @ Tue, 21 Apr 2015 12:08:20: 5000000 INFO @ Tue, 21 Apr 2015 12:08:21: 5000000 INFO @ Tue, 21 Apr 2015 12:08:21: 5000000 INFO @ Tue, 21 Apr 2015 12:08:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:08:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:08:21: #1 total tags in treatment: 5180381 INFO @ Tue, 21 Apr 2015 12:08:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:08:21: #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 12:08:22: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:08:22: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:08:22: #1 total tags in treatment: 5180381 INFO @ Tue, 21 Apr 2015 12:08:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:08:22: #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 12:08:22: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:08:22: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:08:22: #1 total tags in treatment: 5180381 INFO @ Tue, 21 Apr 2015 12:08:22: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:08:22: #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 12:08:22: #1 tags after filtering in treatment: 5179696 INFO @ Tue, 21 Apr 2015 12:08:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:08:22: #1 finished! INFO @ Tue, 21 Apr 2015 12:08:22: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:08:23: #1 tags after filtering in treatment: 5179696 INFO @ Tue, 21 Apr 2015 12:08:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:08:23: #1 finished! INFO @ Tue, 21 Apr 2015 12:08:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:08:23: #1 tags after filtering in treatment: 5179696 INFO @ Tue, 21 Apr 2015 12:08:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:08:23: #1 finished! INFO @ Tue, 21 Apr 2015 12:08:23: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:08:23: #2 number of paired peaks: 152 WARNING @ Tue, 21 Apr 2015 12:08:23: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 21 Apr 2015 12:08:23: start model_add_line... INFO @ Tue, 21 Apr 2015 12:08:24: start X-correlation... INFO @ Tue, 21 Apr 2015 12:08:24: end of X-cor INFO @ Tue, 21 Apr 2015 12:08:24: #2 finished! INFO @ Tue, 21 Apr 2015 12:08:24: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 12:08:24: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 12:08:24: #2.2 Generate R script for model : SRX013080.20_model.r WARNING @ Tue, 21 Apr 2015 12:08:24: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:08:24: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 12:08:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:08:24: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:08:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:08:24: #2 number of paired peaks: 152 WARNING @ Tue, 21 Apr 2015 12:08:24: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 21 Apr 2015 12:08:24: start model_add_line... INFO @ Tue, 21 Apr 2015 12:08:24: #2 number of paired peaks: 152 WARNING @ Tue, 21 Apr 2015 12:08:24: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Tue, 21 Apr 2015 12:08:24: start model_add_line... INFO @ Tue, 21 Apr 2015 12:08:25: start X-correlation... INFO @ Tue, 21 Apr 2015 12:08:25: end of X-cor INFO @ Tue, 21 Apr 2015 12:08:25: #2 finished! INFO @ Tue, 21 Apr 2015 12:08:25: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 12:08:25: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 12:08:25: #2.2 Generate R script for model : SRX013080.10_model.r WARNING @ Tue, 21 Apr 2015 12:08:25: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:08:25: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 12:08:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:08:25: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:08:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:08:25: start X-correlation... INFO @ Tue, 21 Apr 2015 12:08:25: end of X-cor INFO @ Tue, 21 Apr 2015 12:08:25: #2 finished! INFO @ Tue, 21 Apr 2015 12:08:25: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 12:08:25: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 12:08:25: #2.2 Generate R script for model : SRX013080.05_model.r WARNING @ Tue, 21 Apr 2015 12:08:25: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:08:25: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 12:08:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:08:25: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:08:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:08:53: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:08:55: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:08:55: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:14: #4 Write output xls file... SRX013080.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:14: #4 Write peak in narrowPeak format file... SRX013080.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:14: #4 Write summits bed file... SRX013080.20_summits.bed INFO @ Tue, 21 Apr 2015 12:09:14: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:09:17: #4 Write output xls file... SRX013080.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:17: #4 Write peak in narrowPeak format file... SRX013080.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:17: #4 Write summits bed file... SRX013080.10_summits.bed INFO @ Tue, 21 Apr 2015 12:09:17: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (485 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:09:18: #4 Write output xls file... SRX013080.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:18: #4 Write peak in narrowPeak format file... SRX013080.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:18: #4 Write summits bed file... SRX013080.05_summits.bed INFO @ Tue, 21 Apr 2015 12:09:18: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (663 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。