Job ID = 2162162 sra ファイルのダウンロード中... Completed: 85412K bytes transferred in 4 seconds (165861K 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 35441 0 35441 0 0 50399 0 --:--:-- --:--:-- --:--:-- 69356 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 4432677 spots for /home/okishinya/chipatlas/results/dm3/SRX050599/SRR139081.sra Written 4432677 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: 00:01:11 4432677 reads; of these: 4432677 (100.00%) were unpaired; of these: 168660 (3.80%) aligned 0 times 3330365 (75.13%) aligned exactly 1 time 933652 (21.06%) aligned >1 times 96.20% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 112386 / 4264017 = 0.0264 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 13:33:25: # Command line: callpeak -t SRX050599.bam -f BAM -g dm -n SRX050599.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX050599.10 # format = BAM # ChIP-seq file = ['SRX050599.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 13:33:25: # Command line: callpeak -t SRX050599.bam -f BAM -g dm -n SRX050599.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX050599.05 # format = BAM # ChIP-seq file = ['SRX050599.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 13:33:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:33:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:33:25: # Command line: callpeak -t SRX050599.bam -f BAM -g dm -n SRX050599.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX050599.20 # format = BAM # ChIP-seq file = ['SRX050599.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 13:33:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:33:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:33:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:33:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:33:31: 1000000 INFO @ Tue, 21 Apr 2015 13:33:31: 1000000 INFO @ Tue, 21 Apr 2015 13:33:31: 1000000 INFO @ Tue, 21 Apr 2015 13:33:37: 2000000 INFO @ Tue, 21 Apr 2015 13:33:37: 2000000 INFO @ Tue, 21 Apr 2015 13:33:37: 2000000 INFO @ Tue, 21 Apr 2015 13:33:42: 3000000 INFO @ Tue, 21 Apr 2015 13:33:43: 3000000 INFO @ Tue, 21 Apr 2015 13:33:43: 3000000 INFO @ Tue, 21 Apr 2015 13:33:48: 4000000 INFO @ Tue, 21 Apr 2015 13:33:48: 4000000 INFO @ Tue, 21 Apr 2015 13:33:48: 4000000 INFO @ Tue, 21 Apr 2015 13:33:48: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:33:48: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:33:48: #1 total tags in treatment: 4151631 INFO @ Tue, 21 Apr 2015 13:33:48: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:33:48: #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 13:33:49: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:33:49: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:33:49: #1 total tags in treatment: 4151631 INFO @ Tue, 21 Apr 2015 13:33:49: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:33:49: #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 13:33:49: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:33:49: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:33:49: #1 total tags in treatment: 4151631 INFO @ Tue, 21 Apr 2015 13:33:49: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:33:49: #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 13:33:49: #1 tags after filtering in treatment: 4151570 INFO @ Tue, 21 Apr 2015 13:33:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:33:49: #1 finished! INFO @ Tue, 21 Apr 2015 13:33:49: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:33:50: #1 tags after filtering in treatment: 4151570 INFO @ Tue, 21 Apr 2015 13:33:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:33:50: #1 finished! INFO @ Tue, 21 Apr 2015 13:33:50: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:33:50: #1 tags after filtering in treatment: 4151570 INFO @ Tue, 21 Apr 2015 13:33:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:33:50: #1 finished! INFO @ Tue, 21 Apr 2015 13:33:50: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:33:50: #2 number of paired peaks: 151 WARNING @ Tue, 21 Apr 2015 13:33:50: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Tue, 21 Apr 2015 13:33:50: start model_add_line... INFO @ Tue, 21 Apr 2015 13:33:51: #2 number of paired peaks: 151 WARNING @ Tue, 21 Apr 2015 13:33:51: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Tue, 21 Apr 2015 13:33:51: start model_add_line... INFO @ Tue, 21 Apr 2015 13:33:51: start X-correlation... INFO @ Tue, 21 Apr 2015 13:33:51: #2 number of paired peaks: 151 WARNING @ Tue, 21 Apr 2015 13:33:51: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Tue, 21 Apr 2015 13:33:51: start model_add_line... INFO @ Tue, 21 Apr 2015 13:33:51: end of X-cor INFO @ Tue, 21 Apr 2015 13:33:51: #2 finished! INFO @ Tue, 21 Apr 2015 13:33:51: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 13:33:51: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 13:33:51: #2.2 Generate R script for model : SRX050599.20_model.r WARNING @ Tue, 21 Apr 2015 13:33:51: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:33:51: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 13:33:51: #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 13:33:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:33:51: start X-correlation... INFO @ Tue, 21 Apr 2015 13:33:51: end of X-cor INFO @ Tue, 21 Apr 2015 13:33:51: #2 finished! INFO @ Tue, 21 Apr 2015 13:33:51: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 13:33:51: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 13:33:51: #2.2 Generate R script for model : SRX050599.05_model.r WARNING @ Tue, 21 Apr 2015 13:33:51: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:33:51: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 13:33:51: #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 13:33:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:33:51: start X-correlation... INFO @ Tue, 21 Apr 2015 13:33:51: end of X-cor INFO @ Tue, 21 Apr 2015 13:33:51: #2 finished! INFO @ Tue, 21 Apr 2015 13:33:51: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 13:33:51: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 13:33:51: #2.2 Generate R script for model : SRX050599.10_model.r WARNING @ Tue, 21 Apr 2015 13:33:51: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:33:51: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 13:33:51: #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 13:33:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:34:14: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:34:15: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:34:16: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:34:32: #4 Write output xls file... SRX050599.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:34:32: #4 Write peak in narrowPeak format file... SRX050599.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:34:32: #4 Write summits bed file... SRX050599.05_summits.bed INFO @ Tue, 21 Apr 2015 13:34:32: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (862 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:34:33: #4 Write output xls file... SRX050599.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:34:33: #4 Write peak in narrowPeak format file... SRX050599.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:34:33: #4 Write summits bed file... SRX050599.20_summits.bed INFO @ Tue, 21 Apr 2015 13:34:33: 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 13:34:33: #4 Write output xls file... SRX050599.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:34:33: #4 Write peak in narrowPeak format file... SRX050599.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:34:33: #4 Write summits bed file... SRX050599.10_summits.bed INFO @ Tue, 21 Apr 2015 13:34:33: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (405 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。