Job ID = 2161219 sra ファイルのダウンロード中... Completed: 280002K bytes transferred in 5 seconds (386692K 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 --:--:-- --:--:-- --:--:-- 0 101 5467 0 5467 0 0 9909 0 --:--:-- --:--:-- --:--:-- 15144 100 34477 0 34477 0 0 46456 0 --:--:-- --:--:-- --:--:-- 62571 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 10801724 spots for /home/okishinya/chipatlas/results/dm3/SRX013067/SRR030333.sra Written 10801724 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 10801724 reads; of these: 10801724 (100.00%) were unpaired; of these: 7318691 (67.75%) aligned 0 times 3244815 (30.04%) aligned exactly 1 time 238218 (2.21%) aligned >1 times 32.25% 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] 561629 / 3483033 = 0.1612 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 12:06:01: # Command line: callpeak -t SRX013067.bam -f BAM -g dm -n SRX013067.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013067.10 # format = BAM # ChIP-seq file = ['SRX013067.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 12:06:01: # Command line: callpeak -t SRX013067.bam -f BAM -g dm -n SRX013067.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013067.05 # format = BAM # ChIP-seq file = ['SRX013067.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 12:06:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:06:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:06:01: # Command line: callpeak -t SRX013067.bam -f BAM -g dm -n SRX013067.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013067.20 # format = BAM # ChIP-seq file = ['SRX013067.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 12:06:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:06:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:06:01: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:06:01: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:06:06: 1000000 INFO @ Tue, 21 Apr 2015 12:06:07: 1000000 INFO @ Tue, 21 Apr 2015 12:06:07: 1000000 INFO @ Tue, 21 Apr 2015 12:06:12: 2000000 INFO @ Tue, 21 Apr 2015 12:06:14: 2000000 INFO @ Tue, 21 Apr 2015 12:06:14: 2000000 INFO @ Tue, 21 Apr 2015 12:06:18: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:06:18: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:06:18: #1 total tags in treatment: 2921404 INFO @ Tue, 21 Apr 2015 12:06:18: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:06:18: #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 12:06:18: #1 tags after filtering in treatment: 2920655 INFO @ Tue, 21 Apr 2015 12:06:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:06:18: #1 finished! INFO @ Tue, 21 Apr 2015 12:06:18: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:06:19: #2 number of paired peaks: 1929 INFO @ Tue, 21 Apr 2015 12:06:19: start model_add_line... INFO @ Tue, 21 Apr 2015 12:06:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:06:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:06:21: #1 total tags in treatment: 2921404 INFO @ Tue, 21 Apr 2015 12:06:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:06:21: #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 12:06:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:06:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:06:21: #1 total tags in treatment: 2921404 INFO @ Tue, 21 Apr 2015 12:06:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:06:21: #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 12:06:21: #1 tags after filtering in treatment: 2920655 INFO @ Tue, 21 Apr 2015 12:06:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:06:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:06:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:06:21: #1 tags after filtering in treatment: 2920655 INFO @ Tue, 21 Apr 2015 12:06:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:06:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:06:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:06:22: #2 number of paired peaks: 1929 INFO @ Tue, 21 Apr 2015 12:06:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:06:22: #2 number of paired peaks: 1929 INFO @ Tue, 21 Apr 2015 12:06:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:06:23: start X-correlation... INFO @ Tue, 21 Apr 2015 12:06:23: end of X-cor INFO @ Tue, 21 Apr 2015 12:06:23: #2 finished! INFO @ Tue, 21 Apr 2015 12:06:23: #2 predicted fragment length is 59 bps INFO @ Tue, 21 Apr 2015 12:06:23: #2 alternative fragment length(s) may be 4,59 bps INFO @ Tue, 21 Apr 2015 12:06:23: #2.2 Generate R script for model : SRX013067.20_model.r WARNING @ Tue, 21 Apr 2015 12:06:23: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:06:23: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Tue, 21 Apr 2015 12:06:23: #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 12:06:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:06:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:06:26: start X-correlation... INFO @ Tue, 21 Apr 2015 12:06:26: end of X-cor INFO @ Tue, 21 Apr 2015 12:06:26: #2 finished! INFO @ Tue, 21 Apr 2015 12:06:26: #2 predicted fragment length is 59 bps INFO @ Tue, 21 Apr 2015 12:06:26: #2 alternative fragment length(s) may be 4,59 bps INFO @ Tue, 21 Apr 2015 12:06:26: #2.2 Generate R script for model : SRX013067.10_model.r WARNING @ Tue, 21 Apr 2015 12:06:26: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:06:26: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Tue, 21 Apr 2015 12:06:26: #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 12:06:26: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:06:26: start X-correlation... INFO @ Tue, 21 Apr 2015 12:06:26: end of X-cor INFO @ Tue, 21 Apr 2015 12:06:26: #2 finished! INFO @ Tue, 21 Apr 2015 12:06:26: #2 predicted fragment length is 59 bps INFO @ Tue, 21 Apr 2015 12:06:26: #2 alternative fragment length(s) may be 4,59 bps INFO @ Tue, 21 Apr 2015 12:06:26: #2.2 Generate R script for model : SRX013067.05_model.r WARNING @ Tue, 21 Apr 2015 12:06:26: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:06:26: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Tue, 21 Apr 2015 12:06:26: #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 12:06:26: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:06:40: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:06:43: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:06:43: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:06:51: #4 Write output xls file... SRX013067.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:06:51: #4 Write peak in narrowPeak format file... SRX013067.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:06:51: #4 Write summits bed file... SRX013067.20_summits.bed INFO @ Tue, 21 Apr 2015 12:06:51: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (25 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:06:56: #4 Write output xls file... SRX013067.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:06:56: #4 Write peak in narrowPeak format file... SRX013067.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:06:56: #4 Write summits bed file... SRX013067.10_summits.bed INFO @ Tue, 21 Apr 2015 12:06:56: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:06:57: #4 Write output xls file... SRX013067.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:06:57: #4 Write peak in narrowPeak format file... SRX013067.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:06:57: #4 Write summits bed file... SRX013067.05_summits.bed INFO @ Tue, 21 Apr 2015 12:06:57: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (2491 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。