Job ID = 2161547 sra ファイルのダウンロード中... Completed: 8264569K bytes transferred in 65 seconds (1039309K 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 37082 0 37082 0 0 45349 0 --:--:-- --:--:-- --:--:-- 59236 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 13594243 spots for /home/okishinya/chipatlas/results/dm3/SRX027823/SRR067906.sra Written 13594243 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: 00:03:14 13594243 reads; of these: 13594243 (100.00%) were unpaired; of these: 4819376 (35.45%) aligned 0 times 6167508 (45.37%) aligned exactly 1 time 2607359 (19.18%) aligned >1 times 64.55% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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] 1035103 / 8774867 = 0.1180 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 12:51:22: # Command line: callpeak -t SRX027823.bam -f BAM -g dm -n SRX027823.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027823.10 # format = BAM # ChIP-seq file = ['SRX027823.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 12:51:22: # Command line: callpeak -t SRX027823.bam -f BAM -g dm -n SRX027823.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027823.05 # format = BAM # ChIP-seq file = ['SRX027823.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 12:51:22: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:51:22: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:51:22: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:51:22: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:51:22: # Command line: callpeak -t SRX027823.bam -f BAM -g dm -n SRX027823.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027823.20 # format = BAM # ChIP-seq file = ['SRX027823.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 12:51:22: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:51:22: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:51:28: 1000000 INFO @ Tue, 21 Apr 2015 12:51:28: 1000000 INFO @ Tue, 21 Apr 2015 12:51:28: 1000000 INFO @ Tue, 21 Apr 2015 12:51:34: 2000000 INFO @ Tue, 21 Apr 2015 12:51:34: 2000000 INFO @ Tue, 21 Apr 2015 12:51:34: 2000000 INFO @ Tue, 21 Apr 2015 12:51:40: 3000000 INFO @ Tue, 21 Apr 2015 12:51:40: 3000000 INFO @ Tue, 21 Apr 2015 12:51:40: 3000000 INFO @ Tue, 21 Apr 2015 12:51:45: 4000000 INFO @ Tue, 21 Apr 2015 12:51:45: 4000000 INFO @ Tue, 21 Apr 2015 12:51:46: 4000000 INFO @ Tue, 21 Apr 2015 12:51:51: 5000000 INFO @ Tue, 21 Apr 2015 12:51:51: 5000000 INFO @ Tue, 21 Apr 2015 12:51:52: 5000000 INFO @ Tue, 21 Apr 2015 12:51:56: 6000000 INFO @ Tue, 21 Apr 2015 12:51:57: 6000000 INFO @ Tue, 21 Apr 2015 12:51:58: 6000000 INFO @ Tue, 21 Apr 2015 12:52:02: 7000000 INFO @ Tue, 21 Apr 2015 12:52:03: 7000000 INFO @ Tue, 21 Apr 2015 12:52:03: 7000000 INFO @ Tue, 21 Apr 2015 12:52:06: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:52:06: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:52:06: #1 total tags in treatment: 7739764 INFO @ Tue, 21 Apr 2015 12:52:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:52:06: #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 12:52:07: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:52:07: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:52:07: #1 total tags in treatment: 7739764 INFO @ Tue, 21 Apr 2015 12:52:07: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:52:07: #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 12:52:08: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:52:08: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:52:08: #1 total tags in treatment: 7739764 INFO @ Tue, 21 Apr 2015 12:52:08: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:52:08: #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 12:52:08: #1 tags after filtering in treatment: 7739007 INFO @ Tue, 21 Apr 2015 12:52:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:52:08: #1 finished! INFO @ Tue, 21 Apr 2015 12:52:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:52:08: #1 tags after filtering in treatment: 7739007 INFO @ Tue, 21 Apr 2015 12:52:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:52:08: #1 finished! INFO @ Tue, 21 Apr 2015 12:52:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:52:09: #1 tags after filtering in treatment: 7739007 INFO @ Tue, 21 Apr 2015 12:52:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:52:09: #1 finished! INFO @ Tue, 21 Apr 2015 12:52:09: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:52:09: #2 number of paired peaks: 1572 INFO @ Tue, 21 Apr 2015 12:52:09: start model_add_line... INFO @ Tue, 21 Apr 2015 12:52:10: #2 number of paired peaks: 1572 INFO @ Tue, 21 Apr 2015 12:52:10: start model_add_line... INFO @ Tue, 21 Apr 2015 12:52:11: #2 number of paired peaks: 1572 INFO @ Tue, 21 Apr 2015 12:52:11: start model_add_line... INFO @ Tue, 21 Apr 2015 12:52:18: start X-correlation... INFO @ Tue, 21 Apr 2015 12:52:18: end of X-cor INFO @ Tue, 21 Apr 2015 12:52:18: #2 finished! INFO @ Tue, 21 Apr 2015 12:52:18: #2 predicted fragment length is 62 bps INFO @ Tue, 21 Apr 2015 12:52:18: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 21 Apr 2015 12:52:18: #2.2 Generate R script for model : SRX027823.10_model.r WARNING @ Tue, 21 Apr 2015 12:52:18: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:52:18: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 21 Apr 2015 12:52:18: #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 12:52:18: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:52:19: start X-correlation... INFO @ Tue, 21 Apr 2015 12:52:19: end of X-cor INFO @ Tue, 21 Apr 2015 12:52:19: #2 finished! INFO @ Tue, 21 Apr 2015 12:52:19: #2 predicted fragment length is 62 bps INFO @ Tue, 21 Apr 2015 12:52:19: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 21 Apr 2015 12:52:19: #2.2 Generate R script for model : SRX027823.05_model.r WARNING @ Tue, 21 Apr 2015 12:52:19: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:52:19: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 21 Apr 2015 12:52:19: #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 12:52:19: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:52:20: start X-correlation... INFO @ Tue, 21 Apr 2015 12:52:20: end of X-cor INFO @ Tue, 21 Apr 2015 12:52:20: #2 finished! INFO @ Tue, 21 Apr 2015 12:52:20: #2 predicted fragment length is 62 bps INFO @ Tue, 21 Apr 2015 12:52:20: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 21 Apr 2015 12:52:20: #2.2 Generate R script for model : SRX027823.20_model.r WARNING @ Tue, 21 Apr 2015 12:52:20: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:52:20: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 21 Apr 2015 12:52:20: #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 12:52:20: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:52:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:52:59: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:53:01: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:53:04: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:53:32: #4 Write output xls file... SRX027823.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:53:32: #4 Write peak in narrowPeak format file... SRX027823.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:53:32: #4 Write summits bed file... SRX027823.05_summits.bed INFO @ Tue, 21 Apr 2015 12:53:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6965 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:53:33: #4 Write output xls file... SRX027823.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:53:33: #4 Write peak in narrowPeak format file... SRX027823.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:53:33: #4 Write summits bed file... SRX027823.10_summits.bed INFO @ Tue, 21 Apr 2015 12:53:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3727 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:53:36: #4 Write output xls file... SRX027823.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:53:36: #4 Write peak in narrowPeak format file... SRX027823.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:53:36: #4 Write summits bed file... SRX027823.20_summits.bed INFO @ Tue, 21 Apr 2015 12:53:36: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1246 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。