Job ID = 2161312 sra ファイルのダウンロード中... Completed: 240379K bytes transferred in 5 seconds (335396K 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 35366 0 35366 0 0 49991 0 --:--:-- --:--:-- --:--:-- 68538 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 12924744 spots for /home/okishinya/chipatlas/results/dm3/SRX017466/SRR037523.sra Written 12924744 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: 00:03:37 12924744 reads; of these: 12924744 (100.00%) were unpaired; of these: 2807089 (21.72%) aligned 0 times 7496872 (58.00%) aligned exactly 1 time 2620783 (20.28%) aligned >1 times 78.28% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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] 1866294 / 10117655 = 0.1845 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 12:23:43: # Command line: callpeak -t SRX017466.bam -f BAM -g dm -n SRX017466.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX017466.20 # format = BAM # ChIP-seq file = ['SRX017466.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 12:23:43: # Command line: callpeak -t SRX017466.bam -f BAM -g dm -n SRX017466.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX017466.05 # format = BAM # ChIP-seq file = ['SRX017466.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 12:23:43: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:23:43: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:23:43: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:23:43: # Command line: callpeak -t SRX017466.bam -f BAM -g dm -n SRX017466.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX017466.10 # format = BAM # ChIP-seq file = ['SRX017466.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 12:23:43: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:23:43: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:23:43: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:23:48: 1000000 INFO @ Tue, 21 Apr 2015 12:23:48: 1000000 INFO @ Tue, 21 Apr 2015 12:23:48: 1000000 INFO @ Tue, 21 Apr 2015 12:23:53: 2000000 INFO @ Tue, 21 Apr 2015 12:23:53: 2000000 INFO @ Tue, 21 Apr 2015 12:23:53: 2000000 INFO @ Tue, 21 Apr 2015 12:23:58: 3000000 INFO @ Tue, 21 Apr 2015 12:23:58: 3000000 INFO @ Tue, 21 Apr 2015 12:23:59: 3000000 INFO @ Tue, 21 Apr 2015 12:24:03: 4000000 INFO @ Tue, 21 Apr 2015 12:24:04: 4000000 INFO @ Tue, 21 Apr 2015 12:24:04: 4000000 INFO @ Tue, 21 Apr 2015 12:24:09: 5000000 INFO @ Tue, 21 Apr 2015 12:24:09: 5000000 INFO @ Tue, 21 Apr 2015 12:24:09: 5000000 INFO @ Tue, 21 Apr 2015 12:24:14: 6000000 INFO @ Tue, 21 Apr 2015 12:24:14: 6000000 INFO @ Tue, 21 Apr 2015 12:24:15: 6000000 INFO @ Tue, 21 Apr 2015 12:24:19: 7000000 INFO @ Tue, 21 Apr 2015 12:24:20: 7000000 INFO @ Tue, 21 Apr 2015 12:24:21: 7000000 INFO @ Tue, 21 Apr 2015 12:24:24: 8000000 INFO @ Tue, 21 Apr 2015 12:24:25: 8000000 INFO @ Tue, 21 Apr 2015 12:24:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:24:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:24:25: #1 total tags in treatment: 8251361 INFO @ Tue, 21 Apr 2015 12:24:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:24:25: #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 12:24:26: 8000000 INFO @ Tue, 21 Apr 2015 12:24:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:24:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:24:27: #1 total tags in treatment: 8251361 INFO @ Tue, 21 Apr 2015 12:24:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:24:27: #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 12:24:27: #1 tags after filtering in treatment: 8250918 INFO @ Tue, 21 Apr 2015 12:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:24:27: #1 finished! INFO @ Tue, 21 Apr 2015 12:24:27: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:24:28: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:24:28: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:24:28: #1 total tags in treatment: 8251361 INFO @ Tue, 21 Apr 2015 12:24:28: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:24:28: #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 12:24:28: #1 tags after filtering in treatment: 8250918 INFO @ Tue, 21 Apr 2015 12:24:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:24:28: #1 finished! INFO @ Tue, 21 Apr 2015 12:24:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:24:28: #2 number of paired peaks: 232 WARNING @ Tue, 21 Apr 2015 12:24:28: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Tue, 21 Apr 2015 12:24:28: start model_add_line... INFO @ Tue, 21 Apr 2015 12:24:29: #1 tags after filtering in treatment: 8250918 INFO @ Tue, 21 Apr 2015 12:24:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:24:29: #1 finished! INFO @ Tue, 21 Apr 2015 12:24:29: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:24:30: #2 number of paired peaks: 232 WARNING @ Tue, 21 Apr 2015 12:24:30: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Tue, 21 Apr 2015 12:24:30: start model_add_line... INFO @ Tue, 21 Apr 2015 12:24:30: start X-correlation... INFO @ Tue, 21 Apr 2015 12:24:30: end of X-cor INFO @ Tue, 21 Apr 2015 12:24:30: #2 finished! INFO @ Tue, 21 Apr 2015 12:24:30: #2 predicted fragment length is 47 bps INFO @ Tue, 21 Apr 2015 12:24:30: #2 alternative fragment length(s) may be 47 bps INFO @ Tue, 21 Apr 2015 12:24:30: #2.2 Generate R script for model : SRX017466.05_model.r WARNING @ Tue, 21 Apr 2015 12:24:30: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:24:30: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Tue, 21 Apr 2015 12:24:30: #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 12:24:30: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:24:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:24:31: #2 number of paired peaks: 232 WARNING @ Tue, 21 Apr 2015 12:24:31: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Tue, 21 Apr 2015 12:24:31: start model_add_line... INFO @ Tue, 21 Apr 2015 12:24:31: start X-correlation... INFO @ Tue, 21 Apr 2015 12:24:31: end of X-cor INFO @ Tue, 21 Apr 2015 12:24:31: #2 finished! INFO @ Tue, 21 Apr 2015 12:24:31: #2 predicted fragment length is 47 bps INFO @ Tue, 21 Apr 2015 12:24:31: #2 alternative fragment length(s) may be 47 bps INFO @ Tue, 21 Apr 2015 12:24:31: #2.2 Generate R script for model : SRX017466.10_model.r WARNING @ Tue, 21 Apr 2015 12:24:31: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:24:31: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Tue, 21 Apr 2015 12:24:31: #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 12:24:31: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:24:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:24:32: start X-correlation... INFO @ Tue, 21 Apr 2015 12:24:32: end of X-cor INFO @ Tue, 21 Apr 2015 12:24:32: #2 finished! INFO @ Tue, 21 Apr 2015 12:24:32: #2 predicted fragment length is 47 bps INFO @ Tue, 21 Apr 2015 12:24:32: #2 alternative fragment length(s) may be 47 bps INFO @ Tue, 21 Apr 2015 12:24:32: #2.2 Generate R script for model : SRX017466.20_model.r WARNING @ Tue, 21 Apr 2015 12:24:33: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:24:33: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Tue, 21 Apr 2015 12:24:33: #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 12:24:33: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:24:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:25:17: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:25:19: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:25:19: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:25:50: #4 Write output xls file... SRX017466.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:25:50: #4 Write peak in narrowPeak format file... SRX017466.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:25:50: #4 Write summits bed file... SRX017466.20_summits.bed INFO @ Tue, 21 Apr 2015 12:25:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (663 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:25:52: #4 Write output xls file... SRX017466.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:25:52: #4 Write peak in narrowPeak format file... SRX017466.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:25:52: #4 Write summits bed file... SRX017466.10_summits.bed INFO @ Tue, 21 Apr 2015 12:25:52: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1401 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:25:53: #4 Write output xls file... SRX017466.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:25:53: #4 Write peak in narrowPeak format file... SRX017466.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:25:53: #4 Write summits bed file... SRX017466.05_summits.bed INFO @ Tue, 21 Apr 2015 12:25:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2918 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。