Job ID = 2237050 sra ファイルのダウンロード中... Completed: 126084K bytes transferred in 5 seconds (196769K 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 12759 0 12759 0 0 23816 0 --:--:-- --:--:-- --:--:-- 36982 100 38019 0 38019 0 0 52421 0 --:--:-- --:--:-- --:--:-- 71196 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 6268430 spots for /home/okishinya/chipatlas/results/ce10/SRX080105/SRR298925.sra Written 6268430 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: 00:00:28 6268430 reads; of these: 6268430 (100.00%) were unpaired; of these: 5481075 (87.44%) aligned 0 times 657434 (10.49%) aligned exactly 1 time 129921 (2.07%) aligned >1 times 12.56% overall alignment rate Time searching: 00:00:28 Overall time: 00:00:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 21447 / 787355 = 0.0272 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 @ Thu, 30 Apr 2015 11:25:47: # Command line: callpeak -t SRX080105.bam -f BAM -g ce -n SRX080105.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080105.10 # format = BAM # ChIP-seq file = ['SRX080105.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:25:47: # Command line: callpeak -t SRX080105.bam -f BAM -g ce -n SRX080105.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080105.05 # format = BAM # ChIP-seq file = ['SRX080105.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:25:47: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:47: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:47: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:47: # Command line: callpeak -t SRX080105.bam -f BAM -g ce -n SRX080105.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080105.20 # format = BAM # ChIP-seq file = ['SRX080105.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:25:47: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:47: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:47: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:51: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:51: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:51: #1 total tags in treatment: 765908 INFO @ Thu, 30 Apr 2015 11:25:51: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:25:51: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:51: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:51: #1 total tags in treatment: 765908 INFO @ Thu, 30 Apr 2015 11:25:51: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:25:51: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:51: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:51: #1 total tags in treatment: 765908 INFO @ Thu, 30 Apr 2015 11:25:51: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:25:51: #1 tags after filtering in treatment: 765900 INFO @ Thu, 30 Apr 2015 11:25:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:51: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:51: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:51: #1 tags after filtering in treatment: 765900 INFO @ Thu, 30 Apr 2015 11:25:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:51: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:51: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:51: #1 tags after filtering in treatment: 765900 INFO @ Thu, 30 Apr 2015 11:25:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:51: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:51: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:51: #2 number of paired peaks: 353 WARNING @ Thu, 30 Apr 2015 11:25:51: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:51: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:51: #2 number of paired peaks: 353 WARNING @ Thu, 30 Apr 2015 11:25:51: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:51: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:51: #2 number of paired peaks: 353 WARNING @ Thu, 30 Apr 2015 11:25:51: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:51: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:52: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:52: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:52: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:52: #2 predicted fragment length is 33 bps INFO @ Thu, 30 Apr 2015 11:25:52: #2 alternative fragment length(s) may be 33,139,224,252,334,388,427,576 bps INFO @ Thu, 30 Apr 2015 11:25:52: #2.2 Generate R script for model : SRX080105.20_model.r WARNING @ Thu, 30 Apr 2015 11:25:52: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:25:52: #2 You may need to consider one of the other alternative d(s): 33,139,224,252,334,388,427,576 WARNING @ Thu, 30 Apr 2015 11:25:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:25:52: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:52: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:52: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:52: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:52: #2 predicted fragment length is 33 bps INFO @ Thu, 30 Apr 2015 11:25:52: #2 alternative fragment length(s) may be 33,139,224,252,334,388,427,576 bps INFO @ Thu, 30 Apr 2015 11:25:52: #2.2 Generate R script for model : SRX080105.05_model.r WARNING @ Thu, 30 Apr 2015 11:25:52: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:25:52: #2 You may need to consider one of the other alternative d(s): 33,139,224,252,334,388,427,576 WARNING @ Thu, 30 Apr 2015 11:25:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:25:52: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:52: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:52: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:52: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:52: #2 predicted fragment length is 33 bps INFO @ Thu, 30 Apr 2015 11:25:52: #2 alternative fragment length(s) may be 33,139,224,252,334,388,427,576 bps INFO @ Thu, 30 Apr 2015 11:25:52: #2.2 Generate R script for model : SRX080105.10_model.r WARNING @ Thu, 30 Apr 2015 11:25:52: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:25:52: #2 You may need to consider one of the other alternative d(s): 33,139,224,252,334,388,427,576 WARNING @ Thu, 30 Apr 2015 11:25:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 11:25:52: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:56: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:56: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:56: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write output xls file... SRX080105.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write peak in narrowPeak format file... SRX080105.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write summits bed file... SRX080105.20_summits.bed INFO @ Thu, 30 Apr 2015 11:25:59: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write output xls file... SRX080105.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write peak in narrowPeak format file... SRX080105.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write summits bed file... SRX080105.10_summits.bed INFO @ Thu, 30 Apr 2015 11:25:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:59: #4 Write output xls file... SRX080105.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:00: #4 Write peak in narrowPeak format file... SRX080105.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:00: #4 Write summits bed file... SRX080105.05_summits.bed INFO @ Thu, 30 Apr 2015 11:26:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (93 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。