Job ID = 2237053 sra ファイルのダウンロード中... Completed: 372644K bytes transferred in 8 seconds (375830K 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 11300 0 11300 0 0 20924 0 --:--:-- --:--:-- --:--:-- 32378 100 36880 0 36880 0 0 50534 0 --:--:-- --:--:-- --:--:-- 68423 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 12621794 spots for /home/okishinya/chipatlas/results/ce10/SRX094474/SRR340086.sra Written 12621794 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: 00:01:50 12621794 reads; of these: 12621794 (100.00%) were unpaired; of these: 5472346 (43.36%) aligned 0 times 5956143 (47.19%) aligned exactly 1 time 1193305 (9.45%) aligned >1 times 56.64% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 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] 313939 / 7149448 = 0.0439 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 11:29:07: # Command line: callpeak -t SRX094474.bam -f BAM -g ce -n SRX094474.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX094474.05 # format = BAM # ChIP-seq file = ['SRX094474.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 11:29:07: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:07: # Command line: callpeak -t SRX094474.bam -f BAM -g ce -n SRX094474.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX094474.20 # format = BAM # ChIP-seq file = ['SRX094474.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 11:29:07: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:07: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:07: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:07: # Command line: callpeak -t SRX094474.bam -f BAM -g ce -n SRX094474.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX094474.10 # format = BAM # ChIP-seq file = ['SRX094474.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 11:29:07: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:07: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:13: 1000000 INFO @ Thu, 30 Apr 2015 11:29:13: 1000000 INFO @ Thu, 30 Apr 2015 11:29:13: 1000000 INFO @ Thu, 30 Apr 2015 11:29:18: 2000000 INFO @ Thu, 30 Apr 2015 11:29:19: 2000000 INFO @ Thu, 30 Apr 2015 11:29:19: 2000000 INFO @ Thu, 30 Apr 2015 11:29:24: 3000000 INFO @ Thu, 30 Apr 2015 11:29:24: 3000000 INFO @ Thu, 30 Apr 2015 11:29:24: 3000000 INFO @ Thu, 30 Apr 2015 11:29:29: 4000000 INFO @ Thu, 30 Apr 2015 11:29:30: 4000000 INFO @ Thu, 30 Apr 2015 11:29:30: 4000000 INFO @ Thu, 30 Apr 2015 11:29:35: 5000000 INFO @ Thu, 30 Apr 2015 11:29:35: 5000000 INFO @ Thu, 30 Apr 2015 11:29:35: 5000000 INFO @ Thu, 30 Apr 2015 11:29:40: 6000000 INFO @ Thu, 30 Apr 2015 11:29:41: 6000000 INFO @ Thu, 30 Apr 2015 11:29:41: 6000000 INFO @ Thu, 30 Apr 2015 11:29:45: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:29:45: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:29:45: #1 total tags in treatment: 6835509 INFO @ Thu, 30 Apr 2015 11:29:45: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:29:45: #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 11:29:46: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:29:46: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:29:46: #1 total tags in treatment: 6835509 INFO @ Thu, 30 Apr 2015 11:29:46: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:29:46: #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 11:29:46: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:29:46: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:29:46: #1 total tags in treatment: 6835509 INFO @ Thu, 30 Apr 2015 11:29:46: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:29:46: #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 11:29:46: #1 tags after filtering in treatment: 6835246 INFO @ Thu, 30 Apr 2015 11:29:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:29:46: #1 finished! INFO @ Thu, 30 Apr 2015 11:29:46: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:29:47: #1 tags after filtering in treatment: 6835246 INFO @ Thu, 30 Apr 2015 11:29:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:29:47: #1 finished! INFO @ Thu, 30 Apr 2015 11:29:47: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:29:47: #1 tags after filtering in treatment: 6835246 INFO @ Thu, 30 Apr 2015 11:29:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:29:47: #1 finished! INFO @ Thu, 30 Apr 2015 11:29:47: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:29:48: #2 number of paired peaks: 300 WARNING @ Thu, 30 Apr 2015 11:29:48: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Thu, 30 Apr 2015 11:29:48: start model_add_line... INFO @ Thu, 30 Apr 2015 11:29:48: #2 number of paired peaks: 300 WARNING @ Thu, 30 Apr 2015 11:29:48: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Thu, 30 Apr 2015 11:29:48: start model_add_line... INFO @ Thu, 30 Apr 2015 11:29:48: #2 number of paired peaks: 300 WARNING @ Thu, 30 Apr 2015 11:29:48: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Thu, 30 Apr 2015 11:29:48: start model_add_line... INFO @ Thu, 30 Apr 2015 11:29:51: start X-correlation... INFO @ Thu, 30 Apr 2015 11:29:51: end of X-cor INFO @ Thu, 30 Apr 2015 11:29:51: #2 finished! INFO @ Thu, 30 Apr 2015 11:29:51: #2 predicted fragment length is 35 bps INFO @ Thu, 30 Apr 2015 11:29:51: #2 alternative fragment length(s) may be 3,35,575,587 bps INFO @ Thu, 30 Apr 2015 11:29:51: #2.2 Generate R script for model : SRX094474.10_model.r WARNING @ Thu, 30 Apr 2015 11:29:51: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:29:51: #2 You may need to consider one of the other alternative d(s): 3,35,575,587 WARNING @ Thu, 30 Apr 2015 11:29:51: #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 11:29:51: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:29:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:29:51: start X-correlation... INFO @ Thu, 30 Apr 2015 11:29:51: end of X-cor INFO @ Thu, 30 Apr 2015 11:29:51: #2 finished! INFO @ Thu, 30 Apr 2015 11:29:51: #2 predicted fragment length is 35 bps INFO @ Thu, 30 Apr 2015 11:29:51: #2 alternative fragment length(s) may be 3,35,575,587 bps INFO @ Thu, 30 Apr 2015 11:29:51: #2.2 Generate R script for model : SRX094474.05_model.r WARNING @ Thu, 30 Apr 2015 11:29:51: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:29:51: #2 You may need to consider one of the other alternative d(s): 3,35,575,587 WARNING @ Thu, 30 Apr 2015 11:29:51: #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 11:29:51: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:29:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:29:52: start X-correlation... INFO @ Thu, 30 Apr 2015 11:29:52: end of X-cor INFO @ Thu, 30 Apr 2015 11:29:52: #2 finished! INFO @ Thu, 30 Apr 2015 11:29:52: #2 predicted fragment length is 35 bps INFO @ Thu, 30 Apr 2015 11:29:52: #2 alternative fragment length(s) may be 3,35,575,587 bps INFO @ Thu, 30 Apr 2015 11:29:52: #2.2 Generate R script for model : SRX094474.20_model.r WARNING @ Thu, 30 Apr 2015 11:29:52: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:29:52: #2 You may need to consider one of the other alternative d(s): 3,35,575,587 WARNING @ Thu, 30 Apr 2015 11:29:52: #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 11:29:52: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:29:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:30:27: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:30:28: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:30:30: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:30:54: #4 Write output xls file... SRX094474.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:30:54: #4 Write peak in narrowPeak format file... SRX094474.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:30:54: #4 Write summits bed file... SRX094474.20_summits.bed INFO @ Thu, 30 Apr 2015 11:30:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:30:54: #4 Write output xls file... SRX094474.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:30:54: #4 Write peak in narrowPeak format file... SRX094474.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:30:54: #4 Write summits bed file... SRX094474.10_summits.bed INFO @ Thu, 30 Apr 2015 11:30:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:30:58: #4 Write output xls file... SRX094474.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:30:58: #4 Write peak in narrowPeak format file... SRX094474.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:30:58: #4 Write summits bed file... SRX094474.05_summits.bed INFO @ Thu, 30 Apr 2015 11:30:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (462 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。