Job ID = 2236866 sra ファイルのダウンロード中... Completed: 393807K bytes transferred in 9 seconds (353136K 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 19274 0 19274 0 0 25275 0 --:--:-- --:--:-- --:--:-- 33695 100 34660 0 34660 0 0 45396 0 --:--:-- --:--:-- --:--:-- 60488 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 15638416 spots for /home/okishinya/chipatlas/results/ce10/SRX059242/SRR190682.sra Written 15638416 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: 00:02:20 15638416 reads; of these: 15638416 (100.00%) were unpaired; of these: 6938381 (44.37%) aligned 0 times 6913681 (44.21%) aligned exactly 1 time 1786354 (11.42%) aligned >1 times 55.63% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 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] 5407774 / 8700035 = 0.6216 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 11:15:08: # Command line: callpeak -t SRX059242.bam -f BAM -g ce -n SRX059242.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059242.20 # format = BAM # ChIP-seq file = ['SRX059242.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 11:15:08: # Command line: callpeak -t SRX059242.bam -f BAM -g ce -n SRX059242.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059242.05 # format = BAM # ChIP-seq file = ['SRX059242.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 11:15:08: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:15:08: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:15:08: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:15:08: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:15:08: # Command line: callpeak -t SRX059242.bam -f BAM -g ce -n SRX059242.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059242.10 # format = BAM # ChIP-seq file = ['SRX059242.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 11:15:08: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:15:08: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:15:14: 1000000 INFO @ Thu, 30 Apr 2015 11:15:14: 1000000 INFO @ Thu, 30 Apr 2015 11:15:14: 1000000 INFO @ Thu, 30 Apr 2015 11:15:20: 2000000 INFO @ Thu, 30 Apr 2015 11:15:20: 2000000 INFO @ Thu, 30 Apr 2015 11:15:20: 2000000 INFO @ Thu, 30 Apr 2015 11:15:26: 3000000 INFO @ Thu, 30 Apr 2015 11:15:26: 3000000 INFO @ Thu, 30 Apr 2015 11:15:27: 3000000 INFO @ Thu, 30 Apr 2015 11:15:27: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:15:27: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:15:27: #1 total tags in treatment: 3292261 INFO @ Thu, 30 Apr 2015 11:15:27: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:15:27: #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 11:15:28: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:15:28: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:15:28: #1 total tags in treatment: 3292261 INFO @ Thu, 30 Apr 2015 11:15:28: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:15:28: #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 11:15:28: #1 tags after filtering in treatment: 3291824 INFO @ Thu, 30 Apr 2015 11:15:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:15:28: #1 finished! INFO @ Thu, 30 Apr 2015 11:15:28: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:15:28: #1 tags after filtering in treatment: 3291824 INFO @ Thu, 30 Apr 2015 11:15:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:15:28: #1 finished! INFO @ Thu, 30 Apr 2015 11:15:28: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:15:28: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:15:28: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:15:28: #1 total tags in treatment: 3292261 INFO @ Thu, 30 Apr 2015 11:15:28: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:15:28: #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 11:15:29: #2 number of paired peaks: 810 WARNING @ Thu, 30 Apr 2015 11:15:29: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Thu, 30 Apr 2015 11:15:29: start model_add_line... INFO @ Thu, 30 Apr 2015 11:15:29: #2 number of paired peaks: 810 WARNING @ Thu, 30 Apr 2015 11:15:29: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Thu, 30 Apr 2015 11:15:29: start model_add_line... INFO @ Thu, 30 Apr 2015 11:15:29: #1 tags after filtering in treatment: 3291824 INFO @ Thu, 30 Apr 2015 11:15:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:15:29: #1 finished! INFO @ Thu, 30 Apr 2015 11:15:29: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:15:30: #2 number of paired peaks: 810 WARNING @ Thu, 30 Apr 2015 11:15:30: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Thu, 30 Apr 2015 11:15:30: start model_add_line... INFO @ Thu, 30 Apr 2015 11:15:34: start X-correlation... INFO @ Thu, 30 Apr 2015 11:15:34: end of X-cor INFO @ Thu, 30 Apr 2015 11:15:34: #2 finished! INFO @ Thu, 30 Apr 2015 11:15:34: #2 predicted fragment length is 37 bps INFO @ Thu, 30 Apr 2015 11:15:34: #2 alternative fragment length(s) may be 3,37 bps INFO @ Thu, 30 Apr 2015 11:15:34: #2.2 Generate R script for model : SRX059242.05_model.r WARNING @ Thu, 30 Apr 2015 11:15:34: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:15:34: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Thu, 30 Apr 2015 11:15:34: #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 11:15:34: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:15:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:15:34: start X-correlation... INFO @ Thu, 30 Apr 2015 11:15:34: end of X-cor INFO @ Thu, 30 Apr 2015 11:15:34: #2 finished! INFO @ Thu, 30 Apr 2015 11:15:34: #2 predicted fragment length is 37 bps INFO @ Thu, 30 Apr 2015 11:15:34: #2 alternative fragment length(s) may be 3,37 bps INFO @ Thu, 30 Apr 2015 11:15:34: #2.2 Generate R script for model : SRX059242.20_model.r WARNING @ Thu, 30 Apr 2015 11:15:34: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:15:34: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Thu, 30 Apr 2015 11:15:34: #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 11:15:34: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:15:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:15:35: start X-correlation... INFO @ Thu, 30 Apr 2015 11:15:35: end of X-cor INFO @ Thu, 30 Apr 2015 11:15:35: #2 finished! INFO @ Thu, 30 Apr 2015 11:15:35: #2 predicted fragment length is 37 bps INFO @ Thu, 30 Apr 2015 11:15:35: #2 alternative fragment length(s) may be 3,37 bps INFO @ Thu, 30 Apr 2015 11:15:35: #2.2 Generate R script for model : SRX059242.10_model.r WARNING @ Thu, 30 Apr 2015 11:15:35: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:15:35: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Thu, 30 Apr 2015 11:15:35: #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 11:15:35: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:15:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:15:54: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:15:54: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:15:54: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:16:07: #4 Write output xls file... SRX059242.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:16:07: #4 Write peak in narrowPeak format file... SRX059242.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:16:07: #4 Write summits bed file... SRX059242.20_summits.bed INFO @ Thu, 30 Apr 2015 11:16:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:16:07: #4 Write output xls file... SRX059242.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:16:07: #4 Write peak in narrowPeak format file... SRX059242.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:16:07: #4 Write summits bed file... SRX059242.10_summits.bed INFO @ Thu, 30 Apr 2015 11:16:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (468 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:16:08: #4 Write output xls file... SRX059242.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:16:08: #4 Write peak in narrowPeak format file... SRX059242.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:16:08: #4 Write summits bed file... SRX059242.05_summits.bed INFO @ Thu, 30 Apr 2015 11:16:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (862 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。