Job ID = 2236899 sra ファイルのダウンロード中... Completed: 384450K bytes transferred in 6 seconds (475439K 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 35722 0 35722 0 0 46750 0 --:--:-- --:--:-- --:--:-- 62451 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 17659150 spots for /home/okishinya/chipatlas/results/ce10/SRX063960/SRR210888.sra Written 17659150 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: 00:03:36 17659150 reads; of these: 17659150 (100.00%) were unpaired; of these: 1071524 (6.07%) aligned 0 times 13654731 (77.32%) aligned exactly 1 time 2932895 (16.61%) aligned >1 times 93.93% overall alignment rate Time searching: 00:03:36 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: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 8207728 / 16587626 = 0.4948 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 11:19:44: # Command line: callpeak -t SRX063960.bam -f BAM -g ce -n SRX063960.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX063960.20 # format = BAM # ChIP-seq file = ['SRX063960.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 11:19:44: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:19:44: # Command line: callpeak -t SRX063960.bam -f BAM -g ce -n SRX063960.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX063960.10 # format = BAM # ChIP-seq file = ['SRX063960.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 11:19:44: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:19:44: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:19:44: # Command line: callpeak -t SRX063960.bam -f BAM -g ce -n SRX063960.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX063960.05 # format = BAM # ChIP-seq file = ['SRX063960.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 11:19:44: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:19:44: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:19:44: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:19:50: 1000000 INFO @ Thu, 30 Apr 2015 11:19:50: 1000000 INFO @ Thu, 30 Apr 2015 11:19:50: 1000000 INFO @ Thu, 30 Apr 2015 11:19:55: 2000000 INFO @ Thu, 30 Apr 2015 11:19:56: 2000000 INFO @ Thu, 30 Apr 2015 11:19:56: 2000000 INFO @ Thu, 30 Apr 2015 11:20:01: 3000000 INFO @ Thu, 30 Apr 2015 11:20:02: 3000000 INFO @ Thu, 30 Apr 2015 11:20:02: 3000000 INFO @ Thu, 30 Apr 2015 11:20:06: 4000000 INFO @ Thu, 30 Apr 2015 11:20:08: 4000000 INFO @ Thu, 30 Apr 2015 11:20:08: 4000000 INFO @ Thu, 30 Apr 2015 11:20:12: 5000000 INFO @ Thu, 30 Apr 2015 11:20:13: 5000000 INFO @ Thu, 30 Apr 2015 11:20:13: 5000000 INFO @ Thu, 30 Apr 2015 11:20:18: 6000000 INFO @ Thu, 30 Apr 2015 11:20:19: 6000000 INFO @ Thu, 30 Apr 2015 11:20:19: 6000000 INFO @ Thu, 30 Apr 2015 11:20:23: 7000000 INFO @ Thu, 30 Apr 2015 11:20:26: 7000000 INFO @ Thu, 30 Apr 2015 11:20:26: 7000000 INFO @ Thu, 30 Apr 2015 11:20:30: 8000000 INFO @ Thu, 30 Apr 2015 11:20:32: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:20:32: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:20:32: #1 total tags in treatment: 8379898 INFO @ Thu, 30 Apr 2015 11:20:32: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:20:32: #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 11:20:33: 8000000 INFO @ Thu, 30 Apr 2015 11:20:33: 8000000 INFO @ Thu, 30 Apr 2015 11:20:34: #1 tags after filtering in treatment: 8379360 INFO @ Thu, 30 Apr 2015 11:20:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:20:34: #1 finished! INFO @ Thu, 30 Apr 2015 11:20:34: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:20:35: #2 number of paired peaks: 579 WARNING @ Thu, 30 Apr 2015 11:20:35: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Thu, 30 Apr 2015 11:20:35: start model_add_line... INFO @ Thu, 30 Apr 2015 11:20:36: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:20:36: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:20:36: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:20:36: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:20:36: #1 total tags in treatment: 8379898 INFO @ Thu, 30 Apr 2015 11:20:36: #1 total tags in treatment: 8379898 INFO @ Thu, 30 Apr 2015 11:20:36: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:20:36: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:20:36: #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 11:20:36: #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 11:20:38: #1 tags after filtering in treatment: 8379360 INFO @ Thu, 30 Apr 2015 11:20:38: #1 tags after filtering in treatment: 8379360 INFO @ Thu, 30 Apr 2015 11:20:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:20:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:20:38: #1 finished! INFO @ Thu, 30 Apr 2015 11:20:38: #1 finished! INFO @ Thu, 30 Apr 2015 11:20:38: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:20:38: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:20:39: #2 number of paired peaks: 579 WARNING @ Thu, 30 Apr 2015 11:20:39: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Thu, 30 Apr 2015 11:20:39: start model_add_line... INFO @ Thu, 30 Apr 2015 11:20:39: #2 number of paired peaks: 579 WARNING @ Thu, 30 Apr 2015 11:20:39: Fewer paired peaks (579) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 579 pairs to build model! INFO @ Thu, 30 Apr 2015 11:20:39: start model_add_line... INFO @ Thu, 30 Apr 2015 11:20:42: start X-correlation... INFO @ Thu, 30 Apr 2015 11:20:42: end of X-cor INFO @ Thu, 30 Apr 2015 11:20:42: #2 finished! INFO @ Thu, 30 Apr 2015 11:20:42: #2 predicted fragment length is 41 bps INFO @ Thu, 30 Apr 2015 11:20:42: #2 alternative fragment length(s) may be 3,41,574 bps INFO @ Thu, 30 Apr 2015 11:20:42: #2.2 Generate R script for model : SRX063960.05_model.r WARNING @ Thu, 30 Apr 2015 11:20:42: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:20:42: #2 You may need to consider one of the other alternative d(s): 3,41,574 WARNING @ Thu, 30 Apr 2015 11:20:42: #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 11:20:42: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:20:46: start X-correlation... INFO @ Thu, 30 Apr 2015 11:20:46: end of X-cor INFO @ Thu, 30 Apr 2015 11:20:46: #2 finished! INFO @ Thu, 30 Apr 2015 11:20:46: #2 predicted fragment length is 41 bps INFO @ Thu, 30 Apr 2015 11:20:46: #2 alternative fragment length(s) may be 3,41,574 bps INFO @ Thu, 30 Apr 2015 11:20:46: #2.2 Generate R script for model : SRX063960.20_model.r WARNING @ Thu, 30 Apr 2015 11:20:46: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:20:46: #2 You may need to consider one of the other alternative d(s): 3,41,574 WARNING @ Thu, 30 Apr 2015 11:20:46: #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 11:20:46: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:20:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:20:46: start X-correlation... INFO @ Thu, 30 Apr 2015 11:20:46: end of X-cor INFO @ Thu, 30 Apr 2015 11:20:46: #2 finished! INFO @ Thu, 30 Apr 2015 11:20:46: #2 predicted fragment length is 41 bps INFO @ Thu, 30 Apr 2015 11:20:46: #2 alternative fragment length(s) may be 3,41,574 bps INFO @ Thu, 30 Apr 2015 11:20:46: #2.2 Generate R script for model : SRX063960.10_model.r WARNING @ Thu, 30 Apr 2015 11:20:46: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:20:46: #2 You may need to consider one of the other alternative d(s): 3,41,574 WARNING @ Thu, 30 Apr 2015 11:20:46: #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 11:20:46: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:20:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:21:31: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:21:31: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:21:31: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:22:04: #4 Write output xls file... SRX063960.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:22:04: #4 Write peak in narrowPeak format file... SRX063960.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:22:04: #4 Write summits bed file... SRX063960.20_summits.bed INFO @ Thu, 30 Apr 2015 11:22:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (193 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:22:04: #4 Write output xls file... SRX063960.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:22:04: #4 Write peak in narrowPeak format file... SRX063960.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:22:04: #4 Write summits bed file... SRX063960.10_summits.bed INFO @ Thu, 30 Apr 2015 11:22:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (528 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:22:07: #4 Write output xls file... SRX063960.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:22:07: #4 Write peak in narrowPeak format file... SRX063960.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:22:08: #4 Write summits bed file... SRX063960.05_summits.bed INFO @ Thu, 30 Apr 2015 11:22:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (846 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。