Job ID = 2237000 sra ファイルのダウンロード中... Completed: 280203K bytes transferred in 6 seconds (349962K 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 36736 0 36736 0 0 49953 0 --:--:-- --:--:-- --:--:-- 67529 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 16917825 spots for /home/okishinya/chipatlas/results/ce10/SRX076077/SRR275567.sra Written 16917825 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: 00:03:23 16917825 reads; of these: 16917825 (100.00%) were unpaired; of these: 265975 (1.57%) aligned 0 times 13670750 (80.81%) aligned exactly 1 time 2981100 (17.62%) aligned >1 times 98.43% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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] 2382187 / 16651850 = 0.1431 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 11:29:42: # Command line: callpeak -t SRX076077.bam -f BAM -g ce -n SRX076077.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX076077.05 # format = BAM # ChIP-seq file = ['SRX076077.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 11:29:42: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:42: # Command line: callpeak -t SRX076077.bam -f BAM -g ce -n SRX076077.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX076077.20 # format = BAM # ChIP-seq file = ['SRX076077.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 11:29:42: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:42: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:42: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:42: # Command line: callpeak -t SRX076077.bam -f BAM -g ce -n SRX076077.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX076077.10 # format = BAM # ChIP-seq file = ['SRX076077.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 11:29:42: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:29:42: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:29:46: 1000000 INFO @ Thu, 30 Apr 2015 11:29:47: 1000000 INFO @ Thu, 30 Apr 2015 11:29:47: 1000000 INFO @ Thu, 30 Apr 2015 11:29:51: 2000000 INFO @ Thu, 30 Apr 2015 11:29:52: 2000000 INFO @ Thu, 30 Apr 2015 11:29:52: 2000000 INFO @ Thu, 30 Apr 2015 11:29:56: 3000000 INFO @ Thu, 30 Apr 2015 11:29:57: 3000000 INFO @ Thu, 30 Apr 2015 11:29:57: 3000000 INFO @ Thu, 30 Apr 2015 11:30:01: 4000000 INFO @ Thu, 30 Apr 2015 11:30:01: 4000000 INFO @ Thu, 30 Apr 2015 11:30:02: 4000000 INFO @ Thu, 30 Apr 2015 11:30:06: 5000000 INFO @ Thu, 30 Apr 2015 11:30:06: 5000000 INFO @ Thu, 30 Apr 2015 11:30:07: 5000000 INFO @ Thu, 30 Apr 2015 11:30:10: 6000000 INFO @ Thu, 30 Apr 2015 11:30:11: 6000000 INFO @ Thu, 30 Apr 2015 11:30:12: 6000000 INFO @ Thu, 30 Apr 2015 11:30:15: 7000000 INFO @ Thu, 30 Apr 2015 11:30:16: 7000000 INFO @ Thu, 30 Apr 2015 11:30:17: 7000000 INFO @ Thu, 30 Apr 2015 11:30:20: 8000000 INFO @ Thu, 30 Apr 2015 11:30:21: 8000000 INFO @ Thu, 30 Apr 2015 11:30:22: 8000000 INFO @ Thu, 30 Apr 2015 11:30:25: 9000000 INFO @ Thu, 30 Apr 2015 11:30:26: 9000000 INFO @ Thu, 30 Apr 2015 11:30:27: 9000000 INFO @ Thu, 30 Apr 2015 11:30:29: 10000000 INFO @ Thu, 30 Apr 2015 11:30:31: 10000000 INFO @ Thu, 30 Apr 2015 11:30:32: 10000000 INFO @ Thu, 30 Apr 2015 11:30:34: 11000000 INFO @ Thu, 30 Apr 2015 11:30:36: 11000000 INFO @ Thu, 30 Apr 2015 11:30:38: 11000000 INFO @ Thu, 30 Apr 2015 11:30:39: 12000000 INFO @ Thu, 30 Apr 2015 11:30:41: 12000000 INFO @ Thu, 30 Apr 2015 11:30:43: 12000000 INFO @ Thu, 30 Apr 2015 11:30:44: 13000000 INFO @ Thu, 30 Apr 2015 11:30:45: 13000000 INFO @ Thu, 30 Apr 2015 11:30:48: 13000000 INFO @ Thu, 30 Apr 2015 11:30:49: 14000000 INFO @ Thu, 30 Apr 2015 11:30:50: 14000000 INFO @ Thu, 30 Apr 2015 11:30:50: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:30:50: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:30:50: #1 total tags in treatment: 14269663 INFO @ Thu, 30 Apr 2015 11:30:50: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:30:50: #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 11:30:52: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:30:52: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:30:52: #1 total tags in treatment: 14269663 INFO @ Thu, 30 Apr 2015 11:30:52: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:30:52: #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 11:30:53: 14000000 INFO @ Thu, 30 Apr 2015 11:30:53: #1 tags after filtering in treatment: 14268879 INFO @ Thu, 30 Apr 2015 11:30:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:30:53: #1 finished! INFO @ Thu, 30 Apr 2015 11:30:53: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:30:54: #1 tags after filtering in treatment: 14268879 INFO @ Thu, 30 Apr 2015 11:30:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:30:54: #1 finished! INFO @ Thu, 30 Apr 2015 11:30:54: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:30:54: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:30:54: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:30:54: #1 total tags in treatment: 14269663 INFO @ Thu, 30 Apr 2015 11:30:54: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:30:54: #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 11:30:56: #2 number of paired peaks: 273 WARNING @ Thu, 30 Apr 2015 11:30:56: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Thu, 30 Apr 2015 11:30:56: start model_add_line... INFO @ Thu, 30 Apr 2015 11:30:57: #2 number of paired peaks: 273 WARNING @ Thu, 30 Apr 2015 11:30:57: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Thu, 30 Apr 2015 11:30:57: start model_add_line... INFO @ Thu, 30 Apr 2015 11:30:57: #1 tags after filtering in treatment: 14268879 INFO @ Thu, 30 Apr 2015 11:30:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:30:57: #1 finished! INFO @ Thu, 30 Apr 2015 11:30:57: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:31:00: #2 number of paired peaks: 273 WARNING @ Thu, 30 Apr 2015 11:31:00: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Thu, 30 Apr 2015 11:31:00: start model_add_line... INFO @ Thu, 30 Apr 2015 11:31:00: start X-correlation... INFO @ Thu, 30 Apr 2015 11:31:00: end of X-cor INFO @ Thu, 30 Apr 2015 11:31:00: #2 finished! INFO @ Thu, 30 Apr 2015 11:31:00: #2 predicted fragment length is 34 bps INFO @ Thu, 30 Apr 2015 11:31:00: #2 alternative fragment length(s) may be 2,34,577 bps INFO @ Thu, 30 Apr 2015 11:31:00: #2.2 Generate R script for model : SRX076077.05_model.r WARNING @ Thu, 30 Apr 2015 11:31:00: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:31:00: #2 You may need to consider one of the other alternative d(s): 2,34,577 WARNING @ Thu, 30 Apr 2015 11:31:00: #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 11:31:00: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:31:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:31:01: start X-correlation... INFO @ Thu, 30 Apr 2015 11:31:01: end of X-cor INFO @ Thu, 30 Apr 2015 11:31:01: #2 finished! INFO @ Thu, 30 Apr 2015 11:31:01: #2 predicted fragment length is 34 bps INFO @ Thu, 30 Apr 2015 11:31:01: #2 alternative fragment length(s) may be 2,34,577 bps INFO @ Thu, 30 Apr 2015 11:31:01: #2.2 Generate R script for model : SRX076077.10_model.r WARNING @ Thu, 30 Apr 2015 11:31:01: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:31:01: #2 You may need to consider one of the other alternative d(s): 2,34,577 WARNING @ Thu, 30 Apr 2015 11:31:01: #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 11:31:01: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:31:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:31:05: start X-correlation... INFO @ Thu, 30 Apr 2015 11:31:05: end of X-cor INFO @ Thu, 30 Apr 2015 11:31:05: #2 finished! INFO @ Thu, 30 Apr 2015 11:31:05: #2 predicted fragment length is 34 bps INFO @ Thu, 30 Apr 2015 11:31:05: #2 alternative fragment length(s) may be 2,34,577 bps INFO @ Thu, 30 Apr 2015 11:31:05: #2.2 Generate R script for model : SRX076077.20_model.r WARNING @ Thu, 30 Apr 2015 11:31:05: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 11:31:05: #2 You may need to consider one of the other alternative d(s): 2,34,577 WARNING @ Thu, 30 Apr 2015 11:31:05: #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 11:31:05: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:31:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:32:11: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:32:12: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:32:18: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:33:02: #4 Write output xls file... SRX076077.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:33:02: #4 Write peak in narrowPeak format file... SRX076077.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:33:02: #4 Write summits bed file... SRX076077.10_summits.bed INFO @ Thu, 30 Apr 2015 11:33:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (281 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:33:05: #4 Write output xls file... SRX076077.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:33:05: #4 Write peak in narrowPeak format file... SRX076077.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:33:05: #4 Write summits bed file... SRX076077.05_summits.bed INFO @ Thu, 30 Apr 2015 11:33:05: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (620 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:33:09: #4 Write output xls file... SRX076077.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:33:09: #4 Write peak in narrowPeak format file... SRX076077.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:33:09: #4 Write summits bed file... SRX076077.20_summits.bed INFO @ Thu, 30 Apr 2015 11:33:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (84 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。