Job ID = 2237022 sra ファイルのダウンロード中... Completed: 93533K bytes transferred in 4 seconds (170167K 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 6927 0 6927 0 0 13291 0 --:--:-- --:--:-- --:--:-- 20990 100 38139 0 38139 0 0 53668 0 --:--:-- --:--:-- --:--:-- 73344 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 4626948 spots for /home/okishinya/chipatlas/results/ce10/SRX080077/SRR298897.sra Written 4626948 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: 00:00:39 4626948 reads; of these: 4626948 (100.00%) were unpaired; of these: 1908740 (41.25%) aligned 0 times 2219419 (47.97%) aligned exactly 1 time 498789 (10.78%) aligned >1 times 58.75% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 139621 / 2718208 = 0.0514 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 11:25:00: # Command line: callpeak -t SRX080077.bam -f BAM -g ce -n SRX080077.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080077.05 # format = BAM # ChIP-seq file = ['SRX080077.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 11:25:00: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:00: # Command line: callpeak -t SRX080077.bam -f BAM -g ce -n SRX080077.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080077.20 # format = BAM # ChIP-seq file = ['SRX080077.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 11:25:00: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:00: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:00: # Command line: callpeak -t SRX080077.bam -f BAM -g ce -n SRX080077.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080077.10 # format = BAM # ChIP-seq file = ['SRX080077.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 11:25:00: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:00: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:00: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:05: 1000000 INFO @ Thu, 30 Apr 2015 11:25:05: 1000000 INFO @ Thu, 30 Apr 2015 11:25:05: 1000000 INFO @ Thu, 30 Apr 2015 11:25:11: 2000000 INFO @ Thu, 30 Apr 2015 11:25:11: 2000000 INFO @ Thu, 30 Apr 2015 11:25:11: 2000000 INFO @ Thu, 30 Apr 2015 11:25:14: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:14: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:14: #1 total tags in treatment: 2578587 INFO @ Thu, 30 Apr 2015 11:25:14: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:14: #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 11:25:14: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:14: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:14: #1 total tags in treatment: 2578587 INFO @ Thu, 30 Apr 2015 11:25:14: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:14: #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 11:25:14: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:14: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:14: #1 total tags in treatment: 2578587 INFO @ Thu, 30 Apr 2015 11:25:14: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:14: #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 11:25:14: #1 tags after filtering in treatment: 2578540 INFO @ Thu, 30 Apr 2015 11:25:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:14: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:14: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:14: #1 tags after filtering in treatment: 2578540 INFO @ Thu, 30 Apr 2015 11:25:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:14: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:14: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:14: #1 tags after filtering in treatment: 2578540 INFO @ Thu, 30 Apr 2015 11:25:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:14: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:14: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:15: #2 number of paired peaks: 516 WARNING @ Thu, 30 Apr 2015 11:25:15: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:15: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:15: #2 number of paired peaks: 516 WARNING @ Thu, 30 Apr 2015 11:25:15: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:15: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:15: #2 number of paired peaks: 516 WARNING @ Thu, 30 Apr 2015 11:25:15: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Thu, 30 Apr 2015 11:25:15: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:17: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:17: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:17: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:17: #2 predicted fragment length is 34 bps INFO @ Thu, 30 Apr 2015 11:25:17: #2 alternative fragment length(s) may be 4,34,233,481,552,587 bps INFO @ Thu, 30 Apr 2015 11:25:17: #2.2 Generate R script for model : SRX080077.20_model.r WARNING @ Thu, 30 Apr 2015 11:25:17: #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 11:25:17: #2 You may need to consider one of the other alternative d(s): 4,34,233,481,552,587 WARNING @ Thu, 30 Apr 2015 11:25:17: #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 11:25:17: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:17: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:17: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:17: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:17: #2 predicted fragment length is 34 bps INFO @ Thu, 30 Apr 2015 11:25:17: #2 alternative fragment length(s) may be 4,34,233,481,552,587 bps INFO @ Thu, 30 Apr 2015 11:25:17: #2.2 Generate R script for model : SRX080077.10_model.r WARNING @ Thu, 30 Apr 2015 11:25:17: #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 11:25:17: #2 You may need to consider one of the other alternative d(s): 4,34,233,481,552,587 WARNING @ Thu, 30 Apr 2015 11:25:17: #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 11:25:17: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:18: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:18: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:18: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:18: #2 predicted fragment length is 34 bps INFO @ Thu, 30 Apr 2015 11:25:18: #2 alternative fragment length(s) may be 4,34,233,481,552,587 bps INFO @ Thu, 30 Apr 2015 11:25:18: #2.2 Generate R script for model : SRX080077.05_model.r WARNING @ Thu, 30 Apr 2015 11:25:18: #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 11:25:18: #2 You may need to consider one of the other alternative d(s): 4,34,233,481,552,587 WARNING @ Thu, 30 Apr 2015 11:25:18: #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 11:25:18: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:32: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:32: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:34: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:42: #4 Write output xls file... SRX080077.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:42: #4 Write peak in narrowPeak format file... SRX080077.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:42: #4 Write summits bed file... SRX080077.20_summits.bed INFO @ Thu, 30 Apr 2015 11:25:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (27 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:43: #4 Write output xls file... SRX080077.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:43: #4 Write peak in narrowPeak format file... SRX080077.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:43: #4 Write summits bed file... SRX080077.10_summits.bed INFO @ Thu, 30 Apr 2015 11:25:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:25:44: #4 Write output xls file... SRX080077.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:25:44: #4 Write peak in narrowPeak format file... SRX080077.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:25:44: #4 Write summits bed file... SRX080077.05_summits.bed INFO @ Thu, 30 Apr 2015 11:25:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (378 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。