Job ID = 2236844 sra ファイルのダウンロード中... Completed: 213263K bytes transferred in 5 seconds (291637K 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 35635 0 35635 0 0 45649 0 --:--:-- --:--:-- --:--:-- 60500 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 9807251 spots for /home/okishinya/chipatlas/results/ce10/SRX059220/SRR190660.sra Written 9807251 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: 00:01:58 9807251 reads; of these: 9807251 (100.00%) were unpaired; of these: 294233 (3.00%) aligned 0 times 7729380 (78.81%) aligned exactly 1 time 1783638 (18.19%) aligned >1 times 97.00% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 784532 / 9513018 = 0.0825 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 11:14:34: # Command line: callpeak -t SRX059220.bam -f BAM -g ce -n SRX059220.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059220.10 # format = BAM # ChIP-seq file = ['SRX059220.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 11:14:34: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:14:34: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:14:34: # Command line: callpeak -t SRX059220.bam -f BAM -g ce -n SRX059220.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059220.20 # format = BAM # ChIP-seq file = ['SRX059220.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 11:14:34: # Command line: callpeak -t SRX059220.bam -f BAM -g ce -n SRX059220.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059220.05 # format = BAM # ChIP-seq file = ['SRX059220.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 11:14:34: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:14:34: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:14:34: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:14:34: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:14:40: 1000000 INFO @ Thu, 30 Apr 2015 11:14:40: 1000000 INFO @ Thu, 30 Apr 2015 11:14:40: 1000000 INFO @ Thu, 30 Apr 2015 11:14:45: 2000000 INFO @ Thu, 30 Apr 2015 11:14:45: 2000000 INFO @ Thu, 30 Apr 2015 11:14:45: 2000000 INFO @ Thu, 30 Apr 2015 11:14:50: 3000000 INFO @ Thu, 30 Apr 2015 11:14:50: 3000000 INFO @ Thu, 30 Apr 2015 11:14:50: 3000000 INFO @ Thu, 30 Apr 2015 11:14:55: 4000000 INFO @ Thu, 30 Apr 2015 11:14:55: 4000000 INFO @ Thu, 30 Apr 2015 11:14:55: 4000000 INFO @ Thu, 30 Apr 2015 11:15:00: 5000000 INFO @ Thu, 30 Apr 2015 11:15:00: 5000000 INFO @ Thu, 30 Apr 2015 11:15:00: 5000000 INFO @ Thu, 30 Apr 2015 11:15:05: 6000000 INFO @ Thu, 30 Apr 2015 11:15:05: 6000000 INFO @ Thu, 30 Apr 2015 11:15:06: 6000000 INFO @ Thu, 30 Apr 2015 11:15:10: 7000000 INFO @ Thu, 30 Apr 2015 11:15:11: 7000000 INFO @ Thu, 30 Apr 2015 11:15:11: 7000000 INFO @ Thu, 30 Apr 2015 11:15:14: 8000000 INFO @ Thu, 30 Apr 2015 11:15:16: 8000000 INFO @ Thu, 30 Apr 2015 11:15:17: 8000000 INFO @ Thu, 30 Apr 2015 11:15:18: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:15:18: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:15:18: #1 total tags in treatment: 8728486 INFO @ Thu, 30 Apr 2015 11:15:18: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:15:18: #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 11:15:20: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:15:20: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:15:20: #1 total tags in treatment: 8728486 INFO @ Thu, 30 Apr 2015 11:15:20: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:15:20: #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 11:15:20: #1 tags after filtering in treatment: 8727226 INFO @ Thu, 30 Apr 2015 11:15:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:15:20: #1 finished! INFO @ Thu, 30 Apr 2015 11:15:20: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:15:21: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:15:21: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:15:21: #1 total tags in treatment: 8728486 INFO @ Thu, 30 Apr 2015 11:15:21: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:15:21: #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 11:15:21: #1 tags after filtering in treatment: 8727226 INFO @ Thu, 30 Apr 2015 11:15:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:15:21: #1 finished! INFO @ Thu, 30 Apr 2015 11:15:21: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:15:21: #2 number of paired peaks: 321 WARNING @ Thu, 30 Apr 2015 11:15:21: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Thu, 30 Apr 2015 11:15:21: start model_add_line... INFO @ Thu, 30 Apr 2015 11:15:22: #1 tags after filtering in treatment: 8727226 INFO @ Thu, 30 Apr 2015 11:15:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:15:22: #1 finished! INFO @ Thu, 30 Apr 2015 11:15:22: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:15:23: #2 number of paired peaks: 321 WARNING @ Thu, 30 Apr 2015 11:15:23: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Thu, 30 Apr 2015 11:15:23: start model_add_line... INFO @ Thu, 30 Apr 2015 11:15:23: #2 number of paired peaks: 321 WARNING @ Thu, 30 Apr 2015 11:15:23: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Thu, 30 Apr 2015 11:15:23: start model_add_line... INFO @ Thu, 30 Apr 2015 11:15:25: start X-correlation... INFO @ Thu, 30 Apr 2015 11:15:25: end of X-cor INFO @ Thu, 30 Apr 2015 11:15:25: #2 finished! INFO @ Thu, 30 Apr 2015 11:15:25: #2 predicted fragment length is 37 bps INFO @ Thu, 30 Apr 2015 11:15:25: #2 alternative fragment length(s) may be 4,37 bps INFO @ Thu, 30 Apr 2015 11:15:25: #2.2 Generate R script for model : SRX059220.20_model.r WARNING @ Thu, 30 Apr 2015 11:15:25: #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 11:15:25: #2 You may need to consider one of the other alternative d(s): 4,37 WARNING @ Thu, 30 Apr 2015 11:15:25: #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 11:15:25: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:15:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:15:27: start X-correlation... INFO @ Thu, 30 Apr 2015 11:15:27: end of X-cor INFO @ Thu, 30 Apr 2015 11:15:27: #2 finished! INFO @ Thu, 30 Apr 2015 11:15:27: #2 predicted fragment length is 37 bps INFO @ Thu, 30 Apr 2015 11:15:27: #2 alternative fragment length(s) may be 4,37 bps INFO @ Thu, 30 Apr 2015 11:15:27: #2.2 Generate R script for model : SRX059220.05_model.r WARNING @ Thu, 30 Apr 2015 11:15:27: #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 11:15:27: #2 You may need to consider one of the other alternative d(s): 4,37 WARNING @ Thu, 30 Apr 2015 11:15:27: #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 11:15:27: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:15:27: start X-correlation... INFO @ Thu, 30 Apr 2015 11:15:27: end of X-cor INFO @ Thu, 30 Apr 2015 11:15:27: #2 finished! INFO @ Thu, 30 Apr 2015 11:15:27: #2 predicted fragment length is 37 bps INFO @ Thu, 30 Apr 2015 11:15:27: #2 alternative fragment length(s) may be 4,37 bps INFO @ Thu, 30 Apr 2015 11:15:27: #2.2 Generate R script for model : SRX059220.10_model.r WARNING @ Thu, 30 Apr 2015 11:15:27: #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 11:15:27: #2 You may need to consider one of the other alternative d(s): 4,37 WARNING @ Thu, 30 Apr 2015 11:15:27: #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 11:15:27: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:16:10: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:16:13: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:16:14: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:16:44: #4 Write output xls file... SRX059220.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:16:44: #4 Write peak in narrowPeak format file... SRX059220.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:16:44: #4 Write summits bed file... SRX059220.20_summits.bed INFO @ Thu, 30 Apr 2015 11:16:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (101 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:16:48: #4 Write output xls file... SRX059220.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:16:48: #4 Write peak in narrowPeak format file... SRX059220.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:16:48: #4 Write summits bed file... SRX059220.10_summits.bed INFO @ Thu, 30 Apr 2015 11:16:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (352 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:16:48: #4 Write output xls file... SRX059220.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:16:48: #4 Write peak in narrowPeak format file... SRX059220.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:16:48: #4 Write summits bed file... SRX059220.05_summits.bed INFO @ Thu, 30 Apr 2015 11:16:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1299 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。