Job ID = 2161794 sra ファイルのダウンロード中... Completed: 226842K bytes transferred in 5 seconds (328234K bits/sec), in 2 files, 3 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 44462 0 44462 0 0 50913 0 --:--:-- --:--:-- --:--:-- 65098 100 44462 0 44462 0 0 50868 0 --:--:-- --:--:-- --:--:-- 65098 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 3885037 spots for /home/okishinya/chipatlas/results/dm3/SRX033315/SRR080708.sra Written 3885037 spots total Written 4735231 spots for /home/okishinya/chipatlas/results/dm3/SRX033315/SRR080709.sra Written 4735231 spots total 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: 00:01:46 8620268 reads; of these: 8620268 (100.00%) were unpaired; of these: 2921074 (33.89%) aligned 0 times 4292906 (49.80%) aligned exactly 1 time 1406288 (16.31%) aligned >1 times 66.11% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2401713 / 5699194 = 0.4214 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 @ Tue, 21 Apr 2015 13:05:00: # Command line: callpeak -t SRX033315.bam -f BAM -g dm -n SRX033315.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX033315.20 # format = BAM # ChIP-seq file = ['SRX033315.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 13:05:00: # Command line: callpeak -t SRX033315.bam -f BAM -g dm -n SRX033315.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX033315.05 # format = BAM # ChIP-seq file = ['SRX033315.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 13:05:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:05:00: # Command line: callpeak -t SRX033315.bam -f BAM -g dm -n SRX033315.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX033315.10 # format = BAM # ChIP-seq file = ['SRX033315.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 13:05:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:05:00: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:05:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:05:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:05:00: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:05:05: 1000000 INFO @ Tue, 21 Apr 2015 13:05:05: 1000000 INFO @ Tue, 21 Apr 2015 13:05:06: 1000000 INFO @ Tue, 21 Apr 2015 13:05:11: 2000000 INFO @ Tue, 21 Apr 2015 13:05:11: 2000000 INFO @ Tue, 21 Apr 2015 13:05:11: 2000000 INFO @ Tue, 21 Apr 2015 13:05:16: 3000000 INFO @ Tue, 21 Apr 2015 13:05:17: 3000000 INFO @ Tue, 21 Apr 2015 13:05:17: 3000000 INFO @ Tue, 21 Apr 2015 13:05:18: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:05:18: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:05:18: #1 total tags in treatment: 3297481 INFO @ Tue, 21 Apr 2015 13:05:18: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:05:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:05:18: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:05:18: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:05:18: #1 total tags in treatment: 3297481 INFO @ Tue, 21 Apr 2015 13:05:18: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:05:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:05:19: #1 tags after filtering in treatment: 3297275 INFO @ Tue, 21 Apr 2015 13:05:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:05:19: #1 finished! INFO @ Tue, 21 Apr 2015 13:05:19: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:05:19: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:05:19: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:05:19: #1 total tags in treatment: 3297481 INFO @ Tue, 21 Apr 2015 13:05:19: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:05:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 13:05:19: #1 tags after filtering in treatment: 3297275 INFO @ Tue, 21 Apr 2015 13:05:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:05:19: #1 finished! INFO @ Tue, 21 Apr 2015 13:05:19: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:05:19: #2 number of paired peaks: 420 WARNING @ Tue, 21 Apr 2015 13:05:19: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Tue, 21 Apr 2015 13:05:19: start model_add_line... INFO @ Tue, 21 Apr 2015 13:05:20: #1 tags after filtering in treatment: 3297275 INFO @ Tue, 21 Apr 2015 13:05:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:05:20: #1 finished! INFO @ Tue, 21 Apr 2015 13:05:20: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:05:20: #2 number of paired peaks: 420 WARNING @ Tue, 21 Apr 2015 13:05:20: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Tue, 21 Apr 2015 13:05:20: start model_add_line... INFO @ Tue, 21 Apr 2015 13:05:20: #2 number of paired peaks: 420 WARNING @ Tue, 21 Apr 2015 13:05:20: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Tue, 21 Apr 2015 13:05:20: start model_add_line... INFO @ Tue, 21 Apr 2015 13:05:21: start X-correlation... INFO @ Tue, 21 Apr 2015 13:05:21: end of X-cor INFO @ Tue, 21 Apr 2015 13:05:21: #2 finished! INFO @ Tue, 21 Apr 2015 13:05:21: #2 predicted fragment length is 40 bps INFO @ Tue, 21 Apr 2015 13:05:21: #2 alternative fragment length(s) may be 40 bps INFO @ Tue, 21 Apr 2015 13:05:21: #2.2 Generate R script for model : SRX033315.10_model.r WARNING @ Tue, 21 Apr 2015 13:05:21: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:05:21: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Tue, 21 Apr 2015 13:05:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:05:21: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:05:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:05:21: start X-correlation... INFO @ Tue, 21 Apr 2015 13:05:21: end of X-cor INFO @ Tue, 21 Apr 2015 13:05:21: #2 finished! INFO @ Tue, 21 Apr 2015 13:05:21: #2 predicted fragment length is 40 bps INFO @ Tue, 21 Apr 2015 13:05:21: #2 alternative fragment length(s) may be 40 bps INFO @ Tue, 21 Apr 2015 13:05:21: #2.2 Generate R script for model : SRX033315.05_model.r WARNING @ Tue, 21 Apr 2015 13:05:21: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:05:21: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Tue, 21 Apr 2015 13:05:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:05:21: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:05:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:05:22: start X-correlation... INFO @ Tue, 21 Apr 2015 13:05:22: end of X-cor INFO @ Tue, 21 Apr 2015 13:05:22: #2 finished! INFO @ Tue, 21 Apr 2015 13:05:22: #2 predicted fragment length is 40 bps INFO @ Tue, 21 Apr 2015 13:05:22: #2 alternative fragment length(s) may be 40 bps INFO @ Tue, 21 Apr 2015 13:05:22: #2.2 Generate R script for model : SRX033315.20_model.r WARNING @ Tue, 21 Apr 2015 13:05:22: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:05:22: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Tue, 21 Apr 2015 13:05:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 13:05:22: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:05:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:05:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:05:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:05:41: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:05:55: #4 Write output xls file... SRX033315.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:05:55: #4 Write peak in narrowPeak format file... SRX033315.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:05:55: #4 Write summits bed file... SRX033315.10_summits.bed INFO @ Tue, 21 Apr 2015 13:05:55: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (476 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:05:56: #4 Write output xls file... SRX033315.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:05:56: #4 Write peak in narrowPeak format file... SRX033315.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:05:56: #4 Write summits bed file... SRX033315.20_summits.bed INFO @ Tue, 21 Apr 2015 13:05:56: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (376 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:05:56: #4 Write output xls file... SRX033315.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:05:56: #4 Write peak in narrowPeak format file... SRX033315.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:05:56: #4 Write summits bed file... SRX033315.05_summits.bed INFO @ Tue, 21 Apr 2015 13:05:56: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (666 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。