Job ID = 2161355 sra ファイルのダウンロード中... Completed: 158989K bytes transferred in 4 seconds (289553K 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 36761 0 36761 0 0 48644 0 --:--:-- --:--:-- --:--:-- 65179 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 9292856 spots for /home/okishinya/chipatlas/results/dm3/SRX022744/SRR059123.sra Written 9292856 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: 00:02:49 9292856 reads; of these: 9292856 (100.00%) were unpaired; of these: 427320 (4.60%) aligned 0 times 6529811 (70.27%) aligned exactly 1 time 2335725 (25.13%) aligned >1 times 95.40% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 499865 / 8865536 = 0.0564 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 12:32:10: # Command line: callpeak -t SRX022744.bam -f BAM -g dm -n SRX022744.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX022744.05 # format = BAM # ChIP-seq file = ['SRX022744.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 12:32:10: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:32:10: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:32:10: # Command line: callpeak -t SRX022744.bam -f BAM -g dm -n SRX022744.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX022744.10 # format = BAM # ChIP-seq file = ['SRX022744.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 12:32:10: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:32:10: # Command line: callpeak -t SRX022744.bam -f BAM -g dm -n SRX022744.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX022744.20 # format = BAM # ChIP-seq file = ['SRX022744.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 12:32:10: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:32:10: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:32:10: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:32:16: 1000000 INFO @ Tue, 21 Apr 2015 12:32:16: 1000000 INFO @ Tue, 21 Apr 2015 12:32:16: 1000000 INFO @ Tue, 21 Apr 2015 12:32:21: 2000000 INFO @ Tue, 21 Apr 2015 12:32:21: 2000000 INFO @ Tue, 21 Apr 2015 12:32:22: 2000000 INFO @ Tue, 21 Apr 2015 12:32:27: 3000000 INFO @ Tue, 21 Apr 2015 12:32:27: 3000000 INFO @ Tue, 21 Apr 2015 12:32:28: 3000000 INFO @ Tue, 21 Apr 2015 12:32:33: 4000000 INFO @ Tue, 21 Apr 2015 12:32:33: 4000000 INFO @ Tue, 21 Apr 2015 12:32:34: 4000000 INFO @ Tue, 21 Apr 2015 12:32:39: 5000000 INFO @ Tue, 21 Apr 2015 12:32:39: 5000000 INFO @ Tue, 21 Apr 2015 12:32:40: 5000000 INFO @ Tue, 21 Apr 2015 12:32:44: 6000000 INFO @ Tue, 21 Apr 2015 12:32:44: 6000000 INFO @ Tue, 21 Apr 2015 12:32:46: 6000000 INFO @ Tue, 21 Apr 2015 12:32:50: 7000000 INFO @ Tue, 21 Apr 2015 12:32:50: 7000000 INFO @ Tue, 21 Apr 2015 12:32:52: 7000000 INFO @ Tue, 21 Apr 2015 12:32:56: 8000000 INFO @ Tue, 21 Apr 2015 12:32:56: 8000000 INFO @ Tue, 21 Apr 2015 12:32:58: 8000000 INFO @ Tue, 21 Apr 2015 12:32:58: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:32:58: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:32:58: #1 total tags in treatment: 8365671 INFO @ Tue, 21 Apr 2015 12:32:58: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:32:58: #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 12:32:58: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:32:58: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:32:58: #1 total tags in treatment: 8365671 INFO @ Tue, 21 Apr 2015 12:32:58: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:32:58: #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 12:33:00: #1 tags after filtering in treatment: 8365219 INFO @ Tue, 21 Apr 2015 12:33:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:33:00: #1 finished! INFO @ Tue, 21 Apr 2015 12:33:00: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:33:00: #1 tags after filtering in treatment: 8365219 INFO @ Tue, 21 Apr 2015 12:33:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:33:00: #1 finished! INFO @ Tue, 21 Apr 2015 12:33:00: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:33:00: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:33:00: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:33:00: #1 total tags in treatment: 8365671 INFO @ Tue, 21 Apr 2015 12:33:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:33:00: #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 12:33:01: #2 number of paired peaks: 606 WARNING @ Tue, 21 Apr 2015 12:33:01: Fewer paired peaks (606) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 606 pairs to build model! INFO @ Tue, 21 Apr 2015 12:33:01: start model_add_line... INFO @ Tue, 21 Apr 2015 12:33:01: #2 number of paired peaks: 606 WARNING @ Tue, 21 Apr 2015 12:33:01: Fewer paired peaks (606) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 606 pairs to build model! INFO @ Tue, 21 Apr 2015 12:33:01: start model_add_line... INFO @ Tue, 21 Apr 2015 12:33:02: #1 tags after filtering in treatment: 8365219 INFO @ Tue, 21 Apr 2015 12:33:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:33:02: #1 finished! INFO @ Tue, 21 Apr 2015 12:33:02: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:33:03: #2 number of paired peaks: 606 WARNING @ Tue, 21 Apr 2015 12:33:03: Fewer paired peaks (606) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 606 pairs to build model! INFO @ Tue, 21 Apr 2015 12:33:03: start model_add_line... INFO @ Tue, 21 Apr 2015 12:33:05: start X-correlation... INFO @ Tue, 21 Apr 2015 12:33:05: end of X-cor INFO @ Tue, 21 Apr 2015 12:33:05: #2 finished! INFO @ Tue, 21 Apr 2015 12:33:05: #2 predicted fragment length is 41 bps INFO @ Tue, 21 Apr 2015 12:33:05: #2 alternative fragment length(s) may be 41 bps INFO @ Tue, 21 Apr 2015 12:33:05: #2.2 Generate R script for model : SRX022744.05_model.r WARNING @ Tue, 21 Apr 2015 12:33:05: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:33:05: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Tue, 21 Apr 2015 12:33:05: #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 12:33:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:33:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:33:06: start X-correlation... INFO @ Tue, 21 Apr 2015 12:33:06: end of X-cor INFO @ Tue, 21 Apr 2015 12:33:06: #2 finished! INFO @ Tue, 21 Apr 2015 12:33:06: #2 predicted fragment length is 41 bps INFO @ Tue, 21 Apr 2015 12:33:06: #2 alternative fragment length(s) may be 41 bps INFO @ Tue, 21 Apr 2015 12:33:06: #2.2 Generate R script for model : SRX022744.20_model.r WARNING @ Tue, 21 Apr 2015 12:33:06: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:33:06: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Tue, 21 Apr 2015 12:33:06: #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 12:33:06: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:33:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:33:07: start X-correlation... INFO @ Tue, 21 Apr 2015 12:33:07: end of X-cor INFO @ Tue, 21 Apr 2015 12:33:07: #2 finished! INFO @ Tue, 21 Apr 2015 12:33:07: #2 predicted fragment length is 41 bps INFO @ Tue, 21 Apr 2015 12:33:07: #2 alternative fragment length(s) may be 41 bps INFO @ Tue, 21 Apr 2015 12:33:07: #2.2 Generate R script for model : SRX022744.10_model.r WARNING @ Tue, 21 Apr 2015 12:33:07: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:33:07: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Tue, 21 Apr 2015 12:33:07: #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 12:33:07: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:33:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:33:52: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:33:55: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:33:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:34:27: #4 Write output xls file... SRX022744.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:34:27: #4 Write peak in narrowPeak format file... SRX022744.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:34:27: #4 Write summits bed file... SRX022744.05_summits.bed INFO @ Tue, 21 Apr 2015 12:34:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2752 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:34:30: #4 Write output xls file... SRX022744.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:34:30: #4 Write peak in narrowPeak format file... SRX022744.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:34:30: #4 Write summits bed file... SRX022744.10_summits.bed INFO @ Tue, 21 Apr 2015 12:34:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1486 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:34:30: #4 Write output xls file... SRX022744.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:34:30: #4 Write peak in narrowPeak format file... SRX022744.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:34:30: #4 Write summits bed file... SRX022744.20_summits.bed INFO @ Tue, 21 Apr 2015 12:34:30: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (563 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。