Job ID = 2162170 sra ファイルのダウンロード中... Completed: 159063K bytes transferred in 4 seconds (272946K 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 17124 0 17124 0 0 24513 0 --:--:-- --:--:-- --:--:-- 33708 100 35470 0 35470 0 0 50714 0 --:--:-- --:--:-- --:--:-- 69822 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 8148551 spots for /home/okishinya/chipatlas/results/dm3/SRX050604/SRR139086.sra Written 8148551 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:35 8148551 reads; of these: 8148551 (100.00%) were unpaired; of these: 358952 (4.41%) aligned 0 times 5601518 (68.74%) aligned exactly 1 time 2188081 (26.85%) aligned >1 times 95.59% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 707875 / 7789599 = 0.0909 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 13:38:47: # Command line: callpeak -t SRX050604.bam -f BAM -g dm -n SRX050604.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX050604.10 # format = BAM # ChIP-seq file = ['SRX050604.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 13:38:47: # Command line: callpeak -t SRX050604.bam -f BAM -g dm -n SRX050604.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX050604.20 # format = BAM # ChIP-seq file = ['SRX050604.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 13:38:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:38:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:38:47: # Command line: callpeak -t SRX050604.bam -f BAM -g dm -n SRX050604.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX050604.05 # format = BAM # ChIP-seq file = ['SRX050604.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 13:38:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:38:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:38:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:38:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:38:52: 1000000 INFO @ Tue, 21 Apr 2015 13:38:52: 1000000 INFO @ Tue, 21 Apr 2015 13:38:52: 1000000 INFO @ Tue, 21 Apr 2015 13:38:57: 2000000 INFO @ Tue, 21 Apr 2015 13:38:57: 2000000 INFO @ Tue, 21 Apr 2015 13:38:57: 2000000 INFO @ Tue, 21 Apr 2015 13:39:03: 3000000 INFO @ Tue, 21 Apr 2015 13:39:03: 3000000 INFO @ Tue, 21 Apr 2015 13:39:03: 3000000 INFO @ Tue, 21 Apr 2015 13:39:08: 4000000 INFO @ Tue, 21 Apr 2015 13:39:08: 4000000 INFO @ Tue, 21 Apr 2015 13:39:08: 4000000 INFO @ Tue, 21 Apr 2015 13:39:13: 5000000 INFO @ Tue, 21 Apr 2015 13:39:14: 5000000 INFO @ Tue, 21 Apr 2015 13:39:14: 5000000 INFO @ Tue, 21 Apr 2015 13:39:19: 6000000 INFO @ Tue, 21 Apr 2015 13:39:19: 6000000 INFO @ Tue, 21 Apr 2015 13:39:20: 6000000 INFO @ Tue, 21 Apr 2015 13:39:25: 7000000 INFO @ Tue, 21 Apr 2015 13:39:26: 7000000 INFO @ Tue, 21 Apr 2015 13:39:26: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:39:26: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:39:26: #1 total tags in treatment: 7081724 INFO @ Tue, 21 Apr 2015 13:39:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:39:26: #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 13:39:26: 7000000 INFO @ Tue, 21 Apr 2015 13:39:26: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:39:26: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:39:26: #1 total tags in treatment: 7081724 INFO @ Tue, 21 Apr 2015 13:39:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:39:26: #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 13:39:26: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:39:26: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:39:26: #1 total tags in treatment: 7081724 INFO @ Tue, 21 Apr 2015 13:39:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:39:26: #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 13:39:27: #1 tags after filtering in treatment: 7081532 INFO @ Tue, 21 Apr 2015 13:39:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:39:27: #1 finished! INFO @ Tue, 21 Apr 2015 13:39:27: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:39:28: #1 tags after filtering in treatment: 7081532 INFO @ Tue, 21 Apr 2015 13:39:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:39:28: #1 finished! INFO @ Tue, 21 Apr 2015 13:39:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:39:28: #1 tags after filtering in treatment: 7081532 INFO @ Tue, 21 Apr 2015 13:39:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:39:28: #1 finished! INFO @ Tue, 21 Apr 2015 13:39:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:39:28: #2 number of paired peaks: 311 WARNING @ Tue, 21 Apr 2015 13:39:28: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 21 Apr 2015 13:39:28: start model_add_line... INFO @ Tue, 21 Apr 2015 13:39:29: #2 number of paired peaks: 311 WARNING @ Tue, 21 Apr 2015 13:39:29: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 21 Apr 2015 13:39:29: start model_add_line... INFO @ Tue, 21 Apr 2015 13:39:29: #2 number of paired peaks: 311 WARNING @ Tue, 21 Apr 2015 13:39:29: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 21 Apr 2015 13:39:29: start model_add_line... INFO @ Tue, 21 Apr 2015 13:39:30: start X-correlation... INFO @ Tue, 21 Apr 2015 13:39:30: end of X-cor INFO @ Tue, 21 Apr 2015 13:39:30: #2 finished! INFO @ Tue, 21 Apr 2015 13:39:30: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 13:39:30: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 13:39:30: #2.2 Generate R script for model : SRX050604.05_model.r WARNING @ Tue, 21 Apr 2015 13:39:30: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:39:30: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 13:39:30: #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 13:39:30: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:39:30: start X-correlation... INFO @ Tue, 21 Apr 2015 13:39:30: end of X-cor INFO @ Tue, 21 Apr 2015 13:39:30: #2 finished! INFO @ Tue, 21 Apr 2015 13:39:30: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 13:39:30: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 13:39:30: #2.2 Generate R script for model : SRX050604.10_model.r WARNING @ Tue, 21 Apr 2015 13:39:30: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:39:30: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 13:39:30: #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 13:39:30: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:39:30: start X-correlation... INFO @ Tue, 21 Apr 2015 13:39:30: end of X-cor INFO @ Tue, 21 Apr 2015 13:39:30: #2 finished! INFO @ Tue, 21 Apr 2015 13:39:30: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 13:39:30: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 13:39:30: #2.2 Generate R script for model : SRX050604.20_model.r WARNING @ Tue, 21 Apr 2015 13:39:30: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:39:30: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 13:39:30: #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 13:39:30: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:40:09: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:40:09: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:40:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:40:39: #4 Write output xls file... SRX050604.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:40:39: #4 Write peak in narrowPeak format file... SRX050604.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:40:39: #4 Write summits bed file... SRX050604.05_summits.bed INFO @ Tue, 21 Apr 2015 13:40:39: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1495 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:40:39: #4 Write output xls file... SRX050604.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:40:39: #4 Write peak in narrowPeak format file... SRX050604.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:40:39: #4 Write summits bed file... SRX050604.10_summits.bed INFO @ Tue, 21 Apr 2015 13:40:39: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1164 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:40:39: #4 Write output xls file... SRX050604.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:40:39: #4 Write peak in narrowPeak format file... SRX050604.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:40:39: #4 Write summits bed file... SRX050604.20_summits.bed INFO @ Tue, 21 Apr 2015 13:40:39: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (673 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。