Job ID = 2161335 sra ファイルのダウンロード中... Completed: 371614K bytes transferred in 6 seconds (448342K bits/sec), in 4 files, 5 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 35973 0 35973 0 0 51163 0 --:--:-- --:--:-- --:--:-- 70535 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 3122778 spots for /home/okishinya/chipatlas/results/dm3/SRX018631/SRR039099.sra Written 3122778 spots total Written 3254949 spots for /home/okishinya/chipatlas/results/dm3/SRX018631/SRR039100.sra Written 3254949 spots total Written 3345566 spots for /home/okishinya/chipatlas/results/dm3/SRX018631/SRR039101.sra Written 3345566 spots total Written 3413820 spots for /home/okishinya/chipatlas/results/dm3/SRX018631/SRR039102.sra Written 3413820 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: 00:03:24 13137113 reads; of these: 13137113 (100.00%) were unpaired; of these: 4132130 (31.45%) aligned 0 times 6215619 (47.31%) aligned exactly 1 time 2789364 (21.23%) aligned >1 times 68.55% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 846550 / 9004983 = 0.0940 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 12:28:47: # Command line: callpeak -t SRX018631.bam -f BAM -g dm -n SRX018631.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX018631.05 # format = BAM # ChIP-seq file = ['SRX018631.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 12:28:47: # Command line: callpeak -t SRX018631.bam -f BAM -g dm -n SRX018631.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX018631.10 # format = BAM # ChIP-seq file = ['SRX018631.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 12:28:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:28:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:28:47: # Command line: callpeak -t SRX018631.bam -f BAM -g dm -n SRX018631.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX018631.20 # format = BAM # ChIP-seq file = ['SRX018631.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 12:28:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:28:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:28:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:28:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:28:52: 1000000 INFO @ Tue, 21 Apr 2015 12:28:52: 1000000 INFO @ Tue, 21 Apr 2015 12:28:52: 1000000 INFO @ Tue, 21 Apr 2015 12:28:57: 2000000 INFO @ Tue, 21 Apr 2015 12:28:58: 2000000 INFO @ Tue, 21 Apr 2015 12:28:58: 2000000 INFO @ Tue, 21 Apr 2015 12:29:02: 3000000 INFO @ Tue, 21 Apr 2015 12:29:03: 3000000 INFO @ Tue, 21 Apr 2015 12:29:03: 3000000 INFO @ Tue, 21 Apr 2015 12:29:07: 4000000 INFO @ Tue, 21 Apr 2015 12:29:09: 4000000 INFO @ Tue, 21 Apr 2015 12:29:09: 4000000 INFO @ Tue, 21 Apr 2015 12:29:12: 5000000 INFO @ Tue, 21 Apr 2015 12:29:14: 5000000 INFO @ Tue, 21 Apr 2015 12:29:15: 5000000 INFO @ Tue, 21 Apr 2015 12:29:17: 6000000 INFO @ Tue, 21 Apr 2015 12:29:20: 6000000 INFO @ Tue, 21 Apr 2015 12:29:20: 6000000 INFO @ Tue, 21 Apr 2015 12:29:21: 7000000 INFO @ Tue, 21 Apr 2015 12:29:25: 7000000 INFO @ Tue, 21 Apr 2015 12:29:26: 7000000 INFO @ Tue, 21 Apr 2015 12:29:26: 8000000 INFO @ Tue, 21 Apr 2015 12:29:27: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 12:29:27: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 12:29:27: #1 total tags in treatment: 8158433 INFO @ Tue, 21 Apr 2015 12:29:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:29:27: #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 12:29:29: #1 tags after filtering in treatment: 8157838 INFO @ Tue, 21 Apr 2015 12:29:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:29:29: #1 finished! INFO @ Tue, 21 Apr 2015 12:29:29: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:29:30: #2 number of paired peaks: 778 WARNING @ Tue, 21 Apr 2015 12:29:30: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Tue, 21 Apr 2015 12:29:30: start model_add_line... INFO @ Tue, 21 Apr 2015 12:29:31: 8000000 INFO @ Tue, 21 Apr 2015 12:29:32: 8000000 INFO @ Tue, 21 Apr 2015 12:29:32: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 12:29:32: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 12:29:32: #1 total tags in treatment: 8158433 INFO @ Tue, 21 Apr 2015 12:29:32: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:29:32: #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 12:29:33: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 12:29:33: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 12:29:33: #1 total tags in treatment: 8158433 INFO @ Tue, 21 Apr 2015 12:29:33: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:29:33: #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 12:29:34: #1 tags after filtering in treatment: 8157838 INFO @ Tue, 21 Apr 2015 12:29:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:29:34: #1 finished! INFO @ Tue, 21 Apr 2015 12:29:34: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:29:34: #1 tags after filtering in treatment: 8157838 INFO @ Tue, 21 Apr 2015 12:29:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:29:34: #1 finished! INFO @ Tue, 21 Apr 2015 12:29:34: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:29:35: start X-correlation... INFO @ Tue, 21 Apr 2015 12:29:35: end of X-cor INFO @ Tue, 21 Apr 2015 12:29:35: #2 finished! INFO @ Tue, 21 Apr 2015 12:29:35: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 12:29:35: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 12:29:35: #2.2 Generate R script for model : SRX018631.20_model.r WARNING @ Tue, 21 Apr 2015 12:29:35: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:29:35: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 12:29:35: #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 12:29:35: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:29:35: #2 number of paired peaks: 778 WARNING @ Tue, 21 Apr 2015 12:29:35: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Tue, 21 Apr 2015 12:29:35: start model_add_line... INFO @ Tue, 21 Apr 2015 12:29:36: #2 number of paired peaks: 778 WARNING @ Tue, 21 Apr 2015 12:29:36: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Tue, 21 Apr 2015 12:29:36: start model_add_line... INFO @ Tue, 21 Apr 2015 12:29:40: start X-correlation... INFO @ Tue, 21 Apr 2015 12:29:40: end of X-cor INFO @ Tue, 21 Apr 2015 12:29:40: #2 finished! INFO @ Tue, 21 Apr 2015 12:29:40: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 12:29:40: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 12:29:40: #2.2 Generate R script for model : SRX018631.10_model.r WARNING @ Tue, 21 Apr 2015 12:29:40: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:29:40: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 12:29:40: #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 12:29:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:29:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:29:40: start X-correlation... INFO @ Tue, 21 Apr 2015 12:29:40: end of X-cor INFO @ Tue, 21 Apr 2015 12:29:40: #2 finished! INFO @ Tue, 21 Apr 2015 12:29:40: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 12:29:40: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 12:29:40: #2.2 Generate R script for model : SRX018631.05_model.r WARNING @ Tue, 21 Apr 2015 12:29:40: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:29:40: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 12:29:40: #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 12:29:40: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:29:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:30:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:30:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:30:27: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:30:52: #4 Write output xls file... SRX018631.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:30:52: #4 Write peak in narrowPeak format file... SRX018631.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:30:52: #4 Write summits bed file... SRX018631.20_summits.bed INFO @ Tue, 21 Apr 2015 12:30:52: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (870 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:30:59: #4 Write output xls file... SRX018631.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:30:59: #4 Write peak in narrowPeak format file... SRX018631.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:30:59: #4 Write summits bed file... SRX018631.05_summits.bed INFO @ Tue, 21 Apr 2015 12:30:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2759 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:31:01: #4 Write output xls file... SRX018631.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:31:01: #4 Write peak in narrowPeak format file... SRX018631.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:31:01: #4 Write summits bed file... SRX018631.10_summits.bed INFO @ Tue, 21 Apr 2015 12:31:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1696 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。