Job ID = 9029559 sra ファイルのダウンロード中... Completed: 537125K bytes transferred in 8 seconds (531729K 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 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 20109 0 20109 0 0 2525 0 --:--:-- 0:00:07 --:--:-- 14688 100 44725 0 44725 0 0 5087 0 --:--:-- 0:00:08 --:--:-- 20338 100 100k 0 100k 0 0 10494 0 --:--:-- 0:00:09 --:--:-- 32159 100 139k 0 139k 0 0 13931 0 --:--:-- 0:00:10 --:--:-- 38810 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 9523883 spots for /home/okishinya/chipatlas/results/dm3/SRX1840072/SRR3661298.sra Written 9523883 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: 00:08:30 9523883 reads; of these: 9523883 (100.00%) were unpaired; of these: 2370249 (24.89%) aligned 0 times 4528461 (47.55%) aligned exactly 1 time 2625173 (27.56%) aligned >1 times 75.11% overall alignment rate Time searching: 00:08:30 Overall time: 00:08:30 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] 2544960 / 7153634 = 0.3558 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 @ Sat, 03 Jun 2017 14:20:13: # Command line: callpeak -t SRX1840072.bam -f BAM -g dm -n SRX1840072.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1840072.05 # format = BAM # ChIP-seq file = ['SRX1840072.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 @ Sat, 03 Jun 2017 14:20:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:20:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:20:13: # Command line: callpeak -t SRX1840072.bam -f BAM -g dm -n SRX1840072.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1840072.20 # format = BAM # ChIP-seq file = ['SRX1840072.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 @ Sat, 03 Jun 2017 14:20:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:20:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:20:13: # Command line: callpeak -t SRX1840072.bam -f BAM -g dm -n SRX1840072.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1840072.10 # format = BAM # ChIP-seq file = ['SRX1840072.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 @ Sat, 03 Jun 2017 14:20:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:20:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:20:24: 1000000 INFO @ Sat, 03 Jun 2017 14:20:24: 1000000 INFO @ Sat, 03 Jun 2017 14:20:24: 1000000 INFO @ Sat, 03 Jun 2017 14:20:36: 2000000 INFO @ Sat, 03 Jun 2017 14:20:36: 2000000 INFO @ Sat, 03 Jun 2017 14:20:36: 2000000 INFO @ Sat, 03 Jun 2017 14:20:46: 3000000 INFO @ Sat, 03 Jun 2017 14:20:46: 3000000 INFO @ Sat, 03 Jun 2017 14:20:46: 3000000 INFO @ Sat, 03 Jun 2017 14:20:55: 4000000 INFO @ Sat, 03 Jun 2017 14:20:57: 4000000 INFO @ Sat, 03 Jun 2017 14:20:57: 4000000 INFO @ Sat, 03 Jun 2017 14:21:01: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:21:01: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:21:01: #1 total tags in treatment: 4608674 INFO @ Sat, 03 Jun 2017 14:21:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:21:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:21:02: #1 tags after filtering in treatment: 4602547 INFO @ Sat, 03 Jun 2017 14:21:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:21:02: #1 finished! INFO @ Sat, 03 Jun 2017 14:21:02: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:21:03: #2 number of paired peaks: 615 WARNING @ Sat, 03 Jun 2017 14:21:03: Fewer paired peaks (615) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 615 pairs to build model! INFO @ Sat, 03 Jun 2017 14:21:03: start model_add_line... INFO @ Sat, 03 Jun 2017 14:21:03: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:21:03: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:21:03: #1 total tags in treatment: 4608674 INFO @ Sat, 03 Jun 2017 14:21:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:21:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:21:03: #1 tag size is determined as 101 bps INFO @ Sat, 03 Jun 2017 14:21:03: #1 tag size = 101 INFO @ Sat, 03 Jun 2017 14:21:03: #1 total tags in treatment: 4608674 INFO @ Sat, 03 Jun 2017 14:21:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:21:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:21:04: #1 tags after filtering in treatment: 4602547 INFO @ Sat, 03 Jun 2017 14:21:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:21:04: #1 finished! INFO @ Sat, 03 Jun 2017 14:21:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:21:04: #1 tags after filtering in treatment: 4602547 INFO @ Sat, 03 Jun 2017 14:21:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:21:04: #1 finished! INFO @ Sat, 03 Jun 2017 14:21:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:21:05: #2 number of paired peaks: 615 WARNING @ Sat, 03 Jun 2017 14:21:05: Fewer paired peaks (615) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 615 pairs to build model! INFO @ Sat, 03 Jun 2017 14:21:05: start model_add_line... INFO @ Sat, 03 Jun 2017 14:21:05: start X-correlation... INFO @ Sat, 03 Jun 2017 14:21:05: end of X-cor INFO @ Sat, 03 Jun 2017 14:21:05: #2 finished! INFO @ Sat, 03 Jun 2017 14:21:05: #2 predicted fragment length is 96 bps INFO @ Sat, 03 Jun 2017 14:21:05: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 03 Jun 2017 14:21:05: #2.2 Generate R script for model : SRX1840072.10_model.r WARNING @ Sat, 03 Jun 2017 14:21:05: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:21:05: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 03 Jun 2017 14:21:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:21:05: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:21:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:21:05: #2 number of paired peaks: 615 WARNING @ Sat, 03 Jun 2017 14:21:05: Fewer paired peaks (615) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 615 pairs to build model! INFO @ Sat, 03 Jun 2017 14:21:05: start model_add_line... INFO @ Sat, 03 Jun 2017 14:21:07: start X-correlation... INFO @ Sat, 03 Jun 2017 14:21:07: end of X-cor INFO @ Sat, 03 Jun 2017 14:21:07: #2 finished! INFO @ Sat, 03 Jun 2017 14:21:07: #2 predicted fragment length is 96 bps INFO @ Sat, 03 Jun 2017 14:21:07: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 03 Jun 2017 14:21:07: #2.2 Generate R script for model : SRX1840072.05_model.r WARNING @ Sat, 03 Jun 2017 14:21:07: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:21:07: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 03 Jun 2017 14:21:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:21:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:21:07: start X-correlation... INFO @ Sat, 03 Jun 2017 14:21:07: end of X-cor INFO @ Sat, 03 Jun 2017 14:21:07: #2 finished! INFO @ Sat, 03 Jun 2017 14:21:07: #2 predicted fragment length is 96 bps INFO @ Sat, 03 Jun 2017 14:21:07: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 03 Jun 2017 14:21:07: #2.2 Generate R script for model : SRX1840072.20_model.r WARNING @ Sat, 03 Jun 2017 14:21:07: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:21:07: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 03 Jun 2017 14:21:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 14:21:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:21:33: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:21:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:21:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:21:55: #4 Write output xls file... SRX1840072.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:21:55: #4 Write peak in narrowPeak format file... SRX1840072.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:21:55: #4 Write summits bed file... SRX1840072.05_summits.bed INFO @ Sat, 03 Jun 2017 14:21:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1874 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:21:55: #4 Write output xls file... SRX1840072.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:21:55: #4 Write peak in narrowPeak format file... SRX1840072.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:21:55: #4 Write summits bed file... SRX1840072.20_summits.bed INFO @ Sat, 03 Jun 2017 14:21:55: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (812 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:21:56: #4 Write output xls file... SRX1840072.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:21:56: #4 Write peak in narrowPeak format file... SRX1840072.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:21:56: #4 Write summits bed file... SRX1840072.10_summits.bed INFO @ Sat, 03 Jun 2017 14:21:56: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1200 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。