Job ID = 9037572 sra ファイルのダウンロード中... Completed: 180465K bytes transferred in 5 seconds (281135K 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 --:--:-- 0:00:07 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 100 12695 0 12695 0 0 1491 0 --:--:-- 0:00:08 --:--:-- 6097 100 37486 0 37486 0 0 3944 0 --:--:-- 0:00:09 --:--:-- 12182 100 44883 0 44883 0 0 4640 0 --:--:-- 0:00:09 --:--:-- 13835 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 6528113 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876303/SRR1802406.sra Written 6528113 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: 00:00:40 6528113 reads; of these: 6528113 (100.00%) were unpaired; of these: 3801934 (58.24%) aligned 0 times 2093551 (32.07%) aligned exactly 1 time 632628 (9.69%) aligned >1 times 41.76% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 2328622 / 2726179 = 0.8542 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 @ Sun, 04 Jun 2017 04:54:45: # Command line: callpeak -t SRX876303.bam -f BAM -g 12100000 -n SRX876303.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX876303.05 # format = BAM # ChIP-seq file = ['SRX876303.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sun, 04 Jun 2017 04:54:45: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:54:45: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:54:45: # Command line: callpeak -t SRX876303.bam -f BAM -g 12100000 -n SRX876303.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX876303.20 # format = BAM # ChIP-seq file = ['SRX876303.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sun, 04 Jun 2017 04:54:45: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:54:45: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:54:45: # Command line: callpeak -t SRX876303.bam -f BAM -g 12100000 -n SRX876303.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX876303.10 # format = BAM # ChIP-seq file = ['SRX876303.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sun, 04 Jun 2017 04:54:45: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:54:45: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:54:47: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 04:54:47: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 04:54:47: #1 total tags in treatment: 397557 INFO @ Sun, 04 Jun 2017 04:54:47: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:54:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 04:54:47: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 04:54:47: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 04:54:47: #1 total tags in treatment: 397557 INFO @ Sun, 04 Jun 2017 04:54:47: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:54:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 04:54:47: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 04:54:47: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 04:54:47: #1 total tags in treatment: 397557 INFO @ Sun, 04 Jun 2017 04:54:47: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:54:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 04:54:47: #1 tags after filtering in treatment: 397286 INFO @ Sun, 04 Jun 2017 04:54:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:54:47: #1 finished! INFO @ Sun, 04 Jun 2017 04:54:47: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:54:47: #1 tags after filtering in treatment: 397286 INFO @ Sun, 04 Jun 2017 04:54:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:54:47: #1 finished! INFO @ Sun, 04 Jun 2017 04:54:47: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:54:47: #1 tags after filtering in treatment: 397286 INFO @ Sun, 04 Jun 2017 04:54:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:54:47: #1 finished! INFO @ Sun, 04 Jun 2017 04:54:47: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:54:47: #2 number of paired peaks: 251 WARNING @ Sun, 04 Jun 2017 04:54:47: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Sun, 04 Jun 2017 04:54:47: start model_add_line... INFO @ Sun, 04 Jun 2017 04:54:47: #2 number of paired peaks: 251 WARNING @ Sun, 04 Jun 2017 04:54:47: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Sun, 04 Jun 2017 04:54:47: start model_add_line... INFO @ Sun, 04 Jun 2017 04:54:47: #2 number of paired peaks: 251 WARNING @ Sun, 04 Jun 2017 04:54:47: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Sun, 04 Jun 2017 04:54:47: start model_add_line... INFO @ Sun, 04 Jun 2017 04:54:48: start X-correlation... INFO @ Sun, 04 Jun 2017 04:54:48: end of X-cor INFO @ Sun, 04 Jun 2017 04:54:48: #2 finished! INFO @ Sun, 04 Jun 2017 04:54:48: #2 predicted fragment length is 51 bps INFO @ Sun, 04 Jun 2017 04:54:48: #2 alternative fragment length(s) may be 51,230,289,417,448,490,554 bps INFO @ Sun, 04 Jun 2017 04:54:48: #2.2 Generate R script for model : SRX876303.20_model.r WARNING @ Sun, 04 Jun 2017 04:54:48: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 04:54:48: #2 You may need to consider one of the other alternative d(s): 51,230,289,417,448,490,554 WARNING @ Sun, 04 Jun 2017 04:54:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 04:54:48: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:54:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:54:48: start X-correlation... INFO @ Sun, 04 Jun 2017 04:54:48: end of X-cor INFO @ Sun, 04 Jun 2017 04:54:48: #2 finished! INFO @ Sun, 04 Jun 2017 04:54:48: #2 predicted fragment length is 51 bps INFO @ Sun, 04 Jun 2017 04:54:48: #2 alternative fragment length(s) may be 51,230,289,417,448,490,554 bps INFO @ Sun, 04 Jun 2017 04:54:48: #2.2 Generate R script for model : SRX876303.10_model.r WARNING @ Sun, 04 Jun 2017 04:54:48: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 04:54:48: #2 You may need to consider one of the other alternative d(s): 51,230,289,417,448,490,554 WARNING @ Sun, 04 Jun 2017 04:54:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 04:54:48: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:54:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:54:48: start X-correlation... INFO @ Sun, 04 Jun 2017 04:54:48: end of X-cor INFO @ Sun, 04 Jun 2017 04:54:48: #2 finished! INFO @ Sun, 04 Jun 2017 04:54:48: #2 predicted fragment length is 51 bps INFO @ Sun, 04 Jun 2017 04:54:48: #2 alternative fragment length(s) may be 51,230,289,417,448,490,554 bps INFO @ Sun, 04 Jun 2017 04:54:48: #2.2 Generate R script for model : SRX876303.05_model.r WARNING @ Sun, 04 Jun 2017 04:54:48: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 04:54:48: #2 You may need to consider one of the other alternative d(s): 51,230,289,417,448,490,554 WARNING @ Sun, 04 Jun 2017 04:54:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 04:54:48: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:54:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:54:50: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:54:50: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:54:50: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:54:52: #4 Write output xls file... SRX876303.20_peaks.xls INFO @ Sun, 04 Jun 2017 04:54:52: #4 Write output xls file... SRX876303.10_peaks.xls INFO @ Sun, 04 Jun 2017 04:54:52: #4 Write peak in narrowPeak format file... SRX876303.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:54:52: #4 Write summits bed file... SRX876303.20_summits.bed INFO @ Sun, 04 Jun 2017 04:54:52: #4 Write peak in narrowPeak format file... SRX876303.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:54:52: Done! INFO @ Sun, 04 Jun 2017 04:54:52: #4 Write summits bed file... SRX876303.10_summits.bed INFO @ Sun, 04 Jun 2017 04:54:52: Done! pass1 - making usageList (14 chroms): 0 millis pass1 - making usageList (15 chroms)pass2 - checking and writing primary data (26 records, 4 fields): 0 millis : 2 millis pass2 - checking and writing primary data (66 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:54:52: #4 Write output xls file... SRX876303.05_peaks.xls INFO @ Sun, 04 Jun 2017 04:54:52: #4 Write peak in narrowPeak format file... SRX876303.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:54:52: #4 Write summits bed file... SRX876303.05_summits.bed INFO @ Sun, 04 Jun 2017 04:54:52: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (207 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。