Job ID = 9036592 sra ファイルのダウンロード中... Completed: 423318K bytes transferred in 6 seconds (519400K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:10 --:--:-- 0 100 22318 0 22318 0 0 1973 0 --:--:-- 0:00:11 --:--:-- 4526 100 46127 0 46127 0 0 3905 0 --:--:-- 0:00:11 --:--:-- 10419 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 6462137 spots for /home/okishinya/chipatlas/results/sacCer3/SRX360917/SRR1003639.sra Written 6462137 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: 00:02:50 6462137 reads; of these: 6462137 (100.00%) were unpaired; of these: 6451541 (99.84%) aligned 0 times 8301 (0.13%) aligned exactly 1 time 2295 (0.04%) aligned >1 times 0.16% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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] 4805 / 10596 = 0.4535 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 03:26:54: # Command line: callpeak -t SRX360917.bam -f BAM -g 12100000 -n SRX360917.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX360917.20 # format = BAM # ChIP-seq file = ['SRX360917.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 03:26:54: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:26:54: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:26:54: # Command line: callpeak -t SRX360917.bam -f BAM -g 12100000 -n SRX360917.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX360917.05 # format = BAM # ChIP-seq file = ['SRX360917.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 03:26:54: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:26:54: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:26:54: # Command line: callpeak -t SRX360917.bam -f BAM -g 12100000 -n SRX360917.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX360917.10 # format = BAM # ChIP-seq file = ['SRX360917.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 03:26:54: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:26:54: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:26:54: #1 tag size is determined as 102 bps INFO @ Sun, 04 Jun 2017 03:26:54: #1 tag size = 102 INFO @ Sun, 04 Jun 2017 03:26:54: #1 total tags in treatment: 5791 INFO @ Sun, 04 Jun 2017 03:26:54: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:26:54: #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 03:26:54: #1 tags after filtering in treatment: 5753 INFO @ Sun, 04 Jun 2017 03:26:54: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 04 Jun 2017 03:26:54: #1 finished! INFO @ Sun, 04 Jun 2017 03:26:54: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:26:54: #1 tag size is determined as 102 bps INFO @ Sun, 04 Jun 2017 03:26:54: #1 tag size = 102 INFO @ Sun, 04 Jun 2017 03:26:54: #1 total tags in treatment: 5791 INFO @ Sun, 04 Jun 2017 03:26:54: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:26:54: #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 03:26:54: #1 tag size is determined as 102 bps INFO @ Sun, 04 Jun 2017 03:26:54: #1 tag size = 102 INFO @ Sun, 04 Jun 2017 03:26:54: #1 total tags in treatment: 5791 INFO @ Sun, 04 Jun 2017 03:26:54: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:26:54: #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 03:26:54: #1 tags after filtering in treatment: 5753 INFO @ Sun, 04 Jun 2017 03:26:54: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 04 Jun 2017 03:26:54: #1 finished! INFO @ Sun, 04 Jun 2017 03:26:54: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:26:54: #1 tags after filtering in treatment: 5753 INFO @ Sun, 04 Jun 2017 03:26:54: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 04 Jun 2017 03:26:54: #1 finished! INFO @ Sun, 04 Jun 2017 03:26:54: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:26:54: #2 number of paired peaks: 235 WARNING @ Sun, 04 Jun 2017 03:26:54: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Sun, 04 Jun 2017 03:26:54: start model_add_line... INFO @ Sun, 04 Jun 2017 03:26:54: #2 number of paired peaks: 235 WARNING @ Sun, 04 Jun 2017 03:26:54: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Sun, 04 Jun 2017 03:26:54: start model_add_line... INFO @ Sun, 04 Jun 2017 03:26:54: #2 number of paired peaks: 235 WARNING @ Sun, 04 Jun 2017 03:26:54: Fewer paired peaks (235) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 235 pairs to build model! INFO @ Sun, 04 Jun 2017 03:26:54: start model_add_line... INFO @ Sun, 04 Jun 2017 03:26:54: start X-correlation... INFO @ Sun, 04 Jun 2017 03:26:54: start X-correlation... INFO @ Sun, 04 Jun 2017 03:26:54: end of X-cor INFO @ Sun, 04 Jun 2017 03:26:54: #2 finished! INFO @ Sun, 04 Jun 2017 03:26:54: #2 predicted fragment length is 95 bps INFO @ Sun, 04 Jun 2017 03:26:54: #2 alternative fragment length(s) may be 95,144,275,430,593 bps INFO @ Sun, 04 Jun 2017 03:26:54: #2.2 Generate R script for model : SRX360917.20_model.r INFO @ Sun, 04 Jun 2017 03:26:54: start X-correlation... INFO @ Sun, 04 Jun 2017 03:26:54: end of X-cor INFO @ Sun, 04 Jun 2017 03:26:54: #2 finished! INFO @ Sun, 04 Jun 2017 03:26:54: #2 predicted fragment length is 95 bps INFO @ Sun, 04 Jun 2017 03:26:54: #2 alternative fragment length(s) may be 95,144,275,430,593 bps INFO @ Sun, 04 Jun 2017 03:26:54: #2.2 Generate R script for model : SRX360917.10_model.r INFO @ Sun, 04 Jun 2017 03:26:54: end of X-cor INFO @ Sun, 04 Jun 2017 03:26:54: #2 finished! INFO @ Sun, 04 Jun 2017 03:26:54: #2 predicted fragment length is 95 bps INFO @ Sun, 04 Jun 2017 03:26:54: #2 alternative fragment length(s) may be 95,144,275,430,593 bps WARNING @ Sun, 04 Jun 2017 03:26:54: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Sun, 04 Jun 2017 03:26:54: #2.2 Generate R script for model : SRX360917.05_model.r WARNING @ Sun, 04 Jun 2017 03:26:54: #2 You may need to consider one of the other alternative d(s): 95,144,275,430,593 WARNING @ Sun, 04 Jun 2017 03:26:54: #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 03:26:54: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:26:54: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 03:26:54: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 03:26:54: #2 You may need to consider one of the other alternative d(s): 95,144,275,430,593 WARNING @ Sun, 04 Jun 2017 03:26:54: #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 03:26:54: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:26:54: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 03:26:54: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 03:26:54: #2 You may need to consider one of the other alternative d(s): 95,144,275,430,593 WARNING @ Sun, 04 Jun 2017 03:26:54: #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 03:26:54: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:26:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:26:54: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:26:54: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:26:54: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:26:54: #4 Write output xls file... SRX360917.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:26:54: #4 Write peak in narrowPeak format file... SRX360917.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:26:54: #4 Write output xls file... SRX360917.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:26:54: #4 Write summits bed file... SRX360917.10_summits.bed INFO @ Sun, 04 Jun 2017 03:26:54: #4 Write peak in narrowPeak format file... SRX360917.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:26:54: #4 Write output xls file... SRX360917.05_peaks.xls INFO @ Sun, 04 Jun 2017 03:26:54: Done! INFO @ Sun, 04 Jun 2017 03:26:54: #4 Write peak in narrowPeak format file... SRX360917.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:26:54: #4 Write summits bed file... SRX360917.20_summits.bed INFO @ Sun, 04 Jun 2017 03:26:54: Done! INFO @ Sun, 04 Jun 2017 03:26:54: #4 Write summits bed file... SRX360917.05_summits.bed INFO @ Sun, 04 Jun 2017 03:26:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (8 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling