Job ID = 9035900 sra ファイルのダウンロード中... Completed: 267121K bytes transferred in 5 seconds (400499K 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 --:--:-- 0 101 5455 0 5455 0 0 712 0 --:--:-- 0:00:07 --:--:-- 4332 100 30277 0 30277 0 0 3500 0 --:--:-- 0:00:08 --:--:-- 13426 100 32148 0 32148 0 0 3646 0 --:--:-- 0:00:08 --:--:-- 13278 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 7643683 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1054414/SRR2057635.sra Written 7643683 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: 00:01:44 7643683 reads; of these: 7643683 (100.00%) were unpaired; of these: 7623361 (99.73%) aligned 0 times 15572 (0.20%) aligned exactly 1 time 4750 (0.06%) aligned >1 times 0.27% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 2764 / 20322 = 0.1360 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 01:53:59: # Command line: callpeak -t SRX1054414.bam -f BAM -g 12100000 -n SRX1054414.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1054414.10 # format = BAM # ChIP-seq file = ['SRX1054414.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 01:53:59: #1 read tag files... INFO @ Sun, 04 Jun 2017 01:53:59: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 01:53:59: # Command line: callpeak -t SRX1054414.bam -f BAM -g 12100000 -n SRX1054414.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1054414.05 # format = BAM # ChIP-seq file = ['SRX1054414.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 01:53:59: #1 read tag files... INFO @ Sun, 04 Jun 2017 01:53:59: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 01:53:59: # Command line: callpeak -t SRX1054414.bam -f BAM -g 12100000 -n SRX1054414.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1054414.20 # format = BAM # ChIP-seq file = ['SRX1054414.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 01:53:59: #1 read tag files... INFO @ Sun, 04 Jun 2017 01:53:59: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 04 Jun 2017 01:53:59: #1 tag size is determined as 48 bps INFO @ Sun, 04 Jun 2017 01:53:59: #1 tag size = 48 INFO @ Sun, 04 Jun 2017 01:53:59: #1 total tags in treatment: 17558 INFO @ Sun, 04 Jun 2017 01:53:59: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 01:53:59: #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 01:53:59: #1 tags after filtering in treatment: 17472 INFO @ Sun, 04 Jun 2017 01:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 01:53:59: #1 finished! INFO @ Sun, 04 Jun 2017 01:53:59: #2 Build Peak Model... BigWig に変換しました。 INFO @ Sun, 04 Jun 2017 01:53:59: #1 tag size is determined as 48 bps INFO @ Sun, 04 Jun 2017 01:53:59: #1 tag size = 48 INFO @ Sun, 04 Jun 2017 01:53:59: #1 total tags in treatment: 17558 INFO @ Sun, 04 Jun 2017 01:53:59: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 01:53:59: #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 01:53:59: #1 tag size is determined as 48 bps INFO @ Sun, 04 Jun 2017 01:53:59: #1 tag size = 48 INFO @ Sun, 04 Jun 2017 01:53:59: #1 total tags in treatment: 17558 INFO @ Sun, 04 Jun 2017 01:53:59: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 01:53:59: #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 01:53:59: #1 tags after filtering in treatment: 17472 INFO @ Sun, 04 Jun 2017 01:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 01:53:59: #1 finished! INFO @ Sun, 04 Jun 2017 01:53:59: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 01:53:59: #1 tags after filtering in treatment: 17472 INFO @ Sun, 04 Jun 2017 01:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 01:53:59: #1 finished! INFO @ Sun, 04 Jun 2017 01:53:59: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 01:53:59: #2 number of paired peaks: 238 WARNING @ Sun, 04 Jun 2017 01:53:59: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Sun, 04 Jun 2017 01:53:59: start model_add_line... INFO @ Sun, 04 Jun 2017 01:53:59: #2 number of paired peaks: 238 WARNING @ Sun, 04 Jun 2017 01:53:59: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Sun, 04 Jun 2017 01:53:59: start model_add_line... INFO @ Sun, 04 Jun 2017 01:53:59: #2 number of paired peaks: 238 WARNING @ Sun, 04 Jun 2017 01:53:59: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Sun, 04 Jun 2017 01:53:59: start model_add_line... INFO @ Sun, 04 Jun 2017 01:53:59: start X-correlation... INFO @ Sun, 04 Jun 2017 01:53:59: end of X-cor INFO @ Sun, 04 Jun 2017 01:53:59: #2 finished! INFO @ Sun, 04 Jun 2017 01:53:59: #2 predicted fragment length is 47 bps INFO @ Sun, 04 Jun 2017 01:53:59: #2 alternative fragment length(s) may be 47,141,195,239,281,311,415,450,475,520,544,588 bps INFO @ Sun, 04 Jun 2017 01:53:59: #2.2 Generate R script for model : SRX1054414.10_model.r WARNING @ Sun, 04 Jun 2017 01:53:59: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 01:53:59: #2 You may need to consider one of the other alternative d(s): 47,141,195,239,281,311,415,450,475,520,544,588 WARNING @ Sun, 04 Jun 2017 01:53:59: #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 01:53:59: #3 Call peaks... INFO @ Sun, 04 Jun 2017 01:53:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 01:53:59: start X-correlation... INFO @ Sun, 04 Jun 2017 01:53:59: end of X-cor INFO @ Sun, 04 Jun 2017 01:53:59: #2 finished! INFO @ Sun, 04 Jun 2017 01:53:59: #2 predicted fragment length is 47 bps INFO @ Sun, 04 Jun 2017 01:53:59: #2 alternative fragment length(s) may be 47,141,195,239,281,311,415,450,475,520,544,588 bps INFO @ Sun, 04 Jun 2017 01:53:59: #2.2 Generate R script for model : SRX1054414.05_model.r INFO @ Sun, 04 Jun 2017 01:53:59: start X-correlation... WARNING @ Sun, 04 Jun 2017 01:53:59: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 01:53:59: #2 You may need to consider one of the other alternative d(s): 47,141,195,239,281,311,415,450,475,520,544,588 WARNING @ Sun, 04 Jun 2017 01:53:59: #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 01:53:59: #3 Call peaks... INFO @ Sun, 04 Jun 2017 01:53:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 01:53:59: end of X-cor INFO @ Sun, 04 Jun 2017 01:53:59: #2 finished! INFO @ Sun, 04 Jun 2017 01:53:59: #2 predicted fragment length is 47 bps INFO @ Sun, 04 Jun 2017 01:53:59: #2 alternative fragment length(s) may be 47,141,195,239,281,311,415,450,475,520,544,588 bps INFO @ Sun, 04 Jun 2017 01:53:59: #2.2 Generate R script for model : SRX1054414.20_model.r WARNING @ Sun, 04 Jun 2017 01:53:59: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 01:53:59: #2 You may need to consider one of the other alternative d(s): 47,141,195,239,281,311,415,450,475,520,544,588 WARNING @ Sun, 04 Jun 2017 01:53:59: #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 01:53:59: #3 Call peaks... INFO @ Sun, 04 Jun 2017 01:53:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 01:53:59: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 01:53:59: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 01:53:59: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 01:53:59: #4 Write output xls file... SRX1054414.10_peaks.xls INFO @ Sun, 04 Jun 2017 01:53:59: #4 Write peak in narrowPeak format file... SRX1054414.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 01:53:59: #4 Write summits bed file... SRX1054414.10_summits.bed INFO @ Sun, 04 Jun 2017 01:53:59: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 01:53:59: #4 Write output xls file... SRX1054414.05_peaks.xls INFO @ Sun, 04 Jun 2017 01:53:59: #4 Write peak in narrowPeak format file... SRX1054414.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 01:53:59: #4 Write summits bed file... SRX1054414.05_summits.bed INFO @ Sun, 04 Jun 2017 01:53:59: Done! INFO @ Sun, 04 Jun 2017 01:53:59: #4 Write output xls file... SRX1054414.20_peaks.xls INFO @ Sun, 04 Jun 2017 01:53:59: #4 Write peak in narrowPeak format file... SRX1054414.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 01:53:59: #4 Write summits bed file... SRX1054414.20_summits.bed INFO @ Sun, 04 Jun 2017 01:53:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis CompletedMACS2peakCalling