Job ID = 9037569 sra ファイルのダウンロード中... Completed: 105997K bytes transferred in 4 seconds (188289K 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 --:--:-- 0 100 7663 0 7663 0 0 1032 0 --:--:-- 0:00:07 --:--:-- 7851 100 23766 0 23766 0 0 2880 0 --:--:-- 0:00:08 --:--:-- 13159 100 43387 0 43387 0 0 4867 0 --:--:-- 0:00:08 --:--:-- 17572 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 3833689 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876300/SRR1802403.sra Written 3833689 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: 00:00:28 3833689 reads; of these: 3833689 (100.00%) were unpaired; of these: 1894245 (49.41%) aligned 0 times 1507690 (39.33%) aligned exactly 1 time 431754 (11.26%) aligned >1 times 50.59% overall alignment rate Time searching: 00:00:28 Overall time: 00:00:28 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] 1658879 / 1939444 = 0.8553 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 04:54:00: # Command line: callpeak -t SRX876300.bam -f BAM -g 12100000 -n SRX876300.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX876300.10 # format = BAM # ChIP-seq file = ['SRX876300.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 04:54:00: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:54:00: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:54:00: # Command line: callpeak -t SRX876300.bam -f BAM -g 12100000 -n SRX876300.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX876300.20 # format = BAM # ChIP-seq file = ['SRX876300.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 04:54:00: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:54:00: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:54:00: # Command line: callpeak -t SRX876300.bam -f BAM -g 12100000 -n SRX876300.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX876300.05 # format = BAM # ChIP-seq file = ['SRX876300.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 04:54:00: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:54:00: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:54:01: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 04:54:01: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 04:54:01: #1 total tags in treatment: 280565 INFO @ Sun, 04 Jun 2017 04:54:01: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:54:01: #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 04:54:01: #1 tags after filtering in treatment: 280378 INFO @ Sun, 04 Jun 2017 04:54:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:54:01: #1 finished! INFO @ Sun, 04 Jun 2017 04:54:01: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:54:01: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 04:54:01: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 04:54:01: #1 total tags in treatment: 280565 INFO @ Sun, 04 Jun 2017 04:54:01: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:54:01: #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 04:54:01: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 04:54:01: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 04:54:01: #1 total tags in treatment: 280565 INFO @ Sun, 04 Jun 2017 04:54:01: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:54:01: #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 04:54:01: #2 number of paired peaks: 251 WARNING @ Sun, 04 Jun 2017 04:54:01: 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 04:54:01: start model_add_line... INFO @ Sun, 04 Jun 2017 04:54:01: #1 tags after filtering in treatment: 280378 INFO @ Sun, 04 Jun 2017 04:54:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:54:01: #1 finished! INFO @ Sun, 04 Jun 2017 04:54:01: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:54:01: #1 tags after filtering in treatment: 280378 INFO @ Sun, 04 Jun 2017 04:54:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:54:01: #1 finished! INFO @ Sun, 04 Jun 2017 04:54:01: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:54:01: #2 number of paired peaks: 251 WARNING @ Sun, 04 Jun 2017 04:54:01: 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 04:54:01: start model_add_line... INFO @ Sun, 04 Jun 2017 04:54:01: #2 number of paired peaks: 251 WARNING @ Sun, 04 Jun 2017 04:54:01: 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 04:54:01: start model_add_line... INFO @ Sun, 04 Jun 2017 04:54:02: start X-correlation... INFO @ Sun, 04 Jun 2017 04:54:02: end of X-cor INFO @ Sun, 04 Jun 2017 04:54:02: #2 finished! INFO @ Sun, 04 Jun 2017 04:54:02: #2 predicted fragment length is 44 bps INFO @ Sun, 04 Jun 2017 04:54:02: #2 alternative fragment length(s) may be 44,57,136,182,252,327,349,397,443,517,548,567,593 bps INFO @ Sun, 04 Jun 2017 04:54:02: #2.2 Generate R script for model : SRX876300.10_model.r WARNING @ Sun, 04 Jun 2017 04:54:02: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 04:54:02: #2 You may need to consider one of the other alternative d(s): 44,57,136,182,252,327,349,397,443,517,548,567,593 WARNING @ Sun, 04 Jun 2017 04:54:02: #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 04:54:02: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:54:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:54:02: start X-correlation... INFO @ Sun, 04 Jun 2017 04:54:02: start X-correlation... INFO @ Sun, 04 Jun 2017 04:54:02: end of X-cor INFO @ Sun, 04 Jun 2017 04:54:02: #2 finished! INFO @ Sun, 04 Jun 2017 04:54:02: #2 predicted fragment length is 44 bps INFO @ Sun, 04 Jun 2017 04:54:02: #2 alternative fragment length(s) may be 44,57,136,182,252,327,349,397,443,517,548,567,593 bps INFO @ Sun, 04 Jun 2017 04:54:02: #2.2 Generate R script for model : SRX876300.05_model.r INFO @ Sun, 04 Jun 2017 04:54:02: end of X-cor INFO @ Sun, 04 Jun 2017 04:54:02: #2 finished! INFO @ Sun, 04 Jun 2017 04:54:02: #2 predicted fragment length is 44 bps INFO @ Sun, 04 Jun 2017 04:54:02: #2 alternative fragment length(s) may be 44,57,136,182,252,327,349,397,443,517,548,567,593 bps INFO @ Sun, 04 Jun 2017 04:54:02: #2.2 Generate R script for model : SRX876300.20_model.r WARNING @ Sun, 04 Jun 2017 04:54:02: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 04:54:02: #2 You may need to consider one of the other alternative d(s): 44,57,136,182,252,327,349,397,443,517,548,567,593 WARNING @ Sun, 04 Jun 2017 04:54:02: #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 04:54:02: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:54:02: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 04:54:02: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 04:54:02: #2 You may need to consider one of the other alternative d(s): 44,57,136,182,252,327,349,397,443,517,548,567,593 WARNING @ Sun, 04 Jun 2017 04:54:02: #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 04:54:02: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:54:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:54:04: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:54:04: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:54:04: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:54:05: #4 Write output xls file... SRX876300.05_peaks.xls INFO @ Sun, 04 Jun 2017 04:54:05: #4 Write peak in narrowPeak format file... SRX876300.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:54:05: #4 Write summits bed file... SRX876300.05_summits.bed INFO @ Sun, 04 Jun 2017 04:54:05: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:54:05: #4 Write output xls file... SRX876300.20_peaks.xls INFO @ Sun, 04 Jun 2017 04:54:05: #4 Write peak in narrowPeak format file... SRX876300.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:54:05: #4 Write summits bed file... SRX876300.20_summits.bed INFO @ Sun, 04 Jun 2017 04:54:05: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:54:05: #4 Write output xls file... SRX876300.10_peaks.xls INFO @ Sun, 04 Jun 2017 04:54:05: #4 Write peak in narrowPeak format file... SRX876300.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:54:05: #4 Write summits bed file... SRX876300.10_summits.bed INFO @ Sun, 04 Jun 2017 04:54:05: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (18 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。