Job ID = 9037675 sra ファイルのダウンロード中... Completed: 96417K bytes transferred in 4 seconds (187376K 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 1022 0 --:--:-- 0:00:07 --:--:-- 7175 100 31694 0 31694 0 0 3806 0 --:--:-- 0:00:08 --:--:-- 16689 100 44035 0 44035 0 0 4990 0 --:--:-- 0:00:08 --:--:-- 18386 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 4341473 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977466/SRR1951312.sra Written 4341473 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: 00:00:33 4341473 reads; of these: 4341473 (100.00%) were unpaired; of these: 1092758 (25.17%) aligned 0 times 3068101 (70.67%) aligned exactly 1 time 180614 (4.16%) aligned >1 times 74.83% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 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] 3019815 / 3248715 = 0.9295 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 05:09:16: # Command line: callpeak -t SRX977466.bam -f BAM -g 12100000 -n SRX977466.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977466.05 # format = BAM # ChIP-seq file = ['SRX977466.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 05:09:16: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:09:16: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:09:16: # Command line: callpeak -t SRX977466.bam -f BAM -g 12100000 -n SRX977466.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977466.10 # format = BAM # ChIP-seq file = ['SRX977466.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 05:09:16: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:09:16: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:09:16: # Command line: callpeak -t SRX977466.bam -f BAM -g 12100000 -n SRX977466.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977466.20 # format = BAM # ChIP-seq file = ['SRX977466.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 05:09:16: #1 read tag files... INFO @ Sun, 04 Jun 2017 05:09:16: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 05:09:17: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:09:17: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:09:17: #1 total tags in treatment: 228900 INFO @ Sun, 04 Jun 2017 05:09:17: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:09:17: #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 05:09:17: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:09:17: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:09:17: #1 total tags in treatment: 228900 INFO @ Sun, 04 Jun 2017 05:09:17: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:09:17: #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 05:09:17: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 05:09:17: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 05:09:17: #1 total tags in treatment: 228900 INFO @ Sun, 04 Jun 2017 05:09:17: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 05:09:17: #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 05:09:17: #1 tags after filtering in treatment: 228332 INFO @ Sun, 04 Jun 2017 05:09:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:09:17: #1 finished! INFO @ Sun, 04 Jun 2017 05:09:17: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:09:17: #1 tags after filtering in treatment: 228332 INFO @ Sun, 04 Jun 2017 05:09:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:09:17: #1 finished! INFO @ Sun, 04 Jun 2017 05:09:17: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:09:17: #1 tags after filtering in treatment: 228332 INFO @ Sun, 04 Jun 2017 05:09:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 05:09:17: #1 finished! INFO @ Sun, 04 Jun 2017 05:09:17: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 05:09:17: #2 number of paired peaks: 655 WARNING @ Sun, 04 Jun 2017 05:09:17: Fewer paired peaks (655) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 655 pairs to build model! INFO @ Sun, 04 Jun 2017 05:09:17: start model_add_line... INFO @ Sun, 04 Jun 2017 05:09:17: #2 number of paired peaks: 655 WARNING @ Sun, 04 Jun 2017 05:09:17: Fewer paired peaks (655) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 655 pairs to build model! INFO @ Sun, 04 Jun 2017 05:09:17: start model_add_line... INFO @ Sun, 04 Jun 2017 05:09:17: #2 number of paired peaks: 655 WARNING @ Sun, 04 Jun 2017 05:09:17: Fewer paired peaks (655) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 655 pairs to build model! INFO @ Sun, 04 Jun 2017 05:09:17: start model_add_line... INFO @ Sun, 04 Jun 2017 05:09:18: start X-correlation... INFO @ Sun, 04 Jun 2017 05:09:18: end of X-cor INFO @ Sun, 04 Jun 2017 05:09:18: #2 finished! INFO @ Sun, 04 Jun 2017 05:09:18: #2 predicted fragment length is 30 bps INFO @ Sun, 04 Jun 2017 05:09:18: #2 alternative fragment length(s) may be 30 bps INFO @ Sun, 04 Jun 2017 05:09:18: #2.2 Generate R script for model : SRX977466.05_model.r WARNING @ Sun, 04 Jun 2017 05:09:18: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:09:18: #2 You may need to consider one of the other alternative d(s): 30 WARNING @ Sun, 04 Jun 2017 05:09:18: #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 05:09:18: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:09:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:09:18: start X-correlation... INFO @ Sun, 04 Jun 2017 05:09:18: end of X-cor INFO @ Sun, 04 Jun 2017 05:09:18: #2 finished! INFO @ Sun, 04 Jun 2017 05:09:18: #2 predicted fragment length is 30 bps INFO @ Sun, 04 Jun 2017 05:09:18: #2 alternative fragment length(s) may be 30 bps INFO @ Sun, 04 Jun 2017 05:09:18: #2.2 Generate R script for model : SRX977466.10_model.r WARNING @ Sun, 04 Jun 2017 05:09:18: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:09:18: #2 You may need to consider one of the other alternative d(s): 30 WARNING @ Sun, 04 Jun 2017 05:09:18: #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 05:09:18: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:09:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:09:18: start X-correlation... INFO @ Sun, 04 Jun 2017 05:09:18: end of X-cor INFO @ Sun, 04 Jun 2017 05:09:18: #2 finished! INFO @ Sun, 04 Jun 2017 05:09:18: #2 predicted fragment length is 30 bps INFO @ Sun, 04 Jun 2017 05:09:18: #2 alternative fragment length(s) may be 30 bps INFO @ Sun, 04 Jun 2017 05:09:18: #2.2 Generate R script for model : SRX977466.20_model.r WARNING @ Sun, 04 Jun 2017 05:09:18: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 05:09:18: #2 You may need to consider one of the other alternative d(s): 30 WARNING @ Sun, 04 Jun 2017 05:09:18: #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 05:09:18: #3 Call peaks... INFO @ Sun, 04 Jun 2017 05:09:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 05:09:20: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:09:20: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:09:20: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 05:09:21: #4 Write output xls file... SRX977466.10_peaks.xls INFO @ Sun, 04 Jun 2017 05:09:21: #4 Write output xls file... SRX977466.20_peaks.xls INFO @ Sun, 04 Jun 2017 05:09:21: #4 Write peak in narrowPeak format file... SRX977466.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:09:21: #4 Write peak in narrowPeak format file... SRX977466.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:09:21: #4 Write summits bed file... SRX977466.20_summits.bed INFO @ Sun, 04 Jun 2017 05:09:21: #4 Write summits bed file... SRX977466.10_summits.bed INFO @ Sun, 04 Jun 2017 05:09:21: Done! INFO @ Sun, 04 Jun 2017 05:09:21: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (452 records, 4 fields): 2 millis pass1 - making usageList (16 chroms): 0 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (896 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 05:09:21: #4 Write output xls file... SRX977466.05_peaks.xls INFO @ Sun, 04 Jun 2017 05:09:21: #4 Write peak in narrowPeak format file... SRX977466.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 05:09:21: #4 Write summits bed file... SRX977466.05_summits.bed INFO @ Sun, 04 Jun 2017 05:09:21: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1801 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。