Job ID = 9036509 sra ファイルのダウンロード中... Completed: 462979K bytes transferred in 7 seconds (538546K 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 1068 0 --:--:-- 0:00:07 --:--:-- 10163 100 30318 0 30318 0 0 3789 0 --:--:-- 0:00:08 --:--:-- 19152 100 62096 0 62096 0 0 7166 0 --:--:-- 0:00:08 --:--:-- 27635 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 13471171 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2494101/SRR5177918.sra Written 13471171 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: 00:02:53 13471171 reads; of these: 13471171 (100.00%) were unpaired; of these: 1722546 (12.79%) aligned 0 times 10075025 (74.79%) aligned exactly 1 time 1673600 (12.42%) aligned >1 times 87.21% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10131297 / 11748625 = 0.8623 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 03:22:35: # Command line: callpeak -t SRX2494101.bam -f BAM -g 12100000 -n SRX2494101.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2494101.05 # format = BAM # ChIP-seq file = ['SRX2494101.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 03:22:35: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:22:35: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:22:35: # Command line: callpeak -t SRX2494101.bam -f BAM -g 12100000 -n SRX2494101.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2494101.20 # format = BAM # ChIP-seq file = ['SRX2494101.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 03:22:35: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:22:35: # Command line: callpeak -t SRX2494101.bam -f BAM -g 12100000 -n SRX2494101.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2494101.10 # format = BAM # ChIP-seq file = ['SRX2494101.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 03:22:35: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:22:35: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:22:35: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:22:41: 1000000 INFO @ Sun, 04 Jun 2017 03:22:41: 1000000 INFO @ Sun, 04 Jun 2017 03:22:41: 1000000 INFO @ Sun, 04 Jun 2017 03:22:44: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 03:22:44: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 03:22:44: #1 total tags in treatment: 1617328 INFO @ Sun, 04 Jun 2017 03:22:44: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:22:44: #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 03:22:44: #1 tags after filtering in treatment: 1616888 INFO @ Sun, 04 Jun 2017 03:22:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:22:44: #1 finished! INFO @ Sun, 04 Jun 2017 03:22:44: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:22:45: #2 number of paired peaks: 107 WARNING @ Sun, 04 Jun 2017 03:22:45: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Sun, 04 Jun 2017 03:22:45: start model_add_line... INFO @ Sun, 04 Jun 2017 03:22:45: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 03:22:45: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 03:22:45: #1 total tags in treatment: 1617328 INFO @ Sun, 04 Jun 2017 03:22:45: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:22:45: #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 03:22:45: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 03:22:45: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 03:22:45: #1 total tags in treatment: 1617328 INFO @ Sun, 04 Jun 2017 03:22:45: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:22:45: #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 03:22:45: #1 tags after filtering in treatment: 1616888 INFO @ Sun, 04 Jun 2017 03:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:22:45: #1 finished! INFO @ Sun, 04 Jun 2017 03:22:45: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:22:45: #1 tags after filtering in treatment: 1616888 INFO @ Sun, 04 Jun 2017 03:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:22:45: #1 finished! INFO @ Sun, 04 Jun 2017 03:22:45: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:22:45: #2 number of paired peaks: 107 WARNING @ Sun, 04 Jun 2017 03:22:45: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Sun, 04 Jun 2017 03:22:45: start model_add_line... INFO @ Sun, 04 Jun 2017 03:22:45: #2 number of paired peaks: 107 WARNING @ Sun, 04 Jun 2017 03:22:45: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Sun, 04 Jun 2017 03:22:45: start model_add_line... INFO @ Sun, 04 Jun 2017 03:22:46: start X-correlation... INFO @ Sun, 04 Jun 2017 03:22:46: end of X-cor INFO @ Sun, 04 Jun 2017 03:22:46: #2 finished! INFO @ Sun, 04 Jun 2017 03:22:46: #2 predicted fragment length is 50 bps INFO @ Sun, 04 Jun 2017 03:22:46: #2 alternative fragment length(s) may be 3,50,460,465,497,504,508,566,587 bps INFO @ Sun, 04 Jun 2017 03:22:46: #2.2 Generate R script for model : SRX2494101.10_model.r WARNING @ Sun, 04 Jun 2017 03:22:46: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 03:22:46: #2 You may need to consider one of the other alternative d(s): 3,50,460,465,497,504,508,566,587 WARNING @ Sun, 04 Jun 2017 03:22:46: #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 03:22:46: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:22:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:22:47: start X-correlation... INFO @ Sun, 04 Jun 2017 03:22:47: end of X-cor INFO @ Sun, 04 Jun 2017 03:22:47: #2 finished! INFO @ Sun, 04 Jun 2017 03:22:47: #2 predicted fragment length is 50 bps INFO @ Sun, 04 Jun 2017 03:22:47: #2 alternative fragment length(s) may be 3,50,460,465,497,504,508,566,587 bps INFO @ Sun, 04 Jun 2017 03:22:47: #2.2 Generate R script for model : SRX2494101.20_model.r INFO @ Sun, 04 Jun 2017 03:22:47: start X-correlation... INFO @ Sun, 04 Jun 2017 03:22:47: end of X-cor INFO @ Sun, 04 Jun 2017 03:22:47: #2 finished! INFO @ Sun, 04 Jun 2017 03:22:47: #2 predicted fragment length is 50 bps INFO @ Sun, 04 Jun 2017 03:22:47: #2 alternative fragment length(s) may be 3,50,460,465,497,504,508,566,587 bps INFO @ Sun, 04 Jun 2017 03:22:47: #2.2 Generate R script for model : SRX2494101.05_model.r WARNING @ Sun, 04 Jun 2017 03:22:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 03:22:47: #2 You may need to consider one of the other alternative d(s): 3,50,460,465,497,504,508,566,587 WARNING @ Sun, 04 Jun 2017 03:22:47: #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 03:22:47: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:22:47: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 03:22:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 03:22:47: #2 You may need to consider one of the other alternative d(s): 3,50,460,465,497,504,508,566,587 WARNING @ Sun, 04 Jun 2017 03:22:47: #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 03:22:47: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:22:54: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:22:55: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:22:56: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:23:00: #4 Write output xls file... SRX2494101.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:23:00: #4 Write peak in narrowPeak format file... SRX2494101.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:23:00: #4 Write summits bed file... SRX2494101.10_summits.bed INFO @ Sun, 04 Jun 2017 03:23:00: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (158 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:23:01: #4 Write output xls file... SRX2494101.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:23:01: #4 Write peak in narrowPeak format file... SRX2494101.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:23:01: #4 Write summits bed file... SRX2494101.20_summits.bed INFO @ Sun, 04 Jun 2017 03:23:01: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:23:02: #4 Write output xls file... SRX2494101.05_peaks.xls INFO @ Sun, 04 Jun 2017 03:23:02: #4 Write peak in narrowPeak format file... SRX2494101.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:23:02: #4 Write summits bed file... SRX2494101.05_summits.bed INFO @ Sun, 04 Jun 2017 03:23:02: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (505 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。