Job ID = 9302865 sra ファイルのダウンロード中... Completed: 531743K bytes transferred in 7 seconds (565696K bits/sec), in 1 file, 2 directories. 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 19742160 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2022602/SRR4031070.sra Written 19742160 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: 00:02:55 19742160 reads; of these: 19742160 (100.00%) were unpaired; of these: 9495269 (48.10%) aligned 0 times 8480789 (42.96%) aligned exactly 1 time 1766102 (8.95%) aligned >1 times 51.90% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 9218612 / 10246891 = 0.8996 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 @ Fri, 28 Jul 2017 11:31:55: # Command line: callpeak -t SRX2022602.bam -f BAM -g 12100000 -n SRX2022602.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2022602.10 # format = BAM # ChIP-seq file = ['SRX2022602.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 # Paired-End mode is off INFO @ Fri, 28 Jul 2017 11:31:55: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:31:55: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:31:55: # Command line: callpeak -t SRX2022602.bam -f BAM -g 12100000 -n SRX2022602.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2022602.20 # format = BAM # ChIP-seq file = ['SRX2022602.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 # Paired-End mode is off INFO @ Fri, 28 Jul 2017 11:31:55: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:31:55: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:31:55: # Command line: callpeak -t SRX2022602.bam -f BAM -g 12100000 -n SRX2022602.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2022602.05 # format = BAM # ChIP-seq file = ['SRX2022602.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 # Paired-End mode is off INFO @ Fri, 28 Jul 2017 11:31:55: #1 read tag files... INFO @ Fri, 28 Jul 2017 11:31:55: #1 read treatment tags... INFO @ Fri, 28 Jul 2017 11:32:02: 1000000 INFO @ Fri, 28 Jul 2017 11:32:02: #1 tag size is determined as 51 bps INFO @ Fri, 28 Jul 2017 11:32:02: #1 tag size = 51 INFO @ Fri, 28 Jul 2017 11:32:02: #1 total tags in treatment: 1028279 INFO @ Fri, 28 Jul 2017 11:32:02: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:32:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:32:02: #1 tags after filtering in treatment: 1028279 INFO @ Fri, 28 Jul 2017 11:32:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 28 Jul 2017 11:32:02: #1 finished! INFO @ Fri, 28 Jul 2017 11:32:02: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:32:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:32:03: #2 number of paired peaks: 334 WARNING @ Fri, 28 Jul 2017 11:32:03: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Fri, 28 Jul 2017 11:32:03: start model_add_line... INFO @ Fri, 28 Jul 2017 11:32:03: start X-correlation... INFO @ Fri, 28 Jul 2017 11:32:03: 1000000 INFO @ Fri, 28 Jul 2017 11:32:03: end of X-cor INFO @ Fri, 28 Jul 2017 11:32:03: #2 finished! INFO @ Fri, 28 Jul 2017 11:32:03: #2 predicted fragment length is 116 bps INFO @ Fri, 28 Jul 2017 11:32:03: #2 alternative fragment length(s) may be 116 bps INFO @ Fri, 28 Jul 2017 11:32:03: #2.2 Generate R script for model : SRX2022602.10_model.r INFO @ Fri, 28 Jul 2017 11:32:03: 1000000 INFO @ Fri, 28 Jul 2017 11:32:03: #3 Call peaks... INFO @ Fri, 28 Jul 2017 11:32:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 28 Jul 2017 11:32:03: #1 tag size is determined as 51 bps INFO @ Fri, 28 Jul 2017 11:32:03: #1 tag size = 51 INFO @ Fri, 28 Jul 2017 11:32:03: #1 total tags in treatment: 1028279 INFO @ Fri, 28 Jul 2017 11:32:03: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:32:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:32:03: #1 tag size is determined as 51 bps INFO @ Fri, 28 Jul 2017 11:32:03: #1 tag size = 51 INFO @ Fri, 28 Jul 2017 11:32:03: #1 total tags in treatment: 1028279 INFO @ Fri, 28 Jul 2017 11:32:03: #1 user defined the maximum tags... INFO @ Fri, 28 Jul 2017 11:32:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 28 Jul 2017 11:32:03: #1 tags after filtering in treatment: 1028279 INFO @ Fri, 28 Jul 2017 11:32:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 28 Jul 2017 11:32:03: #1 finished! INFO @ Fri, 28 Jul 2017 11:32:03: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:32:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:32:03: #1 tags after filtering in treatment: 1028279 INFO @ Fri, 28 Jul 2017 11:32:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 28 Jul 2017 11:32:03: #1 finished! INFO @ Fri, 28 Jul 2017 11:32:03: #2 Build Peak Model... INFO @ Fri, 28 Jul 2017 11:32:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 28 Jul 2017 11:32:03: #2 number of paired peaks: 334 WARNING @ Fri, 28 Jul 2017 11:32:03: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Fri, 28 Jul 2017 11:32:03: start model_add_line... INFO @ Fri, 28 Jul 2017 11:32:03: #2 number of paired peaks: 334 WARNING @ Fri, 28 Jul 2017 11:32:03: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Fri, 28 Jul 2017 11:32:03: start model_add_line... INFO @ Fri, 28 Jul 2017 11:32:03: start X-correlation... INFO @ Fri, 28 Jul 2017 11:32:03: end of X-cor INFO @ Fri, 28 Jul 2017 11:32:03: #2 finished! INFO @ Fri, 28 Jul 2017 11:32:03: #2 predicted fragment length is 116 bps INFO @ Fri, 28 Jul 2017 11:32:03: #2 alternative fragment length(s) may be 116 bps INFO @ Fri, 28 Jul 2017 11:32:03: #2.2 Generate R script for model : SRX2022602.05_model.r INFO @ Fri, 28 Jul 2017 11:32:03: start X-correlation... INFO @ Fri, 28 Jul 2017 11:32:03: end of X-cor INFO @ Fri, 28 Jul 2017 11:32:03: #2 finished! INFO @ Fri, 28 Jul 2017 11:32:03: #2 predicted fragment length is 116 bps INFO @ Fri, 28 Jul 2017 11:32:03: #2 alternative fragment length(s) may be 116 bps INFO @ Fri, 28 Jul 2017 11:32:03: #2.2 Generate R script for model : SRX2022602.20_model.r INFO @ Fri, 28 Jul 2017 11:32:03: #3 Call peaks... INFO @ Fri, 28 Jul 2017 11:32:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 28 Jul 2017 11:32:03: #3 Call peaks... INFO @ Fri, 28 Jul 2017 11:32:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 28 Jul 2017 11:32:06: #3 Call peaks for each chromosome... INFO @ Fri, 28 Jul 2017 11:32:07: #3 Call peaks for each chromosome... INFO @ Fri, 28 Jul 2017 11:32:07: #3 Call peaks for each chromosome... INFO @ Fri, 28 Jul 2017 11:32:08: #4 Write output xls file... SRX2022602.10_peaks.xls INFO @ Fri, 28 Jul 2017 11:32:08: #4 Write peak in narrowPeak format file... SRX2022602.10_peaks.narrowPeak INFO @ Fri, 28 Jul 2017 11:32:08: #4 Write summits bed file... SRX2022602.10_summits.bed INFO @ Fri, 28 Jul 2017 11:32:08: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (432 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 28 Jul 2017 11:32:08: #4 Write output xls file... SRX2022602.20_peaks.xls INFO @ Fri, 28 Jul 2017 11:32:08: #4 Write peak in narrowPeak format file... SRX2022602.20_peaks.narrowPeak INFO @ Fri, 28 Jul 2017 11:32:08: #4 Write summits bed file... SRX2022602.20_summits.bed INFO @ Fri, 28 Jul 2017 11:32:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 28 Jul 2017 11:32:08: #4 Write output xls file... SRX2022602.05_peaks.xls INFO @ Fri, 28 Jul 2017 11:32:08: #4 Write peak in narrowPeak format file... SRX2022602.05_peaks.narrowPeak INFO @ Fri, 28 Jul 2017 11:32:08: #4 Write summits bed file... SRX2022602.05_summits.bed INFO @ Fri, 28 Jul 2017 11:32:08: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (695 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。