Job ID = 11192924 sra ファイルのダウンロード中... Completed: 54609K bytes transferred in 3 seconds (124804K bits/sec), in 1 file. 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... Read 2816215 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242039/SRR6129623.sra Written 2816215 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242039/SRR6129623.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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 2816215 reads; of these: 2816215 (100.00%) were unpaired; of these: 1093611 (38.83%) aligned 0 times 1525203 (54.16%) aligned exactly 1 time 197401 (7.01%) aligned >1 times 61.17% 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] 1343886 / 1722604 = 0.7801 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 @ Sat, 15 Sep 2018 10:31:32: # Command line: callpeak -t SRX3242039.bam -f BAM -g 12100000 -n SRX3242039.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3242039.20 # format = BAM # ChIP-seq file = ['SRX3242039.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 @ Sat, 15 Sep 2018 10:31:32: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:31:32: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:31:32: # Command line: callpeak -t SRX3242039.bam -f BAM -g 12100000 -n SRX3242039.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3242039.05 # format = BAM # ChIP-seq file = ['SRX3242039.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 @ Sat, 15 Sep 2018 10:31:32: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:31:32: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:31:32: # Command line: callpeak -t SRX3242039.bam -f BAM -g 12100000 -n SRX3242039.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3242039.10 # format = BAM # ChIP-seq file = ['SRX3242039.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 @ Sat, 15 Sep 2018 10:31:32: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:31:32: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:31:35: #1 tag size is determined as 51 bps INFO @ Sat, 15 Sep 2018 10:31:35: #1 tag size = 51 INFO @ Sat, 15 Sep 2018 10:31:35: #1 total tags in treatment: 378718 INFO @ Sat, 15 Sep 2018 10:31:35: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:31:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:31:35: #1 tags after filtering in treatment: 378718 INFO @ Sat, 15 Sep 2018 10:31:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:31:35: #1 finished! INFO @ Sat, 15 Sep 2018 10:31:35: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:31:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:31:35: #2 number of paired peaks: 106 WARNING @ Sat, 15 Sep 2018 10:31:35: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 15 Sep 2018 10:31:35: start model_add_line... INFO @ Sat, 15 Sep 2018 10:31:35: start X-correlation... INFO @ Sat, 15 Sep 2018 10:31:35: end of X-cor INFO @ Sat, 15 Sep 2018 10:31:35: #2 finished! INFO @ Sat, 15 Sep 2018 10:31:35: #2 predicted fragment length is 130 bps INFO @ Sat, 15 Sep 2018 10:31:35: #2 alternative fragment length(s) may be 130 bps INFO @ Sat, 15 Sep 2018 10:31:35: #2.2 Generate R script for model : SRX3242039.10_model.r INFO @ Sat, 15 Sep 2018 10:31:35: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:31:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:31:35: #1 tag size is determined as 51 bps INFO @ Sat, 15 Sep 2018 10:31:35: #1 tag size is determined as 51 bps INFO @ Sat, 15 Sep 2018 10:31:35: #1 tag size = 51 INFO @ Sat, 15 Sep 2018 10:31:35: #1 tag size = 51 INFO @ Sat, 15 Sep 2018 10:31:35: #1 total tags in treatment: 378718 INFO @ Sat, 15 Sep 2018 10:31:35: #1 total tags in treatment: 378718 INFO @ Sat, 15 Sep 2018 10:31:35: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:31:35: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:31:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:31:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:31:35: #1 tags after filtering in treatment: 378718 INFO @ Sat, 15 Sep 2018 10:31:35: #1 tags after filtering in treatment: 378718 INFO @ Sat, 15 Sep 2018 10:31:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:31:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:31:35: #1 finished! INFO @ Sat, 15 Sep 2018 10:31:35: #1 finished! INFO @ Sat, 15 Sep 2018 10:31:35: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:31:35: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:31:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:31:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:31:35: #2 number of paired peaks: 106 WARNING @ Sat, 15 Sep 2018 10:31:35: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 15 Sep 2018 10:31:35: start model_add_line... INFO @ Sat, 15 Sep 2018 10:31:35: #2 number of paired peaks: 106 WARNING @ Sat, 15 Sep 2018 10:31:35: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 15 Sep 2018 10:31:35: start model_add_line... INFO @ Sat, 15 Sep 2018 10:31:35: start X-correlation... INFO @ Sat, 15 Sep 2018 10:31:35: start X-correlation... INFO @ Sat, 15 Sep 2018 10:31:35: end of X-cor INFO @ Sat, 15 Sep 2018 10:31:35: end of X-cor INFO @ Sat, 15 Sep 2018 10:31:35: #2 finished! INFO @ Sat, 15 Sep 2018 10:31:35: #2 finished! INFO @ Sat, 15 Sep 2018 10:31:35: #2 predicted fragment length is 130 bps INFO @ Sat, 15 Sep 2018 10:31:35: #2 predicted fragment length is 130 bps INFO @ Sat, 15 Sep 2018 10:31:35: #2 alternative fragment length(s) may be 130 bps INFO @ Sat, 15 Sep 2018 10:31:35: #2 alternative fragment length(s) may be 130 bps INFO @ Sat, 15 Sep 2018 10:31:35: #2.2 Generate R script for model : SRX3242039.05_model.r INFO @ Sat, 15 Sep 2018 10:31:35: #2.2 Generate R script for model : SRX3242039.20_model.r INFO @ Sat, 15 Sep 2018 10:31:35: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:31:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:31:35: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:31:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:31:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:31:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:31:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:31:37: #4 Write output xls file... SRX3242039.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:31:37: #4 Write peak in narrowPeak format file... SRX3242039.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:31:37: #4 Write summits bed file... SRX3242039.10_summits.bed INFO @ Sat, 15 Sep 2018 10:31:37: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (109 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:31:37: #4 Write output xls file... SRX3242039.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:31:37: #4 Write peak in narrowPeak format file... SRX3242039.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:31:37: #4 Write summits bed file... SRX3242039.20_summits.bed INFO @ Sat, 15 Sep 2018 10:31:37: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (50 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:31:37: #4 Write output xls file... SRX3242039.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:31:37: #4 Write peak in narrowPeak format file... SRX3242039.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:31:37: #4 Write summits bed file... SRX3242039.05_summits.bed INFO @ Sat, 15 Sep 2018 10:31:37: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (246 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。