Job ID = 11193071 sra ファイルのダウンロード中... Completed: 11420K bytes transferred in 2 seconds (31964K 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 503783 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4233962/SRR7361139.sra Written 503783 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4233962/SRR7361139.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: 00:00:05 503783 reads; of these: 503783 (100.00%) were unpaired; of these: 53118 (10.54%) aligned 0 times 382709 (75.97%) aligned exactly 1 time 67956 (13.49%) aligned >1 times 89.46% overall alignment rate Time searching: 00:00:05 Overall time: 00:00:05 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] 38246 / 450665 = 0.0849 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 10:52:33: # Command line: callpeak -t SRX4233962.bam -f BAM -g 12100000 -n SRX4233962.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4233962.10 # format = BAM # ChIP-seq file = ['SRX4233962.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 10:52:33: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:52:33: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:52:33: # Command line: callpeak -t SRX4233962.bam -f BAM -g 12100000 -n SRX4233962.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4233962.05 # format = BAM # ChIP-seq file = ['SRX4233962.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 10:52:33: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:52:33: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:52:33: # Command line: callpeak -t SRX4233962.bam -f BAM -g 12100000 -n SRX4233962.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4233962.20 # format = BAM # ChIP-seq file = ['SRX4233962.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 10:52:33: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:52:33: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:52:36: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:52:36: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:52:36: #1 total tags in treatment: 412419 INFO @ Sat, 15 Sep 2018 10:52:36: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:52:36: #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 10:52:36: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:52:36: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:52:36: #1 total tags in treatment: 412419 INFO @ Sat, 15 Sep 2018 10:52:36: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:52:36: #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 10:52:36: #1 tags after filtering in treatment: 412419 INFO @ Sat, 15 Sep 2018 10:52:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:52:36: #1 finished! INFO @ Sat, 15 Sep 2018 10:52:36: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:52:36: #1 tags after filtering in treatment: 412419 INFO @ Sat, 15 Sep 2018 10:52:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:52:36: #1 finished! INFO @ Sat, 15 Sep 2018 10:52:36: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:52:36: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:52:36: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:52:36: #1 total tags in treatment: 412419 INFO @ Sat, 15 Sep 2018 10:52:36: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:52:36: #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 10:52:36: #1 tags after filtering in treatment: 412419 INFO @ Sat, 15 Sep 2018 10:52:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:52:36: #1 finished! INFO @ Sat, 15 Sep 2018 10:52:36: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:52:36: #2 number of paired peaks: 173 WARNING @ Sat, 15 Sep 2018 10:52:36: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Sep 2018 10:52:36: start model_add_line... INFO @ Sat, 15 Sep 2018 10:52:36: start X-correlation... INFO @ Sat, 15 Sep 2018 10:52:36: end of X-cor INFO @ Sat, 15 Sep 2018 10:52:36: #2 finished! INFO @ Sat, 15 Sep 2018 10:52:36: #2 predicted fragment length is 279 bps INFO @ Sat, 15 Sep 2018 10:52:36: #2 alternative fragment length(s) may be 279 bps INFO @ Sat, 15 Sep 2018 10:52:36: #2.2 Generate R script for model : SRX4233962.10_model.r INFO @ Sat, 15 Sep 2018 10:52:36: #2 number of paired peaks: 173 WARNING @ Sat, 15 Sep 2018 10:52:36: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Sep 2018 10:52:36: start model_add_line... INFO @ Sat, 15 Sep 2018 10:52:36: start X-correlation... INFO @ Sat, 15 Sep 2018 10:52:36: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:52:36: end of X-cor INFO @ Sat, 15 Sep 2018 10:52:36: #2 finished! INFO @ Sat, 15 Sep 2018 10:52:36: #2 predicted fragment length is 279 bps INFO @ Sat, 15 Sep 2018 10:52:36: #2 alternative fragment length(s) may be 279 bps INFO @ Sat, 15 Sep 2018 10:52:36: #2.2 Generate R script for model : SRX4233962.05_model.r INFO @ Sat, 15 Sep 2018 10:52:36: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:52:36: #2 number of paired peaks: 173 WARNING @ Sat, 15 Sep 2018 10:52:36: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Sep 2018 10:52:36: start model_add_line... INFO @ Sat, 15 Sep 2018 10:52:36: start X-correlation... INFO @ Sat, 15 Sep 2018 10:52:36: end of X-cor INFO @ Sat, 15 Sep 2018 10:52:36: #2 finished! INFO @ Sat, 15 Sep 2018 10:52:36: #2 predicted fragment length is 279 bps INFO @ Sat, 15 Sep 2018 10:52:36: #2 alternative fragment length(s) may be 279 bps INFO @ Sat, 15 Sep 2018 10:52:36: #2.2 Generate R script for model : SRX4233962.20_model.r INFO @ Sat, 15 Sep 2018 10:52:36: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:52:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:52:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:52:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:52:38: #4 Write output xls file... SRX4233962.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:52:38: #4 Write peak in narrowPeak format file... SRX4233962.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:52:38: #4 Write summits bed file... SRX4233962.05_summits.bed INFO @ Sat, 15 Sep 2018 10:52:38: Done! INFO @ Sat, 15 Sep 2018 10:52:38: #4 Write output xls file... SRX4233962.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:52:38: #4 Write peak in narrowPeak format file... SRX4233962.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:52:38: #4 Write summits bed file... SRX4233962.10_summits.bed pass1 - making usageList (3 chroms): 0 millis INFO @ Sat, 15 Sep 2018 10:52:38: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 46 millis pass2 - checking and writing primary data (36 records, 4 fields): 66 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:52:38: #4 Write output xls file... SRX4233962.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:52:38: #4 Write peak in narrowPeak format file... SRX4233962.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:52:38: #4 Write summits bed file... SRX4233962.20_summits.bed INFO @ Sat, 15 Sep 2018 10:52:38: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (8 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。