Job ID = 11162571 sra ファイルのダウンロード中... Completed: 442436K bytes transferred in 6 seconds (536662K 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 13851485 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3585185/SRR6495885.sra Written 13851485 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3585185/SRR6495885.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: 00:02:14 13851485 reads; of these: 13851485 (100.00%) were unpaired; of these: 4224908 (30.50%) aligned 0 times 7860272 (56.75%) aligned exactly 1 time 1766305 (12.75%) aligned >1 times 69.50% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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] 7206567 / 9626577 = 0.7486 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 @ Wed, 05 Sep 2018 10:05:12: # Command line: callpeak -t SRX3585185.bam -f BAM -g 12100000 -n SRX3585185.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3585185.10 # format = BAM # ChIP-seq file = ['SRX3585185.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 @ Wed, 05 Sep 2018 10:05:12: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:05:12: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:05:12: # Command line: callpeak -t SRX3585185.bam -f BAM -g 12100000 -n SRX3585185.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3585185.05 # format = BAM # ChIP-seq file = ['SRX3585185.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 @ Wed, 05 Sep 2018 10:05:12: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:05:12: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:05:12: # Command line: callpeak -t SRX3585185.bam -f BAM -g 12100000 -n SRX3585185.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3585185.20 # format = BAM # ChIP-seq file = ['SRX3585185.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 @ Wed, 05 Sep 2018 10:05:12: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:05:12: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:05:19: 1000000 INFO @ Wed, 05 Sep 2018 10:05:20: 1000000 INFO @ Wed, 05 Sep 2018 10:05:20: 1000000 INFO @ Wed, 05 Sep 2018 10:05:26: 2000000 INFO @ Wed, 05 Sep 2018 10:05:27: 2000000 INFO @ Wed, 05 Sep 2018 10:05:27: 2000000 INFO @ Wed, 05 Sep 2018 10:05:29: #1 tag size is determined as 50 bps INFO @ Wed, 05 Sep 2018 10:05:29: #1 tag size = 50 INFO @ Wed, 05 Sep 2018 10:05:29: #1 total tags in treatment: 2420010 INFO @ Wed, 05 Sep 2018 10:05:29: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:05:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:05:29: #1 tags after filtering in treatment: 2420010 INFO @ Wed, 05 Sep 2018 10:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 05 Sep 2018 10:05:29: #1 finished! INFO @ Wed, 05 Sep 2018 10:05:29: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:05:29: #2 number of paired peaks: 241 WARNING @ Wed, 05 Sep 2018 10:05:29: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Wed, 05 Sep 2018 10:05:29: start model_add_line... INFO @ Wed, 05 Sep 2018 10:05:29: start X-correlation... INFO @ Wed, 05 Sep 2018 10:05:29: end of X-cor INFO @ Wed, 05 Sep 2018 10:05:29: #2 finished! INFO @ Wed, 05 Sep 2018 10:05:29: #2 predicted fragment length is 385 bps INFO @ Wed, 05 Sep 2018 10:05:29: #2 alternative fragment length(s) may be 385 bps INFO @ Wed, 05 Sep 2018 10:05:29: #2.2 Generate R script for model : SRX3585185.10_model.r INFO @ Wed, 05 Sep 2018 10:05:29: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:05:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:05:30: #1 tag size is determined as 50 bps INFO @ Wed, 05 Sep 2018 10:05:30: #1 tag size is determined as 50 bps INFO @ Wed, 05 Sep 2018 10:05:30: #1 tag size = 50 INFO @ Wed, 05 Sep 2018 10:05:30: #1 tag size = 50 INFO @ Wed, 05 Sep 2018 10:05:30: #1 total tags in treatment: 2420010 INFO @ Wed, 05 Sep 2018 10:05:30: #1 total tags in treatment: 2420010 INFO @ Wed, 05 Sep 2018 10:05:30: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:05:30: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:05:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:05:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:05:30: #1 tags after filtering in treatment: 2420010 INFO @ Wed, 05 Sep 2018 10:05:30: #1 tags after filtering in treatment: 2420010 INFO @ Wed, 05 Sep 2018 10:05:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 05 Sep 2018 10:05:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 05 Sep 2018 10:05:30: #1 finished! INFO @ Wed, 05 Sep 2018 10:05:30: #1 finished! INFO @ Wed, 05 Sep 2018 10:05:30: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:05:30: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:05:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:05:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:05:30: #2 number of paired peaks: 241 WARNING @ Wed, 05 Sep 2018 10:05:30: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Wed, 05 Sep 2018 10:05:30: start model_add_line... INFO @ Wed, 05 Sep 2018 10:05:30: #2 number of paired peaks: 241 WARNING @ Wed, 05 Sep 2018 10:05:30: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Wed, 05 Sep 2018 10:05:30: start model_add_line... INFO @ Wed, 05 Sep 2018 10:05:30: start X-correlation... INFO @ Wed, 05 Sep 2018 10:05:30: start X-correlation... INFO @ Wed, 05 Sep 2018 10:05:30: end of X-cor INFO @ Wed, 05 Sep 2018 10:05:30: #2 finished! INFO @ Wed, 05 Sep 2018 10:05:30: end of X-cor INFO @ Wed, 05 Sep 2018 10:05:30: #2 predicted fragment length is 385 bps INFO @ Wed, 05 Sep 2018 10:05:30: #2 finished! INFO @ Wed, 05 Sep 2018 10:05:30: #2 alternative fragment length(s) may be 385 bps INFO @ Wed, 05 Sep 2018 10:05:30: #2 predicted fragment length is 385 bps INFO @ Wed, 05 Sep 2018 10:05:30: #2.2 Generate R script for model : SRX3585185.05_model.r INFO @ Wed, 05 Sep 2018 10:05:30: #2 alternative fragment length(s) may be 385 bps INFO @ Wed, 05 Sep 2018 10:05:30: #2.2 Generate R script for model : SRX3585185.20_model.r INFO @ Wed, 05 Sep 2018 10:05:30: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:05:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:05:30: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:05:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:05:46: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:05:47: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:05:47: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:05:49: #4 Write output xls file... SRX3585185.10_peaks.xls INFO @ Wed, 05 Sep 2018 10:05:49: #4 Write peak in narrowPeak format file... SRX3585185.10_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:05:49: #4 Write summits bed file... SRX3585185.10_summits.bed INFO @ Wed, 05 Sep 2018 10:05:49: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (1026 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Wed, 05 Sep 2018 10:05:50: #4 Write output xls file... SRX3585185.20_peaks.xls INFO @ Wed, 05 Sep 2018 10:05:50: #4 Write peak in narrowPeak format file... SRX3585185.20_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:05:50: #4 Write summits bed file... SRX3585185.20_summits.bed INFO @ Wed, 05 Sep 2018 10:05:50: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (730 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 05 Sep 2018 10:05:50: #4 Write output xls file... SRX3585185.05_peaks.xls INFO @ Wed, 05 Sep 2018 10:05:50: #4 Write peak in narrowPeak format file... SRX3585185.05_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:05:50: #4 Write summits bed file... SRX3585185.05_summits.bed INFO @ Wed, 05 Sep 2018 10:05:50: Done! pass1 - making usageList (17 chroms): 3 millis pass2 - checking and writing primary data (1366 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。