Job ID = 10608999 sra ファイルのダウンロード中... Completed: 428194K bytes transferred in 25 seconds (135568K 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... Written 7489966 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2745401/SRR5457341.sra Written 7489966 spots total 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: 00:01:50 7489966 reads; of these: 7489966 (100.00%) were unpaired; of these: 1525811 (20.37%) aligned 0 times 2327421 (31.07%) aligned exactly 1 time 3636734 (48.55%) aligned >1 times 79.63% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 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] 4207955 / 5964155 = 0.7055 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 @ Thu, 03 May 2018 23:01:09: # Command line: callpeak -t SRX2745401.bam -f BAM -g 12100000 -n SRX2745401.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2745401.05 # format = BAM # ChIP-seq file = ['SRX2745401.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 @ Thu, 03 May 2018 23:01:09: # Command line: callpeak -t SRX2745401.bam -f BAM -g 12100000 -n SRX2745401.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2745401.20 # format = BAM # ChIP-seq file = ['SRX2745401.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 @ Thu, 03 May 2018 23:01:09: #1 read tag files... INFO @ Thu, 03 May 2018 23:01:09: #1 read tag files... INFO @ Thu, 03 May 2018 23:01:09: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:01:09: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:01:09: # Command line: callpeak -t SRX2745401.bam -f BAM -g 12100000 -n SRX2745401.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2745401.10 # format = BAM # ChIP-seq file = ['SRX2745401.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 @ Thu, 03 May 2018 23:01:09: #1 read tag files... INFO @ Thu, 03 May 2018 23:01:09: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:01:19: 1000000 INFO @ Thu, 03 May 2018 23:01:20: 1000000 INFO @ Thu, 03 May 2018 23:01:20: 1000000 INFO @ Thu, 03 May 2018 23:01:26: #1 tag size is determined as 101 bps INFO @ Thu, 03 May 2018 23:01:26: #1 tag size = 101 INFO @ Thu, 03 May 2018 23:01:26: #1 total tags in treatment: 1756200 INFO @ Thu, 03 May 2018 23:01:26: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:01:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:01:26: #1 tags after filtering in treatment: 1756200 INFO @ Thu, 03 May 2018 23:01:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:01:26: #1 finished! INFO @ Thu, 03 May 2018 23:01:26: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:01:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:01:26: #2 number of paired peaks: 332 WARNING @ Thu, 03 May 2018 23:01:26: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Thu, 03 May 2018 23:01:26: start model_add_line... INFO @ Thu, 03 May 2018 23:01:26: start X-correlation... INFO @ Thu, 03 May 2018 23:01:26: end of X-cor INFO @ Thu, 03 May 2018 23:01:26: #2 finished! INFO @ Thu, 03 May 2018 23:01:26: #2 predicted fragment length is 310 bps INFO @ Thu, 03 May 2018 23:01:26: #2 alternative fragment length(s) may be 310 bps INFO @ Thu, 03 May 2018 23:01:26: #2.2 Generate R script for model : SRX2745401.20_model.r INFO @ Thu, 03 May 2018 23:01:26: #3 Call peaks... INFO @ Thu, 03 May 2018 23:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:01:27: #1 tag size is determined as 101 bps INFO @ Thu, 03 May 2018 23:01:27: #1 tag size = 101 INFO @ Thu, 03 May 2018 23:01:27: #1 total tags in treatment: 1756200 INFO @ Thu, 03 May 2018 23:01:27: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:01:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:01:27: #1 tags after filtering in treatment: 1756200 INFO @ Thu, 03 May 2018 23:01:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:01:27: #1 finished! INFO @ Thu, 03 May 2018 23:01:27: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:01:27: #1 tag size is determined as 101 bps INFO @ Thu, 03 May 2018 23:01:27: #1 tag size = 101 INFO @ Thu, 03 May 2018 23:01:27: #1 total tags in treatment: 1756200 INFO @ Thu, 03 May 2018 23:01:27: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:01:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:01:27: #1 tags after filtering in treatment: 1756200 INFO @ Thu, 03 May 2018 23:01:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:01:27: #1 finished! INFO @ Thu, 03 May 2018 23:01:27: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:01:28: #2 number of paired peaks: 332 WARNING @ Thu, 03 May 2018 23:01:28: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Thu, 03 May 2018 23:01:28: start model_add_line... INFO @ Thu, 03 May 2018 23:01:28: start X-correlation... INFO @ Thu, 03 May 2018 23:01:28: end of X-cor INFO @ Thu, 03 May 2018 23:01:28: #2 finished! INFO @ Thu, 03 May 2018 23:01:28: #2 predicted fragment length is 310 bps INFO @ Thu, 03 May 2018 23:01:28: #2 alternative fragment length(s) may be 310 bps INFO @ Thu, 03 May 2018 23:01:28: #2.2 Generate R script for model : SRX2745401.05_model.r INFO @ Thu, 03 May 2018 23:01:28: #3 Call peaks... INFO @ Thu, 03 May 2018 23:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:01:28: #2 number of paired peaks: 332 WARNING @ Thu, 03 May 2018 23:01:28: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Thu, 03 May 2018 23:01:28: start model_add_line... INFO @ Thu, 03 May 2018 23:01:28: start X-correlation... INFO @ Thu, 03 May 2018 23:01:28: end of X-cor INFO @ Thu, 03 May 2018 23:01:28: #2 finished! INFO @ Thu, 03 May 2018 23:01:28: #2 predicted fragment length is 310 bps INFO @ Thu, 03 May 2018 23:01:28: #2 alternative fragment length(s) may be 310 bps INFO @ Thu, 03 May 2018 23:01:28: #2.2 Generate R script for model : SRX2745401.10_model.r INFO @ Thu, 03 May 2018 23:01:28: #3 Call peaks... INFO @ Thu, 03 May 2018 23:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 23:01:36: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:01:37: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:01:37: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 23:01:38: #4 Write output xls file... SRX2745401.20_peaks.xls INFO @ Thu, 03 May 2018 23:01:38: #4 Write peak in narrowPeak format file... SRX2745401.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:01:38: #4 Write summits bed file... SRX2745401.20_summits.bed INFO @ Thu, 03 May 2018 23:01:38: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (326 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 23:01:39: #4 Write output xls file... SRX2745401.05_peaks.xls INFO @ Thu, 03 May 2018 23:01:39: #4 Write peak in narrowPeak format file... SRX2745401.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:01:39: #4 Write summits bed file... SRX2745401.05_summits.bed INFO @ Thu, 03 May 2018 23:01:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (531 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 23:01:40: #4 Write output xls file... SRX2745401.10_peaks.xls INFO @ Thu, 03 May 2018 23:01:40: #4 Write peak in narrowPeak format file... SRX2745401.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 23:01:40: #4 Write summits bed file... SRX2745401.10_summits.bed INFO @ Thu, 03 May 2018 23:01:40: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (438 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。