Job ID = 9157421 sra ファイルのダウンロード中... Completed: 272496K bytes transferred in 5 seconds (387572K 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 9709567 spots for /home/okishinya/chipatlas/results/ce10/SRX2144171/SRR4188775.sra Written 9709567 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: 00:01:53 9709567 reads; of these: 9709567 (100.00%) were unpaired; of these: 3748118 (38.60%) aligned 0 times 5180851 (53.36%) aligned exactly 1 time 780598 (8.04%) aligned >1 times 61.40% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1616196 / 5961449 = 0.2711 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 @ Tue, 27 Jun 2017 11:55:01: # Command line: callpeak -t SRX2144171.bam -f BAM -g ce -n SRX2144171.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144171.20 # format = BAM # ChIP-seq file = ['SRX2144171.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 27 Jun 2017 11:55:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:55:01: # Command line: callpeak -t SRX2144171.bam -f BAM -g ce -n SRX2144171.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144171.05 # format = BAM # ChIP-seq file = ['SRX2144171.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 27 Jun 2017 11:55:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:55:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:55:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:55:01: # Command line: callpeak -t SRX2144171.bam -f BAM -g ce -n SRX2144171.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144171.10 # format = BAM # ChIP-seq file = ['SRX2144171.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 27 Jun 2017 11:55:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:55:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:55:08: 1000000 INFO @ Tue, 27 Jun 2017 11:55:09: 1000000 INFO @ Tue, 27 Jun 2017 11:55:10: 1000000 INFO @ Tue, 27 Jun 2017 11:55:15: 2000000 INFO @ Tue, 27 Jun 2017 11:55:16: 2000000 INFO @ Tue, 27 Jun 2017 11:55:18: 2000000 INFO @ Tue, 27 Jun 2017 11:55:22: 3000000 INFO @ Tue, 27 Jun 2017 11:55:23: 3000000 INFO @ Tue, 27 Jun 2017 11:55:26: 3000000 INFO @ Tue, 27 Jun 2017 11:55:28: 4000000 INFO @ Tue, 27 Jun 2017 11:55:30: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:55:30: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:55:30: #1 total tags in treatment: 4345253 INFO @ Tue, 27 Jun 2017 11:55:30: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:55:30: #1 tags after filtering in treatment: 4345253 INFO @ Tue, 27 Jun 2017 11:55:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:30: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:30: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:31: 4000000 INFO @ Tue, 27 Jun 2017 11:55:31: #2 number of paired peaks: 2968 INFO @ Tue, 27 Jun 2017 11:55:31: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:31: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:31: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:31: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:31: #2 predicted fragment length is 132 bps INFO @ Tue, 27 Jun 2017 11:55:31: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 27 Jun 2017 11:55:31: #2.2 Generate R script for model : SRX2144171.20_model.r INFO @ Tue, 27 Jun 2017 11:55:31: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:33: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:55:33: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:55:33: #1 total tags in treatment: 4345253 INFO @ Tue, 27 Jun 2017 11:55:33: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:55:33: #1 tags after filtering in treatment: 4345253 INFO @ Tue, 27 Jun 2017 11:55:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:33: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:33: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:34: #2 number of paired peaks: 2968 INFO @ Tue, 27 Jun 2017 11:55:34: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:34: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:34: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:34: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:34: #2 predicted fragment length is 132 bps INFO @ Tue, 27 Jun 2017 11:55:34: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 27 Jun 2017 11:55:34: #2.2 Generate R script for model : SRX2144171.05_model.r INFO @ Tue, 27 Jun 2017 11:55:34: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:35: 4000000 INFO @ Tue, 27 Jun 2017 11:55:37: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:55:37: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:55:37: #1 total tags in treatment: 4345253 INFO @ Tue, 27 Jun 2017 11:55:37: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:55:37: #1 tags after filtering in treatment: 4345253 INFO @ Tue, 27 Jun 2017 11:55:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:37: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:37: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:38: #2 number of paired peaks: 2968 INFO @ Tue, 27 Jun 2017 11:55:38: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:38: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:38: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:38: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:38: #2 predicted fragment length is 132 bps INFO @ Tue, 27 Jun 2017 11:55:38: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 27 Jun 2017 11:55:38: #2.2 Generate R script for model : SRX2144171.10_model.r INFO @ Tue, 27 Jun 2017 11:55:38: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:43: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:46: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:49: #4 Write output xls file... SRX2144171.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:49: #4 Write peak in narrowPeak format file... SRX2144171.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:49: #4 Write summits bed file... SRX2144171.20_summits.bed INFO @ Tue, 27 Jun 2017 11:55:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (644 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:55:50: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:55:52: #4 Write output xls file... SRX2144171.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:52: #4 Write peak in narrowPeak format file... SRX2144171.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:52: #4 Write summits bed file... SRX2144171.05_summits.bed INFO @ Tue, 27 Jun 2017 11:55:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3718 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:55:57: #4 Write output xls file... SRX2144171.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:55:57: #4 Write peak in narrowPeak format file... SRX2144171.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:55:57: #4 Write summits bed file... SRX2144171.10_summits.bed INFO @ Tue, 27 Jun 2017 11:55:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1816 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。