Job ID = 10714407 sra ファイルのダウンロード中... Completed: 170278K bytes transferred in 7 seconds (195534K 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 8069989 spots for /home/okishinya/chipatlas/results/ce10/SRX4082367/SRR7164185.sra Written 8069989 spots for /home/okishinya/chipatlas/results/ce10/SRX4082367/SRR7164185.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:50 8069989 reads; of these: 8069989 (100.00%) were unpaired; of these: 1423778 (17.64%) aligned 0 times 6083404 (75.38%) aligned exactly 1 time 562807 (6.97%) aligned >1 times 82.36% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 4222866 / 6646211 = 0.6354 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 @ Sun, 03 Jun 2018 12:31:55: # Command line: callpeak -t SRX4082367.bam -f BAM -g ce -n SRX4082367.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082367.05 # format = BAM # ChIP-seq file = ['SRX4082367.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 @ Sun, 03 Jun 2018 12:31:55: # Command line: callpeak -t SRX4082367.bam -f BAM -g ce -n SRX4082367.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082367.10 # format = BAM # ChIP-seq file = ['SRX4082367.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 @ Sun, 03 Jun 2018 12:31:55: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:31:55: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:31:55: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:31:55: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:31:55: # Command line: callpeak -t SRX4082367.bam -f BAM -g ce -n SRX4082367.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082367.20 # format = BAM # ChIP-seq file = ['SRX4082367.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 @ Sun, 03 Jun 2018 12:31:55: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:31:55: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:32:02: 1000000 INFO @ Sun, 03 Jun 2018 12:32:03: 1000000 INFO @ Sun, 03 Jun 2018 12:32:03: 1000000 INFO @ Sun, 03 Jun 2018 12:32:10: 2000000 INFO @ Sun, 03 Jun 2018 12:32:12: 2000000 INFO @ Sun, 03 Jun 2018 12:32:12: 2000000 INFO @ Sun, 03 Jun 2018 12:32:13: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:32:13: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:32:13: #1 total tags in treatment: 2423345 INFO @ Sun, 03 Jun 2018 12:32:13: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:32:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:32:13: #1 tags after filtering in treatment: 2423345 INFO @ Sun, 03 Jun 2018 12:32:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:32:13: #1 finished! INFO @ Sun, 03 Jun 2018 12:32:13: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:32:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:32:13: #2 number of paired peaks: 6023 INFO @ Sun, 03 Jun 2018 12:32:13: start model_add_line... INFO @ Sun, 03 Jun 2018 12:32:13: start X-correlation... INFO @ Sun, 03 Jun 2018 12:32:13: end of X-cor INFO @ Sun, 03 Jun 2018 12:32:13: #2 finished! INFO @ Sun, 03 Jun 2018 12:32:13: #2 predicted fragment length is 197 bps INFO @ Sun, 03 Jun 2018 12:32:13: #2 alternative fragment length(s) may be 4,197 bps INFO @ Sun, 03 Jun 2018 12:32:13: #2.2 Generate R script for model : SRX4082367.05_model.r INFO @ Sun, 03 Jun 2018 12:32:13: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:32:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:32:15: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:32:15: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:32:15: #1 total tags in treatment: 2423345 INFO @ Sun, 03 Jun 2018 12:32:15: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:32:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:32:15: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:32:15: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:32:15: #1 total tags in treatment: 2423345 INFO @ Sun, 03 Jun 2018 12:32:15: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:32:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:32:15: #1 tags after filtering in treatment: 2423345 INFO @ Sun, 03 Jun 2018 12:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:32:15: #1 finished! INFO @ Sun, 03 Jun 2018 12:32:15: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:32:15: #1 tags after filtering in treatment: 2423345 INFO @ Sun, 03 Jun 2018 12:32:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:32:15: #1 finished! INFO @ Sun, 03 Jun 2018 12:32:15: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:32:16: #2 number of paired peaks: 6023 INFO @ Sun, 03 Jun 2018 12:32:16: start model_add_line... INFO @ Sun, 03 Jun 2018 12:32:16: #2 number of paired peaks: 6023 INFO @ Sun, 03 Jun 2018 12:32:16: start model_add_line... INFO @ Sun, 03 Jun 2018 12:32:16: start X-correlation... INFO @ Sun, 03 Jun 2018 12:32:16: end of X-cor INFO @ Sun, 03 Jun 2018 12:32:16: #2 finished! INFO @ Sun, 03 Jun 2018 12:32:16: #2 predicted fragment length is 197 bps INFO @ Sun, 03 Jun 2018 12:32:16: #2 alternative fragment length(s) may be 4,197 bps INFO @ Sun, 03 Jun 2018 12:32:16: #2.2 Generate R script for model : SRX4082367.10_model.r INFO @ Sun, 03 Jun 2018 12:32:16: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:32:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:32:16: start X-correlation... INFO @ Sun, 03 Jun 2018 12:32:16: end of X-cor INFO @ Sun, 03 Jun 2018 12:32:16: #2 finished! INFO @ Sun, 03 Jun 2018 12:32:16: #2 predicted fragment length is 197 bps INFO @ Sun, 03 Jun 2018 12:32:16: #2 alternative fragment length(s) may be 4,197 bps INFO @ Sun, 03 Jun 2018 12:32:16: #2.2 Generate R script for model : SRX4082367.20_model.r INFO @ Sun, 03 Jun 2018 12:32:16: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:32:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:32:20: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:32:23: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:32:23: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:32:23: #4 Write output xls file... SRX4082367.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:32:23: #4 Write peak in narrowPeak format file... SRX4082367.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:32:23: #4 Write summits bed file... SRX4082367.05_summits.bed INFO @ Sun, 03 Jun 2018 12:32:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2899 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:32:26: #4 Write output xls file... SRX4082367.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:32:26: #4 Write output xls file... SRX4082367.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:32:26: #4 Write peak in narrowPeak format file... SRX4082367.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:32:26: #4 Write summits bed file... SRX4082367.20_summits.bed INFO @ Sun, 03 Jun 2018 12:32:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (30 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:32:26: #4 Write peak in narrowPeak format file... SRX4082367.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:32:26: #4 Write summits bed file... SRX4082367.10_summits.bed INFO @ Sun, 03 Jun 2018 12:32:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (515 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。