Job ID = 10924589 sra ファイルのダウンロード中... Completed: 243308K bytes transferred in 12 seconds (162069K 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 12155564 spots for /home/okishinya/chipatlas/results/ce10/SRX4200536/SRR7298002.sra Written 12155564 spots for /home/okishinya/chipatlas/results/ce10/SRX4200536/SRR7298002.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: 00:01:02 12155564 reads; of these: 12155564 (100.00%) were unpaired; of these: 10516259 (86.51%) aligned 0 times 1466797 (12.07%) aligned exactly 1 time 172508 (1.42%) aligned >1 times 13.49% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 622150 / 1639305 = 0.3795 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 @ Mon, 06 Aug 2018 10:27:01: # Command line: callpeak -t SRX4200536.bam -f BAM -g ce -n SRX4200536.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4200536.05 # format = BAM # ChIP-seq file = ['SRX4200536.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 @ Mon, 06 Aug 2018 10:27:01: # Command line: callpeak -t SRX4200536.bam -f BAM -g ce -n SRX4200536.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4200536.20 # format = BAM # ChIP-seq file = ['SRX4200536.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 @ Mon, 06 Aug 2018 10:27:01: # Command line: callpeak -t SRX4200536.bam -f BAM -g ce -n SRX4200536.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4200536.10 # format = BAM # ChIP-seq file = ['SRX4200536.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 @ Mon, 06 Aug 2018 10:27:01: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:27:01: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:27:01: #1 read tag files... INFO @ Mon, 06 Aug 2018 10:27:01: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:27:01: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:27:01: #1 read treatment tags... INFO @ Mon, 06 Aug 2018 10:27:07: 1000000 INFO @ Mon, 06 Aug 2018 10:27:07: 1000000 INFO @ Mon, 06 Aug 2018 10:27:07: #1 tag size is determined as 36 bps INFO @ Mon, 06 Aug 2018 10:27:07: #1 tag size = 36 INFO @ Mon, 06 Aug 2018 10:27:07: #1 total tags in treatment: 1017155 INFO @ Mon, 06 Aug 2018 10:27:07: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:27:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:27:07: #1 tags after filtering in treatment: 1017155 INFO @ Mon, 06 Aug 2018 10:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:27:07: #1 finished! INFO @ Mon, 06 Aug 2018 10:27:07: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:27:08: #1 tag size is determined as 36 bps INFO @ Mon, 06 Aug 2018 10:27:08: #1 tag size = 36 INFO @ Mon, 06 Aug 2018 10:27:08: #1 total tags in treatment: 1017155 INFO @ Mon, 06 Aug 2018 10:27:08: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:27:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:27:08: #1 tags after filtering in treatment: 1017155 INFO @ Mon, 06 Aug 2018 10:27:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:27:08: #1 finished! INFO @ Mon, 06 Aug 2018 10:27:08: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:27:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:27:08: 1000000 INFO @ Mon, 06 Aug 2018 10:27:08: #1 tag size is determined as 36 bps INFO @ Mon, 06 Aug 2018 10:27:08: #1 tag size = 36 INFO @ Mon, 06 Aug 2018 10:27:08: #1 total tags in treatment: 1017155 INFO @ Mon, 06 Aug 2018 10:27:08: #1 user defined the maximum tags... INFO @ Mon, 06 Aug 2018 10:27:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Aug 2018 10:27:08: #1 tags after filtering in treatment: 1017155 INFO @ Mon, 06 Aug 2018 10:27:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Aug 2018 10:27:08: #1 finished! INFO @ Mon, 06 Aug 2018 10:27:08: #2 Build Peak Model... INFO @ Mon, 06 Aug 2018 10:27:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Aug 2018 10:27:08: #2 number of paired peaks: 5724 INFO @ Mon, 06 Aug 2018 10:27:08: start model_add_line... INFO @ Mon, 06 Aug 2018 10:27:08: #2 number of paired peaks: 5724 INFO @ Mon, 06 Aug 2018 10:27:08: start model_add_line... INFO @ Mon, 06 Aug 2018 10:27:08: start X-correlation... INFO @ Mon, 06 Aug 2018 10:27:08: start X-correlation... INFO @ Mon, 06 Aug 2018 10:27:08: #2 number of paired peaks: 5724 INFO @ Mon, 06 Aug 2018 10:27:08: start model_add_line... INFO @ Mon, 06 Aug 2018 10:27:08: start X-correlation... INFO @ Mon, 06 Aug 2018 10:27:08: end of X-cor INFO @ Mon, 06 Aug 2018 10:27:08: end of X-cor INFO @ Mon, 06 Aug 2018 10:27:08: end of X-cor INFO @ Mon, 06 Aug 2018 10:27:08: #2 finished! INFO @ Mon, 06 Aug 2018 10:27:08: #2 finished! INFO @ Mon, 06 Aug 2018 10:27:08: #2 finished! INFO @ Mon, 06 Aug 2018 10:27:08: #2 predicted fragment length is 172 bps INFO @ Mon, 06 Aug 2018 10:27:08: #2 predicted fragment length is 172 bps INFO @ Mon, 06 Aug 2018 10:27:08: #2 predicted fragment length is 172 bps INFO @ Mon, 06 Aug 2018 10:27:08: #2 alternative fragment length(s) may be 172 bps INFO @ Mon, 06 Aug 2018 10:27:08: #2 alternative fragment length(s) may be 172 bps INFO @ Mon, 06 Aug 2018 10:27:08: #2 alternative fragment length(s) may be 172 bps INFO @ Mon, 06 Aug 2018 10:27:08: #2.2 Generate R script for model : SRX4200536.10_model.r INFO @ Mon, 06 Aug 2018 10:27:08: #2.2 Generate R script for model : SRX4200536.05_model.r INFO @ Mon, 06 Aug 2018 10:27:08: #2.2 Generate R script for model : SRX4200536.20_model.r INFO @ Mon, 06 Aug 2018 10:27:08: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:27:08: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:27:08: #3 Call peaks... INFO @ Mon, 06 Aug 2018 10:27:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:27:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:27:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Aug 2018 10:27:11: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:27:11: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:27:11: #3 Call peaks for each chromosome... INFO @ Mon, 06 Aug 2018 10:27:13: #4 Write output xls file... SRX4200536.10_peaks.xls INFO @ Mon, 06 Aug 2018 10:27:13: #4 Write output xls file... SRX4200536.20_peaks.xls INFO @ Mon, 06 Aug 2018 10:27:13: #4 Write peak in narrowPeak format file... SRX4200536.20_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:27:13: #4 Write peak in narrowPeak format file... SRX4200536.10_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:27:13: #4 Write summits bed file... SRX4200536.20_summits.bed INFO @ Mon, 06 Aug 2018 10:27:13: #4 Write output xls file... SRX4200536.05_peaks.xls INFO @ Mon, 06 Aug 2018 10:27:13: Done! INFO @ Mon, 06 Aug 2018 10:27:13: #4 Write summits bed file... SRX4200536.10_summits.bed INFO @ Mon, 06 Aug 2018 10:27:13: #4 Write peak in narrowPeak format file... SRX4200536.05_peaks.narrowPeak INFO @ Mon, 06 Aug 2018 10:27:13: Done! INFO @ Mon, 06 Aug 2018 10:27:13: #4 Write summits bed file... SRX4200536.05_summits.bed INFO @ Mon, 06 Aug 2018 10:27:13: Done! pass1 - making usageList (6 chroms)pass1 - making usageList (6 chroms): 12 millis : 12 millis pass1 - making usageList (6 chroms): 13 millis pass2 - checking and writing primary data (1607 records, 4 fields): 12 millis pass2 - checking and writing primary data (2998 records, 4 fields): 14 millis pass2 - checking and writing primary data (4059 records, 4 fields): 14 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。