Job ID = 11632622 sra ファイルのダウンロード中... Completed: 472945K bytes transferred in 8 seconds (459422K 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 18569086 spots for /home/okishinya/chipatlas/results/rn6/ERX1844924/ERR1780370.sra Written 18569086 spots for /home/okishinya/chipatlas/results/rn6/ERX1844924/ERR1780370.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:49 18569086 reads; of these: 18569086 (100.00%) were unpaired; of these: 3826937 (20.61%) aligned 0 times 11735744 (63.20%) aligned exactly 1 time 3006405 (16.19%) aligned >1 times 79.39% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 12445842 / 14742149 = 0.8442 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 @ Fri, 15 Feb 2019 05:41:44: # Command line: callpeak -t ERX1844924.bam -f BAM -g 2.15e9 -n ERX1844924.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1844924.20 # format = BAM # ChIP-seq file = ['ERX1844924.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 15 Feb 2019 05:41:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 05:41:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 05:41:44: # Command line: callpeak -t ERX1844924.bam -f BAM -g 2.15e9 -n ERX1844924.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1844924.10 # format = BAM # ChIP-seq file = ['ERX1844924.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 15 Feb 2019 05:41:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 05:41:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 05:41:44: # Command line: callpeak -t ERX1844924.bam -f BAM -g 2.15e9 -n ERX1844924.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1844924.05 # format = BAM # ChIP-seq file = ['ERX1844924.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 15 Feb 2019 05:41:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 05:41:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 05:41:51: 1000000 INFO @ Fri, 15 Feb 2019 05:41:51: 1000000 INFO @ Fri, 15 Feb 2019 05:41:51: 1000000 INFO @ Fri, 15 Feb 2019 05:41:59: 2000000 INFO @ Fri, 15 Feb 2019 05:41:59: 2000000 INFO @ Fri, 15 Feb 2019 05:41:59: 2000000 INFO @ Fri, 15 Feb 2019 05:42:01: #1 tag size is determined as 36 bps INFO @ Fri, 15 Feb 2019 05:42:01: #1 tag size is determined as 36 bps INFO @ Fri, 15 Feb 2019 05:42:01: #1 tag size = 36 INFO @ Fri, 15 Feb 2019 05:42:01: #1 tag size = 36 INFO @ Fri, 15 Feb 2019 05:42:01: #1 total tags in treatment: 2296307 INFO @ Fri, 15 Feb 2019 05:42:01: #1 total tags in treatment: 2296307 INFO @ Fri, 15 Feb 2019 05:42:01: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 05:42:01: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 05:42:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 05:42:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 05:42:01: #1 tag size is determined as 36 bps INFO @ Fri, 15 Feb 2019 05:42:01: #1 tag size = 36 INFO @ Fri, 15 Feb 2019 05:42:01: #1 total tags in treatment: 2296307 INFO @ Fri, 15 Feb 2019 05:42:01: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 05:42:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 05:42:01: #1 tags after filtering in treatment: 2296049 INFO @ Fri, 15 Feb 2019 05:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 05:42:01: #1 finished! INFO @ Fri, 15 Feb 2019 05:42:01: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 05:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 05:42:01: #1 tags after filtering in treatment: 2296049 INFO @ Fri, 15 Feb 2019 05:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 05:42:01: #1 finished! INFO @ Fri, 15 Feb 2019 05:42:01: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 05:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 05:42:01: #1 tags after filtering in treatment: 2296049 INFO @ Fri, 15 Feb 2019 05:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 05:42:01: #1 finished! INFO @ Fri, 15 Feb 2019 05:42:01: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 05:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 05:42:04: #2 number of paired peaks: 77491 INFO @ Fri, 15 Feb 2019 05:42:04: start model_add_line... INFO @ Fri, 15 Feb 2019 05:42:04: #2 number of paired peaks: 77491 INFO @ Fri, 15 Feb 2019 05:42:04: start model_add_line... INFO @ Fri, 15 Feb 2019 05:42:04: start X-correlation... INFO @ Fri, 15 Feb 2019 05:42:04: end of X-cor INFO @ Fri, 15 Feb 2019 05:42:04: #2 finished! INFO @ Fri, 15 Feb 2019 05:42:04: #2 predicted fragment length is 93 bps INFO @ Fri, 15 Feb 2019 05:42:04: #2 alternative fragment length(s) may be 93 bps INFO @ Fri, 15 Feb 2019 05:42:04: #2.2 Generate R script for model : ERX1844924.10_model.r INFO @ Fri, 15 Feb 2019 05:42:04: #3 Call peaks... INFO @ Fri, 15 Feb 2019 05:42:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 05:42:04: start X-correlation... INFO @ Fri, 15 Feb 2019 05:42:04: end of X-cor INFO @ Fri, 15 Feb 2019 05:42:04: #2 finished! INFO @ Fri, 15 Feb 2019 05:42:04: #2 predicted fragment length is 93 bps INFO @ Fri, 15 Feb 2019 05:42:04: #2 alternative fragment length(s) may be 93 bps INFO @ Fri, 15 Feb 2019 05:42:04: #2.2 Generate R script for model : ERX1844924.20_model.r INFO @ Fri, 15 Feb 2019 05:42:04: #3 Call peaks... INFO @ Fri, 15 Feb 2019 05:42:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 05:42:04: #2 number of paired peaks: 77491 INFO @ Fri, 15 Feb 2019 05:42:04: start model_add_line... INFO @ Fri, 15 Feb 2019 05:42:04: start X-correlation... INFO @ Fri, 15 Feb 2019 05:42:05: end of X-cor INFO @ Fri, 15 Feb 2019 05:42:05: #2 finished! INFO @ Fri, 15 Feb 2019 05:42:05: #2 predicted fragment length is 93 bps INFO @ Fri, 15 Feb 2019 05:42:05: #2 alternative fragment length(s) may be 93 bps INFO @ Fri, 15 Feb 2019 05:42:05: #2.2 Generate R script for model : ERX1844924.05_model.r INFO @ Fri, 15 Feb 2019 05:42:05: #3 Call peaks... INFO @ Fri, 15 Feb 2019 05:42:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 05:42:10: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 05:42:10: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 05:42:10: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 05:42:13: #4 Write output xls file... ERX1844924.20_peaks.xls INFO @ Fri, 15 Feb 2019 05:42:13: #4 Write peak in narrowPeak format file... ERX1844924.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 05:42:13: #4 Write summits bed file... ERX1844924.20_summits.bed INFO @ Fri, 15 Feb 2019 05:42:13: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (420 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 05:42:13: #4 Write output xls file... ERX1844924.10_peaks.xls INFO @ Fri, 15 Feb 2019 05:42:13: #4 Write peak in narrowPeak format file... ERX1844924.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 05:42:13: #4 Write output xls file... ERX1844924.05_peaks.xls INFO @ Fri, 15 Feb 2019 05:42:13: #4 Write summits bed file... ERX1844924.10_summits.bed INFO @ Fri, 15 Feb 2019 05:42:13: Done! INFO @ Fri, 15 Feb 2019 05:42:13: #4 Write peak in narrowPeak format file... ERX1844924.05_peaks.narrowPeak pass1 - making usageList (52 chroms): 3 millis pass2 - checking and writing primary data (1392 records, 4 fields): 6 millis INFO @ Fri, 15 Feb 2019 05:42:13: #4 Write summits bed file... ERX1844924.05_summits.bed CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 05:42:14: Done! pass1 - making usageList (68 chroms): 2 millis pass2 - checking and writing primary data (3930 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。