Job ID = 11192570 sra ファイルのダウンロード中... Completed: 666783K bytes transferred in 10 seconds (513209K 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 20613196 spots for /home/okishinya/chipatlas/results/rn6/SRX2226582/SRR4374832.sra Written 20613196 spots for /home/okishinya/chipatlas/results/rn6/SRX2226582/SRR4374832.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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:15:21 20613196 reads; of these: 20613196 (100.00%) were unpaired; of these: 2690776 (13.05%) aligned 0 times 13596422 (65.96%) aligned exactly 1 time 4325998 (20.99%) aligned >1 times 86.95% overall alignment rate Time searching: 00:15:26 Overall time: 00:15:26 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5365800 / 17922420 = 0.2994 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 @ Sat, 15 Sep 2018 09:18:40: # Command line: callpeak -t SRX2226582.bam -f BAM -g 2.15e9 -n SRX2226582.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226582.20 # format = BAM # ChIP-seq file = ['SRX2226582.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 @ Sat, 15 Sep 2018 09:18:40: # Command line: callpeak -t SRX2226582.bam -f BAM -g 2.15e9 -n SRX2226582.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226582.10 # format = BAM # ChIP-seq file = ['SRX2226582.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 @ Sat, 15 Sep 2018 09:18:40: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:18:40: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:18:40: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:18:40: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:18:40: # Command line: callpeak -t SRX2226582.bam -f BAM -g 2.15e9 -n SRX2226582.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226582.05 # format = BAM # ChIP-seq file = ['SRX2226582.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 @ Sat, 15 Sep 2018 09:18:40: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:18:40: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:18:49: 1000000 INFO @ Sat, 15 Sep 2018 09:18:49: 1000000 INFO @ Sat, 15 Sep 2018 09:18:49: 1000000 INFO @ Sat, 15 Sep 2018 09:18:57: 2000000 INFO @ Sat, 15 Sep 2018 09:18:58: 2000000 INFO @ Sat, 15 Sep 2018 09:18:58: 2000000 INFO @ Sat, 15 Sep 2018 09:19:05: 3000000 INFO @ Sat, 15 Sep 2018 09:19:07: 3000000 INFO @ Sat, 15 Sep 2018 09:19:07: 3000000 INFO @ Sat, 15 Sep 2018 09:19:14: 4000000 INFO @ Sat, 15 Sep 2018 09:19:16: 4000000 INFO @ Sat, 15 Sep 2018 09:19:16: 4000000 INFO @ Sat, 15 Sep 2018 09:19:23: 5000000 INFO @ Sat, 15 Sep 2018 09:19:25: 5000000 INFO @ Sat, 15 Sep 2018 09:19:25: 5000000 INFO @ Sat, 15 Sep 2018 09:19:32: 6000000 INFO @ Sat, 15 Sep 2018 09:19:33: 6000000 INFO @ Sat, 15 Sep 2018 09:19:34: 6000000 INFO @ Sat, 15 Sep 2018 09:19:41: 7000000 INFO @ Sat, 15 Sep 2018 09:19:42: 7000000 INFO @ Sat, 15 Sep 2018 09:19:42: 7000000 INFO @ Sat, 15 Sep 2018 09:19:50: 8000000 INFO @ Sat, 15 Sep 2018 09:19:51: 8000000 INFO @ Sat, 15 Sep 2018 09:19:51: 8000000 INFO @ Sat, 15 Sep 2018 09:19:59: 9000000 INFO @ Sat, 15 Sep 2018 09:19:59: 9000000 INFO @ Sat, 15 Sep 2018 09:19:59: 9000000 INFO @ Sat, 15 Sep 2018 09:20:08: 10000000 INFO @ Sat, 15 Sep 2018 09:20:08: 10000000 INFO @ Sat, 15 Sep 2018 09:20:08: 10000000 INFO @ Sat, 15 Sep 2018 09:20:16: 11000000 INFO @ Sat, 15 Sep 2018 09:20:16: 11000000 INFO @ Sat, 15 Sep 2018 09:20:17: 11000000 INFO @ Sat, 15 Sep 2018 09:20:24: 12000000 INFO @ Sat, 15 Sep 2018 09:20:24: 12000000 INFO @ Sat, 15 Sep 2018 09:20:26: 12000000 INFO @ Sat, 15 Sep 2018 09:20:29: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:20:29: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:20:29: #1 total tags in treatment: 12556620 INFO @ Sat, 15 Sep 2018 09:20:29: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:20:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:20:29: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:20:29: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:20:29: #1 total tags in treatment: 12556620 INFO @ Sat, 15 Sep 2018 09:20:29: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:20:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:20:30: #1 tags after filtering in treatment: 12556456 INFO @ Sat, 15 Sep 2018 09:20:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:20:30: #1 finished! INFO @ Sat, 15 Sep 2018 09:20:30: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:20:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:20:30: #1 tags after filtering in treatment: 12556456 INFO @ Sat, 15 Sep 2018 09:20:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:20:30: #1 finished! INFO @ Sat, 15 Sep 2018 09:20:30: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:20:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:20:31: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:20:31: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:20:31: #1 total tags in treatment: 12556620 INFO @ Sat, 15 Sep 2018 09:20:31: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:20:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:20:31: #1 tags after filtering in treatment: 12556456 INFO @ Sat, 15 Sep 2018 09:20:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:20:31: #1 finished! INFO @ Sat, 15 Sep 2018 09:20:31: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:20:32: #2 number of paired peaks: 18800 INFO @ Sat, 15 Sep 2018 09:20:32: start model_add_line... INFO @ Sat, 15 Sep 2018 09:20:32: #2 number of paired peaks: 18800 INFO @ Sat, 15 Sep 2018 09:20:32: start model_add_line... INFO @ Sat, 15 Sep 2018 09:20:32: start X-correlation... INFO @ Sat, 15 Sep 2018 09:20:32: end of X-cor INFO @ Sat, 15 Sep 2018 09:20:32: #2 finished! INFO @ Sat, 15 Sep 2018 09:20:32: #2 predicted fragment length is 229 bps INFO @ Sat, 15 Sep 2018 09:20:32: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 15 Sep 2018 09:20:32: #2.2 Generate R script for model : SRX2226582.05_model.r INFO @ Sat, 15 Sep 2018 09:20:32: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:20:32: start X-correlation... INFO @ Sat, 15 Sep 2018 09:20:32: end of X-cor INFO @ Sat, 15 Sep 2018 09:20:32: #2 finished! INFO @ Sat, 15 Sep 2018 09:20:32: #2 predicted fragment length is 229 bps INFO @ Sat, 15 Sep 2018 09:20:32: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 15 Sep 2018 09:20:32: #2.2 Generate R script for model : SRX2226582.20_model.r INFO @ Sat, 15 Sep 2018 09:20:32: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:20:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:20:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:20:33: #2 number of paired peaks: 18800 INFO @ Sat, 15 Sep 2018 09:20:33: start model_add_line... INFO @ Sat, 15 Sep 2018 09:20:34: start X-correlation... INFO @ Sat, 15 Sep 2018 09:20:34: end of X-cor INFO @ Sat, 15 Sep 2018 09:20:34: #2 finished! INFO @ Sat, 15 Sep 2018 09:20:34: #2 predicted fragment length is 229 bps INFO @ Sat, 15 Sep 2018 09:20:34: #2 alternative fragment length(s) may be 229 bps INFO @ Sat, 15 Sep 2018 09:20:34: #2.2 Generate R script for model : SRX2226582.10_model.r INFO @ Sat, 15 Sep 2018 09:20:34: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:21:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:21:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:21:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:21:23: #4 Write output xls file... SRX2226582.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:21:23: #4 Write peak in narrowPeak format file... SRX2226582.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:21:23: #4 Write summits bed file... SRX2226582.05_summits.bed INFO @ Sat, 15 Sep 2018 09:21:23: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (2456 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:21:24: #4 Write output xls file... SRX2226582.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:21:24: #4 Write peak in narrowPeak format file... SRX2226582.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:21:24: #4 Write summits bed file... SRX2226582.20_summits.bed INFO @ Sat, 15 Sep 2018 09:21:24: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (406 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:21:24: #4 Write output xls file... SRX2226582.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:21:24: #4 Write peak in narrowPeak format file... SRX2226582.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:21:24: #4 Write summits bed file... SRX2226582.10_summits.bed INFO @ Sat, 15 Sep 2018 09:21:24: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (1130 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。