Job ID = 10194820 sra ファイルのダウンロード中... Completed: 346675K bytes transferred in 12 seconds (222890K 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... Written 11812267 spots for /home/okishinya/chipatlas/results/rn6/SRX1927034/SRR3831681.sra Written 11812267 spots total 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: 00:00:04 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:10:31 11812267 reads; of these: 11812267 (100.00%) were unpaired; of these: 2949376 (24.97%) aligned 0 times 8062702 (68.26%) aligned exactly 1 time 800189 (6.77%) aligned >1 times 75.03% overall alignment rate Time searching: 00:10:38 Overall time: 00:10:38 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] 4597921 / 8862891 = 0.5188 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, 10 Nov 2017 22:09:31: # Command line: callpeak -t SRX1927034.bam -f BAM -g 2.15e9 -n SRX1927034.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1927034.10 # format = BAM # ChIP-seq file = ['SRX1927034.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, 10 Nov 2017 22:09:31: # Command line: callpeak -t SRX1927034.bam -f BAM -g 2.15e9 -n SRX1927034.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1927034.20 # format = BAM # ChIP-seq file = ['SRX1927034.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, 10 Nov 2017 22:09:31: # Command line: callpeak -t SRX1927034.bam -f BAM -g 2.15e9 -n SRX1927034.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1927034.05 # format = BAM # ChIP-seq file = ['SRX1927034.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, 10 Nov 2017 22:09:31: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:09:31: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:09:31: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:09:31: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:09:31: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:09:31: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:09:46: 1000000 INFO @ Fri, 10 Nov 2017 22:09:47: 1000000 INFO @ Fri, 10 Nov 2017 22:09:48: 1000000 INFO @ Fri, 10 Nov 2017 22:10:00: 2000000 INFO @ Fri, 10 Nov 2017 22:10:03: 2000000 INFO @ Fri, 10 Nov 2017 22:10:05: 2000000 INFO @ Fri, 10 Nov 2017 22:10:15: 3000000 INFO @ Fri, 10 Nov 2017 22:10:19: 3000000 INFO @ Fri, 10 Nov 2017 22:10:22: 3000000 INFO @ Fri, 10 Nov 2017 22:10:29: 4000000 INFO @ Fri, 10 Nov 2017 22:10:33: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 22:10:33: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 22:10:33: #1 total tags in treatment: 4264970 INFO @ Fri, 10 Nov 2017 22:10:33: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:10:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:10:33: #1 tags after filtering in treatment: 4264663 INFO @ Fri, 10 Nov 2017 22:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:10:33: #1 finished! INFO @ Fri, 10 Nov 2017 22:10:33: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:10:35: 4000000 INFO @ Fri, 10 Nov 2017 22:10:35: #2 number of paired peaks: 26191 INFO @ Fri, 10 Nov 2017 22:10:35: start model_add_line... INFO @ Fri, 10 Nov 2017 22:10:36: start X-correlation... INFO @ Fri, 10 Nov 2017 22:10:36: end of X-cor INFO @ Fri, 10 Nov 2017 22:10:36: #2 finished! INFO @ Fri, 10 Nov 2017 22:10:36: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Nov 2017 22:10:36: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Nov 2017 22:10:36: #2.2 Generate R script for model : SRX1927034.05_model.r INFO @ Fri, 10 Nov 2017 22:10:36: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:10:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:10:39: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 22:10:39: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 22:10:39: #1 total tags in treatment: 4264970 INFO @ Fri, 10 Nov 2017 22:10:39: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:10:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:10:39: 4000000 INFO @ Fri, 10 Nov 2017 22:10:39: #1 tags after filtering in treatment: 4264663 INFO @ Fri, 10 Nov 2017 22:10:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:10:39: #1 finished! INFO @ Fri, 10 Nov 2017 22:10:39: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:10:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:10:41: #2 number of paired peaks: 26191 INFO @ Fri, 10 Nov 2017 22:10:41: start model_add_line... INFO @ Fri, 10 Nov 2017 22:10:41: start X-correlation... INFO @ Fri, 10 Nov 2017 22:10:41: end of X-cor INFO @ Fri, 10 Nov 2017 22:10:41: #2 finished! INFO @ Fri, 10 Nov 2017 22:10:41: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Nov 2017 22:10:41: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Nov 2017 22:10:41: #2.2 Generate R script for model : SRX1927034.20_model.r INFO @ Fri, 10 Nov 2017 22:10:41: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:10:44: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 22:10:44: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 22:10:44: #1 total tags in treatment: 4264970 INFO @ Fri, 10 Nov 2017 22:10:44: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:10:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:10:44: #1 tags after filtering in treatment: 4264663 INFO @ Fri, 10 Nov 2017 22:10:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:10:44: #1 finished! INFO @ Fri, 10 Nov 2017 22:10:44: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:10:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:10:46: #2 number of paired peaks: 26191 INFO @ Fri, 10 Nov 2017 22:10:46: start model_add_line... INFO @ Fri, 10 Nov 2017 22:10:46: start X-correlation... INFO @ Fri, 10 Nov 2017 22:10:46: end of X-cor INFO @ Fri, 10 Nov 2017 22:10:46: #2 finished! INFO @ Fri, 10 Nov 2017 22:10:46: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Nov 2017 22:10:46: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Nov 2017 22:10:46: #2.2 Generate R script for model : SRX1927034.10_model.r INFO @ Fri, 10 Nov 2017 22:10:46: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:10:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:10:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:10:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:10:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:11:00: #4 Write output xls file... SRX1927034.05_peaks.xls INFO @ Fri, 10 Nov 2017 22:11:00: #4 Write peak in narrowPeak format file... SRX1927034.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:11:00: #4 Write summits bed file... SRX1927034.05_summits.bed INFO @ Fri, 10 Nov 2017 22:11:00: Done! pass1 - making usageList (104 chroms): 13 millis pass2 - checking and writing primary data (24701 records, 4 fields): 118 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:11:04: #4 Write output xls file... SRX1927034.20_peaks.xls INFO @ Fri, 10 Nov 2017 22:11:04: #4 Write peak in narrowPeak format file... SRX1927034.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:11:04: #4 Write summits bed file... SRX1927034.20_summits.bed INFO @ Fri, 10 Nov 2017 22:11:04: Done! pass1 - making usageList (63 chroms): 4 millis pass2 - checking and writing primary data (10809 records, 4 fields): 64 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:11:09: #4 Write output xls file... SRX1927034.10_peaks.xls INFO @ Fri, 10 Nov 2017 22:11:09: #4 Write peak in narrowPeak format file... SRX1927034.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:11:09: #4 Write summits bed file... SRX1927034.10_summits.bed INFO @ Fri, 10 Nov 2017 22:11:09: Done! pass1 - making usageList (87 chroms): 6 millis pass2 - checking and writing primary data (18555 records, 4 fields): 50 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。