Job ID = 10195020 sra ファイルのダウンロード中... Completed: 142857K bytes transferred in 4 seconds (286699K 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 4786128 spots for /home/okishinya/chipatlas/results/rn6/SRX913489/SRR1870919.sra Written 4786128 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:03:01 4786128 reads; of these: 4786128 (100.00%) were unpaired; of these: 186950 (3.91%) aligned 0 times 3168596 (66.20%) aligned exactly 1 time 1430582 (29.89%) aligned >1 times 96.09% overall alignment rate Time searching: 00:03:03 Overall time: 00:03:03 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 226570 / 4599178 = 0.0493 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, 11 Nov 2017 06:20:17: # Command line: callpeak -t SRX913489.bam -f BAM -g 2.15e9 -n SRX913489.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913489.05 # format = BAM # ChIP-seq file = ['SRX913489.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, 11 Nov 2017 06:20:17: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:20:17: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:20:17: # Command line: callpeak -t SRX913489.bam -f BAM -g 2.15e9 -n SRX913489.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913489.20 # format = BAM # ChIP-seq file = ['SRX913489.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, 11 Nov 2017 06:20:17: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:20:17: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:20:17: # Command line: callpeak -t SRX913489.bam -f BAM -g 2.15e9 -n SRX913489.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913489.10 # format = BAM # ChIP-seq file = ['SRX913489.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, 11 Nov 2017 06:20:17: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:20:17: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:20:24: 1000000 INFO @ Sat, 11 Nov 2017 06:20:24: 1000000 INFO @ Sat, 11 Nov 2017 06:20:24: 1000000 INFO @ Sat, 11 Nov 2017 06:20:31: 2000000 INFO @ Sat, 11 Nov 2017 06:20:31: 2000000 INFO @ Sat, 11 Nov 2017 06:20:32: 2000000 INFO @ Sat, 11 Nov 2017 06:20:38: 3000000 INFO @ Sat, 11 Nov 2017 06:20:38: 3000000 INFO @ Sat, 11 Nov 2017 06:20:39: 3000000 INFO @ Sat, 11 Nov 2017 06:20:46: 4000000 INFO @ Sat, 11 Nov 2017 06:20:46: 4000000 INFO @ Sat, 11 Nov 2017 06:20:47: 4000000 INFO @ Sat, 11 Nov 2017 06:20:49: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 06:20:49: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 06:20:49: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 06:20:49: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 06:20:49: #1 total tags in treatment: 4372608 INFO @ Sat, 11 Nov 2017 06:20:49: #1 total tags in treatment: 4372608 INFO @ Sat, 11 Nov 2017 06:20:49: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:20:49: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:20:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 06:20:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 06:20:49: #1 tags after filtering in treatment: 4372303 INFO @ Sat, 11 Nov 2017 06:20:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:20:49: #1 finished! INFO @ Sat, 11 Nov 2017 06:20:49: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:20:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:20:49: #1 tags after filtering in treatment: 4372303 INFO @ Sat, 11 Nov 2017 06:20:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:20:49: #1 finished! INFO @ Sat, 11 Nov 2017 06:20:49: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:20:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:20:50: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 06:20:50: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 06:20:50: #1 total tags in treatment: 4372608 INFO @ Sat, 11 Nov 2017 06:20:50: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:20:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 06:20:50: #1 tags after filtering in treatment: 4372303 INFO @ Sat, 11 Nov 2017 06:20:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:20:50: #1 finished! INFO @ Sat, 11 Nov 2017 06:20:50: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:20:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:20:52: #2 number of paired peaks: 15978 INFO @ Sat, 11 Nov 2017 06:20:52: start model_add_line... INFO @ Sat, 11 Nov 2017 06:20:52: start X-correlation... INFO @ Sat, 11 Nov 2017 06:20:52: end of X-cor INFO @ Sat, 11 Nov 2017 06:20:52: #2 finished! INFO @ Sat, 11 Nov 2017 06:20:52: #2 predicted fragment length is 261 bps INFO @ Sat, 11 Nov 2017 06:20:52: #2 alternative fragment length(s) may be 52,208,261 bps INFO @ Sat, 11 Nov 2017 06:20:52: #2.2 Generate R script for model : SRX913489.05_model.r INFO @ Sat, 11 Nov 2017 06:20:52: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:20:52: #2 number of paired peaks: 15978 INFO @ Sat, 11 Nov 2017 06:20:52: start model_add_line... INFO @ Sat, 11 Nov 2017 06:20:52: start X-correlation... INFO @ Sat, 11 Nov 2017 06:20:52: end of X-cor INFO @ Sat, 11 Nov 2017 06:20:52: #2 finished! INFO @ Sat, 11 Nov 2017 06:20:52: #2 predicted fragment length is 261 bps INFO @ Sat, 11 Nov 2017 06:20:52: #2 alternative fragment length(s) may be 52,208,261 bps INFO @ Sat, 11 Nov 2017 06:20:52: #2.2 Generate R script for model : SRX913489.20_model.r INFO @ Sat, 11 Nov 2017 06:20:52: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:20:53: #2 number of paired peaks: 15978 INFO @ Sat, 11 Nov 2017 06:20:53: start model_add_line... INFO @ Sat, 11 Nov 2017 06:20:53: start X-correlation... INFO @ Sat, 11 Nov 2017 06:20:53: end of X-cor INFO @ Sat, 11 Nov 2017 06:20:53: #2 finished! INFO @ Sat, 11 Nov 2017 06:20:53: #2 predicted fragment length is 261 bps INFO @ Sat, 11 Nov 2017 06:20:53: #2 alternative fragment length(s) may be 52,208,261 bps INFO @ Sat, 11 Nov 2017 06:20:53: #2.2 Generate R script for model : SRX913489.10_model.r INFO @ Sat, 11 Nov 2017 06:20:53: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:20:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:21:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:21:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:21:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:21:08: #4 Write output xls file... SRX913489.20_peaks.xls INFO @ Sat, 11 Nov 2017 06:21:08: #4 Write peak in narrowPeak format file... SRX913489.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:21:08: #4 Write summits bed file... SRX913489.20_summits.bed INFO @ Sat, 11 Nov 2017 06:21:08: Done! pass1 - making usageList (18 chroms): 1 millis pass2 - checking and writing primary data (55 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 06:21:09: #4 Write output xls file... SRX913489.05_peaks.xls INFO @ Sat, 11 Nov 2017 06:21:09: #4 Write peak in narrowPeak format file... SRX913489.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:21:09: #4 Write summits bed file... SRX913489.05_summits.bed INFO @ Sat, 11 Nov 2017 06:21:09: Done! pass1 - making usageList (29 chroms): 0 millis pass2 - checking and writing primary data (326 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 06:21:11: #4 Write output xls file... SRX913489.10_peaks.xls INFO @ Sat, 11 Nov 2017 06:21:11: #4 Write peak in narrowPeak format file... SRX913489.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:21:11: #4 Write summits bed file... SRX913489.10_summits.bed INFO @ Sat, 11 Nov 2017 06:21:11: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (186 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。