Job ID = 10480719 sra ファイルのダウンロード中... Completed: 332897K bytes transferred in 35 seconds (76280K 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 10688864 spots for /home/okishinya/chipatlas/results/dm3/SRX3068990/SRR5907466.sra Written 10688864 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:29 10688864 reads; of these: 10688864 (100.00%) were unpaired; of these: 3636958 (34.03%) aligned 0 times 6237485 (58.35%) aligned exactly 1 time 814421 (7.62%) aligned >1 times 65.97% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 3311056 / 7051906 = 0.4695 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, 16 Mar 2018 07:47:18: # Command line: callpeak -t SRX3068990.bam -f BAM -g dm -n SRX3068990.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068990.05 # format = BAM # ChIP-seq file = ['SRX3068990.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:47:18: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:47:18: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:47:18: # Command line: callpeak -t SRX3068990.bam -f BAM -g dm -n SRX3068990.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068990.10 # format = BAM # ChIP-seq file = ['SRX3068990.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:47:18: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:47:18: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:47:18: # Command line: callpeak -t SRX3068990.bam -f BAM -g dm -n SRX3068990.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068990.20 # format = BAM # ChIP-seq file = ['SRX3068990.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 16 Mar 2018 07:47:18: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:47:18: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:47:24: 1000000 INFO @ Fri, 16 Mar 2018 07:47:24: 1000000 INFO @ Fri, 16 Mar 2018 07:47:25: 1000000 INFO @ Fri, 16 Mar 2018 07:47:31: 2000000 INFO @ Fri, 16 Mar 2018 07:47:31: 2000000 INFO @ Fri, 16 Mar 2018 07:47:31: 2000000 INFO @ Fri, 16 Mar 2018 07:47:37: 3000000 INFO @ Fri, 16 Mar 2018 07:47:37: 3000000 INFO @ Fri, 16 Mar 2018 07:47:38: 3000000 INFO @ Fri, 16 Mar 2018 07:47:42: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:47:42: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:47:42: #1 total tags in treatment: 3740850 INFO @ Fri, 16 Mar 2018 07:47:42: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:47:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:47:42: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:47:42: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:47:42: #1 total tags in treatment: 3740850 INFO @ Fri, 16 Mar 2018 07:47:42: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:47:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:47:42: #1 tags after filtering in treatment: 3740850 INFO @ Fri, 16 Mar 2018 07:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:47:42: #1 finished! INFO @ Fri, 16 Mar 2018 07:47:42: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:47:42: #1 tags after filtering in treatment: 3740850 INFO @ Fri, 16 Mar 2018 07:47:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:47:42: #1 finished! INFO @ Fri, 16 Mar 2018 07:47:42: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:47:43: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:47:43: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:47:43: #1 total tags in treatment: 3740850 INFO @ Fri, 16 Mar 2018 07:47:43: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:47:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:47:43: #1 tags after filtering in treatment: 3740850 INFO @ Fri, 16 Mar 2018 07:47:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:47:43: #1 finished! INFO @ Fri, 16 Mar 2018 07:47:43: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:47:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:47:43: #2 number of paired peaks: 3600 INFO @ Fri, 16 Mar 2018 07:47:43: start model_add_line... INFO @ Fri, 16 Mar 2018 07:47:43: #2 number of paired peaks: 3600 INFO @ Fri, 16 Mar 2018 07:47:43: start model_add_line... INFO @ Fri, 16 Mar 2018 07:47:43: start X-correlation... INFO @ Fri, 16 Mar 2018 07:47:43: end of X-cor INFO @ Fri, 16 Mar 2018 07:47:43: #2 finished! INFO @ Fri, 16 Mar 2018 07:47:43: #2 predicted fragment length is 141 bps INFO @ Fri, 16 Mar 2018 07:47:43: #2 alternative fragment length(s) may be 141 bps INFO @ Fri, 16 Mar 2018 07:47:43: #2.2 Generate R script for model : SRX3068990.20_model.r INFO @ Fri, 16 Mar 2018 07:47:43: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:47:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:47:43: start X-correlation... INFO @ Fri, 16 Mar 2018 07:47:43: end of X-cor INFO @ Fri, 16 Mar 2018 07:47:43: #2 finished! INFO @ Fri, 16 Mar 2018 07:47:43: #2 predicted fragment length is 141 bps INFO @ Fri, 16 Mar 2018 07:47:43: #2 alternative fragment length(s) may be 141 bps INFO @ Fri, 16 Mar 2018 07:47:43: #2.2 Generate R script for model : SRX3068990.05_model.r INFO @ Fri, 16 Mar 2018 07:47:43: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:47:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:47:43: #2 number of paired peaks: 3600 INFO @ Fri, 16 Mar 2018 07:47:43: start model_add_line... INFO @ Fri, 16 Mar 2018 07:47:43: start X-correlation... INFO @ Fri, 16 Mar 2018 07:47:43: end of X-cor INFO @ Fri, 16 Mar 2018 07:47:43: #2 finished! INFO @ Fri, 16 Mar 2018 07:47:43: #2 predicted fragment length is 141 bps INFO @ Fri, 16 Mar 2018 07:47:43: #2 alternative fragment length(s) may be 141 bps INFO @ Fri, 16 Mar 2018 07:47:43: #2.2 Generate R script for model : SRX3068990.10_model.r INFO @ Fri, 16 Mar 2018 07:47:43: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:47:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:47:52: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:47:53: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:47:53: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:47:57: #4 Write output xls file... SRX3068990.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:47:57: #4 Write peak in narrowPeak format file... SRX3068990.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:47:57: #4 Write summits bed file... SRX3068990.05_summits.bed INFO @ Fri, 16 Mar 2018 07:47:57: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6537 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:47:58: #4 Write output xls file... SRX3068990.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:47:58: #4 Write peak in narrowPeak format file... SRX3068990.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:47:58: #4 Write summits bed file... SRX3068990.20_summits.bed INFO @ Fri, 16 Mar 2018 07:47:58: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1800 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:47:58: #4 Write output xls file... SRX3068990.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:47:58: #4 Write peak in narrowPeak format file... SRX3068990.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:47:58: #4 Write summits bed file... SRX3068990.10_summits.bed INFO @ Fri, 16 Mar 2018 07:47:58: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (3777 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。