Job ID = 10480717 sra ファイルのダウンロード中... Completed: 341676K bytes transferred in 33 seconds (84407K 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 11173045 spots for /home/okishinya/chipatlas/results/dm3/SRX3068988/SRR5907464.sra Written 11173045 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: 00:00:00 Multiseed full-index search: 00:02:30 11173045 reads; of these: 11173045 (100.00%) were unpaired; of these: 4927905 (44.11%) aligned 0 times 5449614 (48.77%) aligned exactly 1 time 795526 (7.12%) aligned >1 times 55.89% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 3250059 / 6245140 = 0.5204 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 07:47:01: # Command line: callpeak -t SRX3068988.bam -f BAM -g dm -n SRX3068988.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068988.20 # format = BAM # ChIP-seq file = ['SRX3068988.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 07:47:01: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:47:01: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:47:01: # Command line: callpeak -t SRX3068988.bam -f BAM -g dm -n SRX3068988.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068988.10 # format = BAM # ChIP-seq file = ['SRX3068988.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 07:47:01: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:47:01: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:47:01: # Command line: callpeak -t SRX3068988.bam -f BAM -g dm -n SRX3068988.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068988.05 # format = BAM # ChIP-seq file = ['SRX3068988.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 07:47:01: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:47:01: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:47:08: 1000000 INFO @ Fri, 16 Mar 2018 07:47:09: 1000000 INFO @ Fri, 16 Mar 2018 07:47:09: 1000000 INFO @ Fri, 16 Mar 2018 07:47:15: 2000000 INFO @ Fri, 16 Mar 2018 07:47:16: 2000000 INFO @ Fri, 16 Mar 2018 07:47:16: 2000000 INFO @ Fri, 16 Mar 2018 07:47:23: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:47:23: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:47:23: #1 total tags in treatment: 2995081 INFO @ Fri, 16 Mar 2018 07:47:23: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:47:23: #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 07:47:23: #1 tags after filtering in treatment: 2995081 INFO @ Fri, 16 Mar 2018 07:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:47:23: #1 finished! INFO @ Fri, 16 Mar 2018 07:47:23: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:47:23: #2 number of paired peaks: 3235 INFO @ Fri, 16 Mar 2018 07:47:23: start model_add_line... INFO @ Fri, 16 Mar 2018 07:47:23: start X-correlation... INFO @ Fri, 16 Mar 2018 07:47:23: end of X-cor INFO @ Fri, 16 Mar 2018 07:47:23: #2 finished! INFO @ Fri, 16 Mar 2018 07:47:23: #2 predicted fragment length is 231 bps INFO @ Fri, 16 Mar 2018 07:47:23: #2 alternative fragment length(s) may be 231 bps INFO @ Fri, 16 Mar 2018 07:47:23: #2.2 Generate R script for model : SRX3068988.05_model.r INFO @ Fri, 16 Mar 2018 07:47:23: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:47:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:47:24: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:47:24: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:47:24: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:47:24: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:47:24: #1 total tags in treatment: 2995081 INFO @ Fri, 16 Mar 2018 07:47:24: #1 total tags in treatment: 2995081 INFO @ Fri, 16 Mar 2018 07:47:24: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:47:24: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:47:24: #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 07:47:24: #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 07:47:24: #1 tags after filtering in treatment: 2995081 INFO @ Fri, 16 Mar 2018 07:47:24: #1 tags after filtering in treatment: 2995081 INFO @ Fri, 16 Mar 2018 07:47:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:47:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:47:24: #1 finished! INFO @ Fri, 16 Mar 2018 07:47:24: #1 finished! INFO @ Fri, 16 Mar 2018 07:47:24: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:47:24: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:47:24: #2 number of paired peaks: 3235 INFO @ Fri, 16 Mar 2018 07:47:24: start model_add_line... INFO @ Fri, 16 Mar 2018 07:47:24: #2 number of paired peaks: 3235 INFO @ Fri, 16 Mar 2018 07:47:24: start model_add_line... INFO @ Fri, 16 Mar 2018 07:47:24: start X-correlation... INFO @ Fri, 16 Mar 2018 07:47:24: end of X-cor INFO @ Fri, 16 Mar 2018 07:47:24: #2 finished! INFO @ Fri, 16 Mar 2018 07:47:24: #2 predicted fragment length is 231 bps INFO @ Fri, 16 Mar 2018 07:47:24: #2 alternative fragment length(s) may be 231 bps INFO @ Fri, 16 Mar 2018 07:47:24: start X-correlation... INFO @ Fri, 16 Mar 2018 07:47:24: #2.2 Generate R script for model : SRX3068988.10_model.r INFO @ Fri, 16 Mar 2018 07:47:24: end of X-cor INFO @ Fri, 16 Mar 2018 07:47:24: #2 finished! INFO @ Fri, 16 Mar 2018 07:47:24: #2 predicted fragment length is 231 bps INFO @ Fri, 16 Mar 2018 07:47:24: #2 alternative fragment length(s) may be 231 bps INFO @ Fri, 16 Mar 2018 07:47:24: #2.2 Generate R script for model : SRX3068988.20_model.r INFO @ Fri, 16 Mar 2018 07:47:24: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:47:24: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:47:31: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:47:32: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:47:33: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:47:35: #4 Write output xls file... SRX3068988.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:47:35: #4 Write peak in narrowPeak format file... SRX3068988.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:47:35: #4 Write summits bed file... SRX3068988.05_summits.bed INFO @ Fri, 16 Mar 2018 07:47:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4533 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:47:36: #4 Write output xls file... SRX3068988.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:47:36: #4 Write peak in narrowPeak format file... SRX3068988.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:47:36: #4 Write summits bed file... SRX3068988.10_summits.bed INFO @ Fri, 16 Mar 2018 07:47:36: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (2589 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:47:37: #4 Write output xls file... SRX3068988.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:47:37: #4 Write peak in narrowPeak format file... SRX3068988.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:47:37: #4 Write summits bed file... SRX3068988.20_summits.bed INFO @ Fri, 16 Mar 2018 07:47:37: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1163 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。