Job ID = 11240796 sra ファイルのダウンロード中... Completed: 463481K bytes transferred in 7 seconds (477830K 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 13268717 spots for /home/okishinya/chipatlas/results/dm3/SRX4798834/SRR7965235.sra Written 13268717 spots for /home/okishinya/chipatlas/results/dm3/SRX4798834/SRR7965235.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:26 13268717 reads; of these: 13268717 (100.00%) were unpaired; of these: 3050296 (22.99%) aligned 0 times 8806737 (66.37%) aligned exactly 1 time 1411684 (10.64%) aligned >1 times 77.01% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2913550 / 10218421 = 0.2851 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 @ Sun, 07 Oct 2018 20:47:15: # Command line: callpeak -t SRX4798834.bam -f BAM -g dm -n SRX4798834.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798834.05 # format = BAM # ChIP-seq file = ['SRX4798834.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 @ Sun, 07 Oct 2018 20:47:15: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:47:15: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:15: # Command line: callpeak -t SRX4798834.bam -f BAM -g dm -n SRX4798834.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798834.20 # format = BAM # ChIP-seq file = ['SRX4798834.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 @ Sun, 07 Oct 2018 20:47:15: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:47:15: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:15: # Command line: callpeak -t SRX4798834.bam -f BAM -g dm -n SRX4798834.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798834.10 # format = BAM # ChIP-seq file = ['SRX4798834.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 @ Sun, 07 Oct 2018 20:47:15: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:47:15: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:23: 1000000 INFO @ Sun, 07 Oct 2018 20:47:23: 1000000 INFO @ Sun, 07 Oct 2018 20:47:23: 1000000 INFO @ Sun, 07 Oct 2018 20:47:31: 2000000 INFO @ Sun, 07 Oct 2018 20:47:31: 2000000 INFO @ Sun, 07 Oct 2018 20:47:31: 2000000 INFO @ Sun, 07 Oct 2018 20:47:38: 3000000 INFO @ Sun, 07 Oct 2018 20:47:38: 3000000 INFO @ Sun, 07 Oct 2018 20:47:39: 3000000 INFO @ Sun, 07 Oct 2018 20:47:45: 4000000 INFO @ Sun, 07 Oct 2018 20:47:45: 4000000 INFO @ Sun, 07 Oct 2018 20:47:47: 4000000 INFO @ Sun, 07 Oct 2018 20:47:53: 5000000 INFO @ Sun, 07 Oct 2018 20:47:53: 5000000 INFO @ Sun, 07 Oct 2018 20:47:55: 5000000 INFO @ Sun, 07 Oct 2018 20:48:00: 6000000 INFO @ Sun, 07 Oct 2018 20:48:00: 6000000 INFO @ Sun, 07 Oct 2018 20:48:03: 6000000 INFO @ Sun, 07 Oct 2018 20:48:07: 7000000 INFO @ Sun, 07 Oct 2018 20:48:07: 7000000 INFO @ Sun, 07 Oct 2018 20:48:09: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:48:09: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:48:09: #1 total tags in treatment: 7304871 INFO @ Sun, 07 Oct 2018 20:48:09: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:48:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:48:09: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:48:09: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:48:09: #1 total tags in treatment: 7304871 INFO @ Sun, 07 Oct 2018 20:48:09: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:48:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:48:10: #1 tags after filtering in treatment: 7304871 INFO @ Sun, 07 Oct 2018 20:48:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:48:10: #1 finished! INFO @ Sun, 07 Oct 2018 20:48:10: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:48:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:48:10: #1 tags after filtering in treatment: 7304871 INFO @ Sun, 07 Oct 2018 20:48:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:48:10: #1 finished! INFO @ Sun, 07 Oct 2018 20:48:10: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:48:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:48:10: #2 number of paired peaks: 127 WARNING @ Sun, 07 Oct 2018 20:48:10: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Sun, 07 Oct 2018 20:48:10: start model_add_line... INFO @ Sun, 07 Oct 2018 20:48:10: #2 number of paired peaks: 127 WARNING @ Sun, 07 Oct 2018 20:48:10: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Sun, 07 Oct 2018 20:48:10: start model_add_line... INFO @ Sun, 07 Oct 2018 20:48:10: start X-correlation... INFO @ Sun, 07 Oct 2018 20:48:10: start X-correlation... INFO @ Sun, 07 Oct 2018 20:48:10: end of X-cor INFO @ Sun, 07 Oct 2018 20:48:10: end of X-cor INFO @ Sun, 07 Oct 2018 20:48:10: #2 finished! INFO @ Sun, 07 Oct 2018 20:48:10: #2 finished! INFO @ Sun, 07 Oct 2018 20:48:10: #2 predicted fragment length is 122 bps INFO @ Sun, 07 Oct 2018 20:48:10: #2 predicted fragment length is 122 bps INFO @ Sun, 07 Oct 2018 20:48:10: #2 alternative fragment length(s) may be 68,95,122,147,585 bps INFO @ Sun, 07 Oct 2018 20:48:10: #2 alternative fragment length(s) may be 68,95,122,147,585 bps INFO @ Sun, 07 Oct 2018 20:48:10: #2.2 Generate R script for model : SRX4798834.20_model.r INFO @ Sun, 07 Oct 2018 20:48:10: #2.2 Generate R script for model : SRX4798834.05_model.r INFO @ Sun, 07 Oct 2018 20:48:10: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:48:10: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:48:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:48:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:48:12: 7000000 INFO @ Sun, 07 Oct 2018 20:48:14: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:48:14: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:48:14: #1 total tags in treatment: 7304871 INFO @ Sun, 07 Oct 2018 20:48:14: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:48:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:48:14: #1 tags after filtering in treatment: 7304871 INFO @ Sun, 07 Oct 2018 20:48:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:48:14: #1 finished! INFO @ Sun, 07 Oct 2018 20:48:14: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:48:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:48:15: #2 number of paired peaks: 127 WARNING @ Sun, 07 Oct 2018 20:48:15: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Sun, 07 Oct 2018 20:48:15: start model_add_line... INFO @ Sun, 07 Oct 2018 20:48:15: start X-correlation... INFO @ Sun, 07 Oct 2018 20:48:15: end of X-cor INFO @ Sun, 07 Oct 2018 20:48:15: #2 finished! INFO @ Sun, 07 Oct 2018 20:48:15: #2 predicted fragment length is 122 bps INFO @ Sun, 07 Oct 2018 20:48:15: #2 alternative fragment length(s) may be 68,95,122,147,585 bps INFO @ Sun, 07 Oct 2018 20:48:15: #2.2 Generate R script for model : SRX4798834.10_model.r INFO @ Sun, 07 Oct 2018 20:48:15: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:48:26: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:27: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:32: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:36: #4 Write output xls file... SRX4798834.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:36: #4 Write peak in narrowPeak format file... SRX4798834.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:36: #4 Write summits bed file... SRX4798834.20_summits.bed INFO @ Sun, 07 Oct 2018 20:48:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (157 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:48:37: #4 Write output xls file... SRX4798834.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:37: #4 Write peak in narrowPeak format file... SRX4798834.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:37: #4 Write summits bed file... SRX4798834.05_summits.bed INFO @ Sun, 07 Oct 2018 20:48:37: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (420 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:48:40: #4 Write output xls file... SRX4798834.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:40: #4 Write peak in narrowPeak format file... SRX4798834.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:40: #4 Write summits bed file... SRX4798834.10_summits.bed INFO @ Sun, 07 Oct 2018 20:48:40: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (281 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。