Job ID = 10714578 sra ファイルのダウンロード中... Completed: 43032K bytes transferred in 8 seconds (43788K 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 2722424 spots for /home/okishinya/chipatlas/results/dm3/SRX4053332/SRR7132381.sra Written 2722424 spots for /home/okishinya/chipatlas/results/dm3/SRX4053332/SRR7132381.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: 00:00:52 2722424 reads; of these: 2722424 (100.00%) were unpaired; of these: 391766 (14.39%) aligned 0 times 1894400 (69.59%) aligned exactly 1 time 436258 (16.02%) aligned >1 times 85.61% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 313506 / 2330658 = 0.1345 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, 03 Jun 2018 13:35:52: # Command line: callpeak -t SRX4053332.bam -f BAM -g dm -n SRX4053332.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053332.10 # format = BAM # ChIP-seq file = ['SRX4053332.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, 03 Jun 2018 13:35:52: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:35:52: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:35:52: # Command line: callpeak -t SRX4053332.bam -f BAM -g dm -n SRX4053332.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053332.20 # format = BAM # ChIP-seq file = ['SRX4053332.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, 03 Jun 2018 13:35:52: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:35:52: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:35:52: # Command line: callpeak -t SRX4053332.bam -f BAM -g dm -n SRX4053332.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053332.05 # format = BAM # ChIP-seq file = ['SRX4053332.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, 03 Jun 2018 13:35:52: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:35:52: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:35:58: 1000000 INFO @ Sun, 03 Jun 2018 13:35:58: 1000000 INFO @ Sun, 03 Jun 2018 13:35:58: 1000000 INFO @ Sun, 03 Jun 2018 13:36:04: 2000000 INFO @ Sun, 03 Jun 2018 13:36:04: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:36:04: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:36:04: #1 total tags in treatment: 2017152 INFO @ Sun, 03 Jun 2018 13:36:04: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:36:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:36:04: #1 tags after filtering in treatment: 2017152 INFO @ Sun, 03 Jun 2018 13:36:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:36:04: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:04: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:05: #2 number of paired peaks: 6336 INFO @ Sun, 03 Jun 2018 13:36:05: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:05: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:05: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:05: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:05: #2 predicted fragment length is 247 bps INFO @ Sun, 03 Jun 2018 13:36:05: #2 alternative fragment length(s) may be 4,226,247,263 bps INFO @ Sun, 03 Jun 2018 13:36:05: #2.2 Generate R script for model : SRX4053332.20_model.r INFO @ Sun, 03 Jun 2018 13:36:05: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:05: 2000000 INFO @ Sun, 03 Jun 2018 13:36:05: 2000000 INFO @ Sun, 03 Jun 2018 13:36:05: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:36:05: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:36:05: #1 total tags in treatment: 2017152 INFO @ Sun, 03 Jun 2018 13:36:05: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:36:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:36:05: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:36:05: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:36:05: #1 total tags in treatment: 2017152 INFO @ Sun, 03 Jun 2018 13:36:05: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:36:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:36:05: #1 tags after filtering in treatment: 2017152 INFO @ Sun, 03 Jun 2018 13:36:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:36:05: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:05: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:05: #1 tags after filtering in treatment: 2017152 INFO @ Sun, 03 Jun 2018 13:36:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:36:05: #1 finished! INFO @ Sun, 03 Jun 2018 13:36:05: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:36:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:36:06: #2 number of paired peaks: 6336 INFO @ Sun, 03 Jun 2018 13:36:06: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:06: #2 number of paired peaks: 6336 INFO @ Sun, 03 Jun 2018 13:36:06: start model_add_line... INFO @ Sun, 03 Jun 2018 13:36:06: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:06: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:06: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:06: #2 predicted fragment length is 247 bps INFO @ Sun, 03 Jun 2018 13:36:06: #2 alternative fragment length(s) may be 4,226,247,263 bps INFO @ Sun, 03 Jun 2018 13:36:06: #2.2 Generate R script for model : SRX4053332.05_model.r INFO @ Sun, 03 Jun 2018 13:36:06: start X-correlation... INFO @ Sun, 03 Jun 2018 13:36:06: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:06: end of X-cor INFO @ Sun, 03 Jun 2018 13:36:06: #2 finished! INFO @ Sun, 03 Jun 2018 13:36:06: #2 predicted fragment length is 247 bps INFO @ Sun, 03 Jun 2018 13:36:06: #2 alternative fragment length(s) may be 4,226,247,263 bps INFO @ Sun, 03 Jun 2018 13:36:06: #2.2 Generate R script for model : SRX4053332.10_model.r INFO @ Sun, 03 Jun 2018 13:36:06: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:36:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:11: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:36:12: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:36:12: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:36:14: #4 Write output xls file... SRX4053332.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:36:14: #4 Write peak in narrowPeak format file... SRX4053332.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:36:14: #4 Write summits bed file... SRX4053332.20_summits.bed INFO @ Sun, 03 Jun 2018 13:36:14: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (97 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:36:15: #4 Write output xls file... SRX4053332.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:36:15: #4 Write peak in narrowPeak format file... SRX4053332.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:36:15: #4 Write summits bed file... SRX4053332.05_summits.bed INFO @ Sun, 03 Jun 2018 13:36:15: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (505 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:36:15: #4 Write output xls file... SRX4053332.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:36:15: #4 Write peak in narrowPeak format file... SRX4053332.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:36:15: #4 Write summits bed file... SRX4053332.10_summits.bed INFO @ Sun, 03 Jun 2018 13:36:15: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (214 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。