Job ID = 10714553 sra ファイルのダウンロード中... Completed: 151111K bytes transferred in 16 seconds (76985K 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 9847608 spots for /home/okishinya/chipatlas/results/dm3/SRX4047176/SRR7126157.sra Written 9847608 spots for /home/okishinya/chipatlas/results/dm3/SRX4047176/SRR7126157.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: 00:01:17 9847608 reads; of these: 9847608 (100.00%) were unpaired; of these: 7074460 (71.84%) aligned 0 times 2256299 (22.91%) aligned exactly 1 time 516849 (5.25%) aligned >1 times 28.16% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 436762 / 2773148 = 0.1575 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 13:23:04: # Command line: callpeak -t SRX4047176.bam -f BAM -g dm -n SRX4047176.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4047176.20 # format = BAM # ChIP-seq file = ['SRX4047176.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 13:23:04: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:23:04: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:23:04: # Command line: callpeak -t SRX4047176.bam -f BAM -g dm -n SRX4047176.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4047176.10 # format = BAM # ChIP-seq file = ['SRX4047176.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 13:23:04: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:23:04: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:23:04: # Command line: callpeak -t SRX4047176.bam -f BAM -g dm -n SRX4047176.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4047176.05 # format = BAM # ChIP-seq file = ['SRX4047176.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 13:23:04: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:23:04: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:23:10: 1000000 INFO @ Sun, 03 Jun 2018 13:23:10: 1000000 INFO @ Sun, 03 Jun 2018 13:23:10: 1000000 INFO @ Sun, 03 Jun 2018 13:23:16: 2000000 INFO @ Sun, 03 Jun 2018 13:23:16: 2000000 INFO @ Sun, 03 Jun 2018 13:23:16: 2000000 INFO @ Sun, 03 Jun 2018 13:23:18: #1 tag size is determined as 36 bps INFO @ Sun, 03 Jun 2018 13:23:18: #1 tag size = 36 INFO @ Sun, 03 Jun 2018 13:23:18: #1 total tags in treatment: 2336386 INFO @ Sun, 03 Jun 2018 13:23:18: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:23:18: #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 13:23:18: #1 tags after filtering in treatment: 2336386 INFO @ Sun, 03 Jun 2018 13:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:23:18: #1 finished! INFO @ Sun, 03 Jun 2018 13:23:18: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:23:18: #2 number of paired peaks: 378 WARNING @ Sun, 03 Jun 2018 13:23:18: Fewer paired peaks (378) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 378 pairs to build model! INFO @ Sun, 03 Jun 2018 13:23:18: start model_add_line... INFO @ Sun, 03 Jun 2018 13:23:18: #1 tag size is determined as 36 bps INFO @ Sun, 03 Jun 2018 13:23:18: #1 tag size = 36 INFO @ Sun, 03 Jun 2018 13:23:18: #1 total tags in treatment: 2336386 INFO @ Sun, 03 Jun 2018 13:23:18: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:23:18: #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 13:23:18: start X-correlation... INFO @ Sun, 03 Jun 2018 13:23:18: end of X-cor INFO @ Sun, 03 Jun 2018 13:23:18: #2 finished! INFO @ Sun, 03 Jun 2018 13:23:18: #2 predicted fragment length is 74 bps INFO @ Sun, 03 Jun 2018 13:23:18: #2 alternative fragment length(s) may be 74 bps INFO @ Sun, 03 Jun 2018 13:23:18: #2.2 Generate R script for model : SRX4047176.05_model.r INFO @ Sun, 03 Jun 2018 13:23:18: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:23:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:23:18: #1 tags after filtering in treatment: 2336386 INFO @ Sun, 03 Jun 2018 13:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:23:18: #1 finished! INFO @ Sun, 03 Jun 2018 13:23:18: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:23:18: #1 tag size is determined as 36 bps INFO @ Sun, 03 Jun 2018 13:23:18: #1 tag size = 36 INFO @ Sun, 03 Jun 2018 13:23:18: #1 total tags in treatment: 2336386 INFO @ Sun, 03 Jun 2018 13:23:18: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:23:18: #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 13:23:18: #1 tags after filtering in treatment: 2336386 INFO @ Sun, 03 Jun 2018 13:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:23:18: #1 finished! INFO @ Sun, 03 Jun 2018 13:23:18: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:23:18: #2 number of paired peaks: 378 WARNING @ Sun, 03 Jun 2018 13:23:18: Fewer paired peaks (378) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 378 pairs to build model! INFO @ Sun, 03 Jun 2018 13:23:18: start model_add_line... INFO @ Sun, 03 Jun 2018 13:23:18: start X-correlation... INFO @ Sun, 03 Jun 2018 13:23:18: end of X-cor INFO @ Sun, 03 Jun 2018 13:23:18: #2 finished! INFO @ Sun, 03 Jun 2018 13:23:18: #2 predicted fragment length is 74 bps INFO @ Sun, 03 Jun 2018 13:23:18: #2 alternative fragment length(s) may be 74 bps INFO @ Sun, 03 Jun 2018 13:23:18: #2.2 Generate R script for model : SRX4047176.20_model.r INFO @ Sun, 03 Jun 2018 13:23:18: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:23:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:23:18: #2 number of paired peaks: 378 WARNING @ Sun, 03 Jun 2018 13:23:18: Fewer paired peaks (378) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 378 pairs to build model! INFO @ Sun, 03 Jun 2018 13:23:18: start model_add_line... INFO @ Sun, 03 Jun 2018 13:23:18: start X-correlation... INFO @ Sun, 03 Jun 2018 13:23:18: end of X-cor INFO @ Sun, 03 Jun 2018 13:23:18: #2 finished! INFO @ Sun, 03 Jun 2018 13:23:18: #2 predicted fragment length is 74 bps INFO @ Sun, 03 Jun 2018 13:23:18: #2 alternative fragment length(s) may be 74 bps INFO @ Sun, 03 Jun 2018 13:23:18: #2.2 Generate R script for model : SRX4047176.10_model.r INFO @ Sun, 03 Jun 2018 13:23:18: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:23:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:23:24: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:23:24: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:23:24: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:23:27: #4 Write output xls file... SRX4047176.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:23:27: #4 Write peak in narrowPeak format file... SRX4047176.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:23:27: #4 Write summits bed file... SRX4047176.10_summits.bed INFO @ Sun, 03 Jun 2018 13:23:27: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:23:27: #4 Write output xls file... SRX4047176.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:23:27: #4 Write peak in narrowPeak format file... SRX4047176.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:23:27: #4 Write summits bed file... SRX4047176.20_summits.bed INFO @ Sun, 03 Jun 2018 13:23:27: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:23:27: #4 Write output xls file... SRX4047176.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:23:27: #4 Write peak in narrowPeak format file... SRX4047176.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:23:27: #4 Write summits bed file... SRX4047176.05_summits.bed INFO @ Sun, 03 Jun 2018 13:23:27: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (704 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。