Job ID = 11193094 sra ファイルのダウンロード中... Completed: 134409K bytes transferred in 14 seconds (78602K 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 7058959 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4234064/SRR7361037.sra Written 7058959 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4234064/SRR7361037.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: 00:01:15 7058959 reads; of these: 7058959 (100.00%) were unpaired; of these: 1112870 (15.77%) aligned 0 times 5118089 (72.50%) aligned exactly 1 time 828000 (11.73%) aligned >1 times 84.23% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 3305822 / 5946089 = 0.5560 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 @ Sat, 15 Sep 2018 10:57:47: # Command line: callpeak -t SRX4234064.bam -f BAM -g 12100000 -n SRX4234064.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4234064.20 # format = BAM # ChIP-seq file = ['SRX4234064.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 15 Sep 2018 10:57:47: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:57:47: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:57:47: # Command line: callpeak -t SRX4234064.bam -f BAM -g 12100000 -n SRX4234064.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4234064.05 # format = BAM # ChIP-seq file = ['SRX4234064.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 15 Sep 2018 10:57:47: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:57:47: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:57:47: # Command line: callpeak -t SRX4234064.bam -f BAM -g 12100000 -n SRX4234064.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4234064.10 # format = BAM # ChIP-seq file = ['SRX4234064.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 15 Sep 2018 10:57:47: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:57:47: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:57:53: 1000000 INFO @ Sat, 15 Sep 2018 10:57:54: 1000000 INFO @ Sat, 15 Sep 2018 10:57:54: 1000000 INFO @ Sat, 15 Sep 2018 10:58:01: 2000000 INFO @ Sat, 15 Sep 2018 10:58:02: 2000000 INFO @ Sat, 15 Sep 2018 10:58:02: 2000000 INFO @ Sat, 15 Sep 2018 10:58:05: #1 tag size is determined as 48 bps INFO @ Sat, 15 Sep 2018 10:58:05: #1 tag size = 48 INFO @ Sat, 15 Sep 2018 10:58:05: #1 total tags in treatment: 2640267 INFO @ Sat, 15 Sep 2018 10:58:05: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:58:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:58:05: #1 tags after filtering in treatment: 2640267 INFO @ Sat, 15 Sep 2018 10:58:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:58:05: #1 finished! INFO @ Sat, 15 Sep 2018 10:58:05: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:58:05: #2 number of paired peaks: 161 WARNING @ Sat, 15 Sep 2018 10:58:05: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 15 Sep 2018 10:58:05: start model_add_line... INFO @ Sat, 15 Sep 2018 10:58:05: start X-correlation... INFO @ Sat, 15 Sep 2018 10:58:05: end of X-cor INFO @ Sat, 15 Sep 2018 10:58:05: #2 finished! INFO @ Sat, 15 Sep 2018 10:58:05: #2 predicted fragment length is 195 bps INFO @ Sat, 15 Sep 2018 10:58:05: #2 alternative fragment length(s) may be 3,122,176,195,238,248,267 bps INFO @ Sat, 15 Sep 2018 10:58:05: #2.2 Generate R script for model : SRX4234064.20_model.r INFO @ Sat, 15 Sep 2018 10:58:05: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:58:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:58:07: #1 tag size is determined as 48 bps INFO @ Sat, 15 Sep 2018 10:58:07: #1 tag size = 48 INFO @ Sat, 15 Sep 2018 10:58:07: #1 total tags in treatment: 2640267 INFO @ Sat, 15 Sep 2018 10:58:07: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:58:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:58:07: #1 tag size is determined as 48 bps INFO @ Sat, 15 Sep 2018 10:58:07: #1 tag size = 48 INFO @ Sat, 15 Sep 2018 10:58:07: #1 total tags in treatment: 2640267 INFO @ Sat, 15 Sep 2018 10:58:07: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:58:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:58:07: #1 tags after filtering in treatment: 2640267 INFO @ Sat, 15 Sep 2018 10:58:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:58:07: #1 finished! INFO @ Sat, 15 Sep 2018 10:58:07: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:58:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:58:07: #1 tags after filtering in treatment: 2640267 INFO @ Sat, 15 Sep 2018 10:58:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:58:07: #1 finished! INFO @ Sat, 15 Sep 2018 10:58:07: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:58:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:58:07: #2 number of paired peaks: 161 WARNING @ Sat, 15 Sep 2018 10:58:07: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 15 Sep 2018 10:58:07: start model_add_line... INFO @ Sat, 15 Sep 2018 10:58:07: start X-correlation... INFO @ Sat, 15 Sep 2018 10:58:07: end of X-cor INFO @ Sat, 15 Sep 2018 10:58:07: #2 finished! INFO @ Sat, 15 Sep 2018 10:58:07: #2 predicted fragment length is 195 bps INFO @ Sat, 15 Sep 2018 10:58:07: #2 alternative fragment length(s) may be 3,122,176,195,238,248,267 bps INFO @ Sat, 15 Sep 2018 10:58:07: #2.2 Generate R script for model : SRX4234064.05_model.r INFO @ Sat, 15 Sep 2018 10:58:07: #2 number of paired peaks: 161 WARNING @ Sat, 15 Sep 2018 10:58:07: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 15 Sep 2018 10:58:07: start model_add_line... INFO @ Sat, 15 Sep 2018 10:58:07: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:58:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:58:07: start X-correlation... INFO @ Sat, 15 Sep 2018 10:58:07: end of X-cor INFO @ Sat, 15 Sep 2018 10:58:07: #2 finished! INFO @ Sat, 15 Sep 2018 10:58:07: #2 predicted fragment length is 195 bps INFO @ Sat, 15 Sep 2018 10:58:07: #2 alternative fragment length(s) may be 3,122,176,195,238,248,267 bps INFO @ Sat, 15 Sep 2018 10:58:07: #2.2 Generate R script for model : SRX4234064.10_model.r INFO @ Sat, 15 Sep 2018 10:58:07: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:58:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:58:15: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:58:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:58:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:58:18: #4 Write output xls file... SRX4234064.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:58:18: #4 Write peak in narrowPeak format file... SRX4234064.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:58:18: #4 Write summits bed file... SRX4234064.20_summits.bed INFO @ Sat, 15 Sep 2018 10:58:18: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:58:20: #4 Write output xls file... SRX4234064.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:58:20: #4 Write peak in narrowPeak format file... SRX4234064.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:58:20: #4 Write summits bed file... SRX4234064.05_summits.bed INFO @ Sat, 15 Sep 2018 10:58:20: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1121 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:58:20: #4 Write output xls file... SRX4234064.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:58:20: #4 Write peak in narrowPeak format file... SRX4234064.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:58:20: #4 Write summits bed file... SRX4234064.10_summits.bed INFO @ Sat, 15 Sep 2018 10:58:20: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (586 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。