Job ID = 11193122 sra ファイルのダウンロード中... Completed: 97202K bytes transferred in 4 seconds (189305K 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 4369396 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4234145/SRR7360956.sra Written 4369396 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4234145/SRR7360956.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: 00:01:02 4369396 reads; of these: 4369396 (100.00%) were unpaired; of these: 368603 (8.44%) aligned 0 times 3452584 (79.02%) aligned exactly 1 time 548209 (12.55%) aligned >1 times 91.56% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 946124 / 4000793 = 0.2365 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 11:00:01: # Command line: callpeak -t SRX4234145.bam -f BAM -g 12100000 -n SRX4234145.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4234145.10 # format = BAM # ChIP-seq file = ['SRX4234145.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 11:00:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:00:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:00:01: # Command line: callpeak -t SRX4234145.bam -f BAM -g 12100000 -n SRX4234145.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4234145.20 # format = BAM # ChIP-seq file = ['SRX4234145.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 11:00:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:00:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:00:01: # Command line: callpeak -t SRX4234145.bam -f BAM -g 12100000 -n SRX4234145.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4234145.05 # format = BAM # ChIP-seq file = ['SRX4234145.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 11:00:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:00:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:00:10: 1000000 INFO @ Sat, 15 Sep 2018 11:00:10: 1000000 INFO @ Sat, 15 Sep 2018 11:00:10: 1000000 INFO @ Sat, 15 Sep 2018 11:00:19: 2000000 INFO @ Sat, 15 Sep 2018 11:00:19: 2000000 INFO @ Sat, 15 Sep 2018 11:00:19: 2000000 INFO @ Sat, 15 Sep 2018 11:00:26: 3000000 INFO @ Sat, 15 Sep 2018 11:00:27: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 11:00:27: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 11:00:27: #1 total tags in treatment: 3054669 INFO @ Sat, 15 Sep 2018 11:00:27: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:00:27: #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 11:00:27: #1 tags after filtering in treatment: 3054669 INFO @ Sat, 15 Sep 2018 11:00:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:00:27: #1 finished! INFO @ Sat, 15 Sep 2018 11:00:27: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:00:27: #2 number of paired peaks: 175 WARNING @ Sat, 15 Sep 2018 11:00:27: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Sep 2018 11:00:27: start model_add_line... INFO @ Sat, 15 Sep 2018 11:00:27: start X-correlation... INFO @ Sat, 15 Sep 2018 11:00:27: end of X-cor INFO @ Sat, 15 Sep 2018 11:00:27: #2 finished! INFO @ Sat, 15 Sep 2018 11:00:27: #2 predicted fragment length is 170 bps INFO @ Sat, 15 Sep 2018 11:00:27: #2 alternative fragment length(s) may be 3,135,157,170,187 bps INFO @ Sat, 15 Sep 2018 11:00:27: #2.2 Generate R script for model : SRX4234145.05_model.r INFO @ Sat, 15 Sep 2018 11:00:27: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:00:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:00:28: 3000000 INFO @ Sat, 15 Sep 2018 11:00:28: 3000000 INFO @ Sat, 15 Sep 2018 11:00:28: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 11:00:28: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 11:00:28: #1 total tags in treatment: 3054669 INFO @ Sat, 15 Sep 2018 11:00:28: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:00:28: #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 11:00:28: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 11:00:28: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 11:00:28: #1 total tags in treatment: 3054669 INFO @ Sat, 15 Sep 2018 11:00:28: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:00:28: #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 11:00:28: #1 tags after filtering in treatment: 3054669 INFO @ Sat, 15 Sep 2018 11:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:00:28: #1 finished! INFO @ Sat, 15 Sep 2018 11:00:28: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:00:28: #1 tags after filtering in treatment: 3054669 INFO @ Sat, 15 Sep 2018 11:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:00:28: #1 finished! INFO @ Sat, 15 Sep 2018 11:00:28: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:00:28: #2 number of paired peaks: 175 WARNING @ Sat, 15 Sep 2018 11:00:28: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Sep 2018 11:00:28: start model_add_line... INFO @ Sat, 15 Sep 2018 11:00:28: #2 number of paired peaks: 175 WARNING @ Sat, 15 Sep 2018 11:00:28: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Sep 2018 11:00:28: start model_add_line... INFO @ Sat, 15 Sep 2018 11:00:28: start X-correlation... INFO @ Sat, 15 Sep 2018 11:00:28: end of X-cor INFO @ Sat, 15 Sep 2018 11:00:28: #2 finished! INFO @ Sat, 15 Sep 2018 11:00:28: #2 predicted fragment length is 170 bps INFO @ Sat, 15 Sep 2018 11:00:28: #2 alternative fragment length(s) may be 3,135,157,170,187 bps INFO @ Sat, 15 Sep 2018 11:00:28: #2.2 Generate R script for model : SRX4234145.10_model.r INFO @ Sat, 15 Sep 2018 11:00:28: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:00:28: start X-correlation... INFO @ Sat, 15 Sep 2018 11:00:28: end of X-cor INFO @ Sat, 15 Sep 2018 11:00:28: #2 finished! INFO @ Sat, 15 Sep 2018 11:00:28: #2 predicted fragment length is 170 bps INFO @ Sat, 15 Sep 2018 11:00:28: #2 alternative fragment length(s) may be 3,135,157,170,187 bps INFO @ Sat, 15 Sep 2018 11:00:28: #2.2 Generate R script for model : SRX4234145.20_model.r INFO @ Sat, 15 Sep 2018 11:00:29: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:00:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:00:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:00:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:00:42: #4 Write output xls file... SRX4234145.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:00:42: #4 Write peak in narrowPeak format file... SRX4234145.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:00:42: #4 Write summits bed file... SRX4234145.05_summits.bed INFO @ Sat, 15 Sep 2018 11:00:42: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1195 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:00:43: #4 Write output xls file... SRX4234145.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:00:43: #4 Write peak in narrowPeak format file... SRX4234145.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:00:43: #4 Write summits bed file... SRX4234145.10_summits.bed INFO @ Sat, 15 Sep 2018 11:00:43: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (758 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:00:44: #4 Write output xls file... SRX4234145.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:00:44: #4 Write peak in narrowPeak format file... SRX4234145.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:00:44: #4 Write summits bed file... SRX4234145.20_summits.bed INFO @ Sat, 15 Sep 2018 11:00:44: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (443 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。