Job ID = 10453673 sra ファイルのダウンロード中... Completed: 427618K bytes transferred in 7 seconds (453382K 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... Written 17231243 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3531161/SRR6439792.sra Written 17231243 spots total 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: 00:02:29 17231243 reads; of these: 17231243 (100.00%) were unpaired; of these: 15346839 (89.06%) aligned 0 times 1609349 (9.34%) aligned exactly 1 time 275055 (1.60%) aligned >1 times 10.94% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 686636 / 1884404 = 0.3644 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 @ Thu, 08 Feb 2018 17:46:44: # Command line: callpeak -t SRX3531161.bam -f BAM -g 12100000 -n SRX3531161.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3531161.20 # format = BAM # ChIP-seq file = ['SRX3531161.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 @ Thu, 08 Feb 2018 17:46:44: #1 read tag files... INFO @ Thu, 08 Feb 2018 17:46:44: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 17:46:44: # Command line: callpeak -t SRX3531161.bam -f BAM -g 12100000 -n SRX3531161.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3531161.10 # format = BAM # ChIP-seq file = ['SRX3531161.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 @ Thu, 08 Feb 2018 17:46:44: #1 read tag files... INFO @ Thu, 08 Feb 2018 17:46:44: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 17:46:52: 1000000 INFO @ Thu, 08 Feb 2018 17:46:54: #1 tag size is determined as 40 bps INFO @ Thu, 08 Feb 2018 17:46:54: #1 tag size = 40 INFO @ Thu, 08 Feb 2018 17:46:54: #1 total tags in treatment: 1197768 INFO @ Thu, 08 Feb 2018 17:46:54: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 17:46:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 17:46:54: #1 tags after filtering in treatment: 1197768 INFO @ Thu, 08 Feb 2018 17:46:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 17:46:54: #1 finished! INFO @ Thu, 08 Feb 2018 17:46:54: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 17:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 17:46:54: #2 number of paired peaks: 211 WARNING @ Thu, 08 Feb 2018 17:46:54: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Thu, 08 Feb 2018 17:46:54: start model_add_line... INFO @ Thu, 08 Feb 2018 17:46:54: start X-correlation... INFO @ Thu, 08 Feb 2018 17:46:54: end of X-cor INFO @ Thu, 08 Feb 2018 17:46:54: #2 finished! INFO @ Thu, 08 Feb 2018 17:46:54: #2 predicted fragment length is 261 bps INFO @ Thu, 08 Feb 2018 17:46:54: #2 alternative fragment length(s) may be 261 bps INFO @ Thu, 08 Feb 2018 17:46:54: #2.2 Generate R script for model : SRX3531161.10_model.r INFO @ Thu, 08 Feb 2018 17:46:54: #3 Call peaks... INFO @ Thu, 08 Feb 2018 17:46:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 17:46:58: 1000000 INFO @ Thu, 08 Feb 2018 17:47:00: #1 tag size is determined as 40 bps INFO @ Thu, 08 Feb 2018 17:47:00: #1 tag size = 40 INFO @ Thu, 08 Feb 2018 17:47:00: #1 total tags in treatment: 1197768 INFO @ Thu, 08 Feb 2018 17:47:00: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 17:47:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 17:47:00: #1 tags after filtering in treatment: 1197768 INFO @ Thu, 08 Feb 2018 17:47:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 17:47:00: #1 finished! INFO @ Thu, 08 Feb 2018 17:47:00: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 17:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 17:47:00: #2 number of paired peaks: 211 WARNING @ Thu, 08 Feb 2018 17:47:00: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Thu, 08 Feb 2018 17:47:00: start model_add_line... INFO @ Thu, 08 Feb 2018 17:47:00: start X-correlation... INFO @ Thu, 08 Feb 2018 17:47:00: end of X-cor INFO @ Thu, 08 Feb 2018 17:47:00: #2 finished! INFO @ Thu, 08 Feb 2018 17:47:00: #2 predicted fragment length is 261 bps INFO @ Thu, 08 Feb 2018 17:47:00: #2 alternative fragment length(s) may be 261 bps INFO @ Thu, 08 Feb 2018 17:47:00: #2.2 Generate R script for model : SRX3531161.20_model.r INFO @ Thu, 08 Feb 2018 17:47:00: #3 Call peaks... INFO @ Thu, 08 Feb 2018 17:47:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 17:47:00: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 17:47:02: #4 Write output xls file... SRX3531161.10_peaks.xls INFO @ Thu, 08 Feb 2018 17:47:03: #4 Write peak in narrowPeak format file... SRX3531161.10_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 17:47:03: #4 Write summits bed file... SRX3531161.10_summits.bed INFO @ Thu, 08 Feb 2018 17:47:03: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (512 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 17:47:05: # Command line: callpeak -t SRX3531161.bam -f BAM -g 12100000 -n SRX3531161.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3531161.05 # format = BAM # ChIP-seq file = ['SRX3531161.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 @ Thu, 08 Feb 2018 17:47:05: #1 read tag files... INFO @ Thu, 08 Feb 2018 17:47:05: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 17:47:06: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 17:47:08: #4 Write output xls file... SRX3531161.20_peaks.xls INFO @ Thu, 08 Feb 2018 17:47:08: #4 Write peak in narrowPeak format file... SRX3531161.20_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 17:47:08: #4 Write summits bed file... SRX3531161.20_summits.bed INFO @ Thu, 08 Feb 2018 17:47:08: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (290 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 17:47:13: 1000000 INFO @ Thu, 08 Feb 2018 17:47:14: #1 tag size is determined as 40 bps INFO @ Thu, 08 Feb 2018 17:47:14: #1 tag size = 40 INFO @ Thu, 08 Feb 2018 17:47:14: #1 total tags in treatment: 1197768 INFO @ Thu, 08 Feb 2018 17:47:14: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 17:47:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 17:47:14: #1 tags after filtering in treatment: 1197768 INFO @ Thu, 08 Feb 2018 17:47:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 17:47:14: #1 finished! INFO @ Thu, 08 Feb 2018 17:47:14: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 17:47:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 17:47:15: #2 number of paired peaks: 211 WARNING @ Thu, 08 Feb 2018 17:47:15: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Thu, 08 Feb 2018 17:47:15: start model_add_line... INFO @ Thu, 08 Feb 2018 17:47:15: start X-correlation... INFO @ Thu, 08 Feb 2018 17:47:15: end of X-cor INFO @ Thu, 08 Feb 2018 17:47:15: #2 finished! INFO @ Thu, 08 Feb 2018 17:47:15: #2 predicted fragment length is 261 bps INFO @ Thu, 08 Feb 2018 17:47:15: #2 alternative fragment length(s) may be 261 bps INFO @ Thu, 08 Feb 2018 17:47:15: #2.2 Generate R script for model : SRX3531161.05_model.r INFO @ Thu, 08 Feb 2018 17:47:15: #3 Call peaks... INFO @ Thu, 08 Feb 2018 17:47:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 17:47:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Feb 2018 17:47:22: #4 Write output xls file... SRX3531161.05_peaks.xls INFO @ Thu, 08 Feb 2018 17:47:22: #4 Write peak in narrowPeak format file... SRX3531161.05_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 17:47:22: #4 Write summits bed file... SRX3531161.05_summits.bed INFO @ Thu, 08 Feb 2018 17:47:22: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (844 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。