Job ID = 11633821 sra ファイルのダウンロード中... Completed: 19659K bytes transferred in 3 seconds (52100K 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 593505 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420438/ERR1348914.sra Written 593505 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420438/ERR1348914.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: 00:00:06 593505 reads; of these: 593505 (100.00%) were unpaired; of these: 44458 (7.49%) aligned 0 times 444521 (74.90%) aligned exactly 1 time 104526 (17.61%) aligned >1 times 92.51% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 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] 57885 / 549047 = 0.1054 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 @ Fri, 15 Feb 2019 09:13:38: # Command line: callpeak -t ERX1420438.bam -f BAM -g 12100000 -n ERX1420438.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1420438.05 # format = BAM # ChIP-seq file = ['ERX1420438.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 @ Fri, 15 Feb 2019 09:13:38: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:13:38: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:13:38: # Command line: callpeak -t ERX1420438.bam -f BAM -g 12100000 -n ERX1420438.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1420438.20 # format = BAM # ChIP-seq file = ['ERX1420438.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 @ Fri, 15 Feb 2019 09:13:38: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:13:38: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:13:38: # Command line: callpeak -t ERX1420438.bam -f BAM -g 12100000 -n ERX1420438.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1420438.10 # format = BAM # ChIP-seq file = ['ERX1420438.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 @ Fri, 15 Feb 2019 09:13:38: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:13:38: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:13:41: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:13:41: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:13:41: #1 total tags in treatment: 491162 INFO @ Fri, 15 Feb 2019 09:13:41: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:13:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:13:41: #1 tags after filtering in treatment: 491162 INFO @ Fri, 15 Feb 2019 09:13:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:13:41: #1 finished! INFO @ Fri, 15 Feb 2019 09:13:41: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:13:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:13:41: #2 number of paired peaks: 177 WARNING @ Fri, 15 Feb 2019 09:13:41: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 15 Feb 2019 09:13:41: start model_add_line... INFO @ Fri, 15 Feb 2019 09:13:41: start X-correlation... INFO @ Fri, 15 Feb 2019 09:13:41: end of X-cor INFO @ Fri, 15 Feb 2019 09:13:41: #2 finished! INFO @ Fri, 15 Feb 2019 09:13:41: #2 predicted fragment length is 276 bps INFO @ Fri, 15 Feb 2019 09:13:41: #2 alternative fragment length(s) may be 0,10,84,165,204,226,253,276,320,341,375,380,446,474,520,522,594,598 bps INFO @ Fri, 15 Feb 2019 09:13:41: #2.2 Generate R script for model : ERX1420438.10_model.r INFO @ Fri, 15 Feb 2019 09:13:41: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:13:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:13:41: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:13:41: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:13:41: #1 total tags in treatment: 491162 INFO @ Fri, 15 Feb 2019 09:13:41: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:13:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:13:41: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:13:41: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:13:41: #1 total tags in treatment: 491162 INFO @ Fri, 15 Feb 2019 09:13:41: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:13:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:13:41: #1 tags after filtering in treatment: 491162 INFO @ Fri, 15 Feb 2019 09:13:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:13:41: #1 finished! INFO @ Fri, 15 Feb 2019 09:13:41: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:13:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:13:41: #1 tags after filtering in treatment: 491162 INFO @ Fri, 15 Feb 2019 09:13:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:13:41: #1 finished! INFO @ Fri, 15 Feb 2019 09:13:41: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:13:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:13:41: #2 number of paired peaks: 177 WARNING @ Fri, 15 Feb 2019 09:13:41: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 15 Feb 2019 09:13:41: start model_add_line... INFO @ Fri, 15 Feb 2019 09:13:41: start X-correlation... INFO @ Fri, 15 Feb 2019 09:13:41: end of X-cor INFO @ Fri, 15 Feb 2019 09:13:41: #2 finished! INFO @ Fri, 15 Feb 2019 09:13:41: #2 predicted fragment length is 276 bps INFO @ Fri, 15 Feb 2019 09:13:41: #2 number of paired peaks: 177 INFO @ Fri, 15 Feb 2019 09:13:41: #2 alternative fragment length(s) may be 0,10,84,165,204,226,253,276,320,341,375,380,446,474,520,522,594,598 bps WARNING @ Fri, 15 Feb 2019 09:13:41: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 15 Feb 2019 09:13:41: #2.2 Generate R script for model : ERX1420438.05_model.r INFO @ Fri, 15 Feb 2019 09:13:41: start model_add_line... INFO @ Fri, 15 Feb 2019 09:13:41: start X-correlation... INFO @ Fri, 15 Feb 2019 09:13:41: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:13:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:13:41: end of X-cor INFO @ Fri, 15 Feb 2019 09:13:41: #2 finished! INFO @ Fri, 15 Feb 2019 09:13:41: #2 predicted fragment length is 276 bps INFO @ Fri, 15 Feb 2019 09:13:41: #2 alternative fragment length(s) may be 0,10,84,165,204,226,253,276,320,341,375,380,446,474,520,522,594,598 bps INFO @ Fri, 15 Feb 2019 09:13:41: #2.2 Generate R script for model : ERX1420438.20_model.r INFO @ Fri, 15 Feb 2019 09:13:41: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:13:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:13:43: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:13:43: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:13:43: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:13:44: #4 Write output xls file... ERX1420438.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:13:44: #4 Write peak in narrowPeak format file... ERX1420438.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:13:44: #4 Write summits bed file... ERX1420438.10_summits.bed INFO @ Fri, 15 Feb 2019 09:13:44: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:13:44: #4 Write output xls file... ERX1420438.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:13:44: #4 Write peak in narrowPeak format file... ERX1420438.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:13:44: #4 Write summits bed file... ERX1420438.05_summits.bed INFO @ Fri, 15 Feb 2019 09:13:44: Done! INFO @ Fri, 15 Feb 2019 09:13:44: #4 Write output xls file... ERX1420438.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:13:44: #4 Write peak in narrowPeak format file... ERX1420438.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:13:44: #4 Write summits bed file... ERX1420438.20_summits.bed INFO @ Fri, 15 Feb 2019 09:13:44: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (17 records, 4 fields): 9 millis CompletedMACS2peakCalling pass1 - making usageList (1 chroms): 2 millis pass2 - checking and writing primary data (3 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。