Job ID = 11633894 sra ファイルのダウンロード中... Completed: 9859K bytes transferred in 2 seconds (28090K 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 305241 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420509/ERR1348985.sra Written 305241 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420509/ERR1348985.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: 00:00:03 305241 reads; of these: 305241 (100.00%) were unpaired; of these: 55593 (18.21%) aligned 0 times 185469 (60.76%) aligned exactly 1 time 64179 (21.03%) aligned >1 times 81.79% overall alignment rate Time searching: 00:00:03 Overall time: 00:00:03 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] 42256 / 249648 = 0.1693 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 09:17:28: # Command line: callpeak -t ERX1420509.bam -f BAM -g 12100000 -n ERX1420509.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1420509.10 # format = BAM # ChIP-seq file = ['ERX1420509.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 09:17:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:17:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:17:28: # Command line: callpeak -t ERX1420509.bam -f BAM -g 12100000 -n ERX1420509.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1420509.20 # format = BAM # ChIP-seq file = ['ERX1420509.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 09:17:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:17:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:17:28: # Command line: callpeak -t ERX1420509.bam -f BAM -g 12100000 -n ERX1420509.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1420509.05 # format = BAM # ChIP-seq file = ['ERX1420509.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 09:17:28: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:17:28: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:17:30: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:17:30: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:17:30: #1 total tags in treatment: 207392 INFO @ Fri, 15 Feb 2019 09:17:30: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:17:30: #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 09:17:30: #1 tags after filtering in treatment: 207392 INFO @ Fri, 15 Feb 2019 09:17:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:17:30: #1 finished! INFO @ Fri, 15 Feb 2019 09:17:30: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:17:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:17:30: #2 number of paired peaks: 361 WARNING @ Fri, 15 Feb 2019 09:17:30: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 15 Feb 2019 09:17:30: start model_add_line... INFO @ Fri, 15 Feb 2019 09:17:30: start X-correlation... INFO @ Fri, 15 Feb 2019 09:17:30: end of X-cor INFO @ Fri, 15 Feb 2019 09:17:30: #2 finished! INFO @ Fri, 15 Feb 2019 09:17:30: #2 predicted fragment length is 208 bps INFO @ Fri, 15 Feb 2019 09:17:30: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 15 Feb 2019 09:17:30: #2.2 Generate R script for model : ERX1420509.10_model.r INFO @ Fri, 15 Feb 2019 09:17:30: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:17:30: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:17:30: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:17:30: #1 total tags in treatment: 207392 INFO @ Fri, 15 Feb 2019 09:17:30: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:17:30: #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 09:17:30: #1 tags after filtering in treatment: 207392 INFO @ Fri, 15 Feb 2019 09:17:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:17:30: #1 finished! INFO @ Fri, 15 Feb 2019 09:17:30: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:17:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:17:30: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:17:30: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:17:30: #1 total tags in treatment: 207392 INFO @ Fri, 15 Feb 2019 09:17:30: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:17:30: #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 09:17:30: #2 number of paired peaks: 361 WARNING @ Fri, 15 Feb 2019 09:17:30: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 15 Feb 2019 09:17:30: start model_add_line... INFO @ Fri, 15 Feb 2019 09:17:30: #1 tags after filtering in treatment: 207392 INFO @ Fri, 15 Feb 2019 09:17:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:17:30: #1 finished! INFO @ Fri, 15 Feb 2019 09:17:30: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:17:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:17:30: start X-correlation... INFO @ Fri, 15 Feb 2019 09:17:30: end of X-cor INFO @ Fri, 15 Feb 2019 09:17:30: #2 finished! INFO @ Fri, 15 Feb 2019 09:17:30: #2 predicted fragment length is 208 bps INFO @ Fri, 15 Feb 2019 09:17:30: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 15 Feb 2019 09:17:30: #2.2 Generate R script for model : ERX1420509.20_model.r INFO @ Fri, 15 Feb 2019 09:17:30: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:17:30: #2 number of paired peaks: 361 WARNING @ Fri, 15 Feb 2019 09:17:30: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Fri, 15 Feb 2019 09:17:30: start model_add_line... INFO @ Fri, 15 Feb 2019 09:17:30: start X-correlation... INFO @ Fri, 15 Feb 2019 09:17:30: end of X-cor INFO @ Fri, 15 Feb 2019 09:17:30: #2 finished! INFO @ Fri, 15 Feb 2019 09:17:30: #2 predicted fragment length is 208 bps INFO @ Fri, 15 Feb 2019 09:17:30: #2 alternative fragment length(s) may be 208 bps INFO @ Fri, 15 Feb 2019 09:17:30: #2.2 Generate R script for model : ERX1420509.05_model.r INFO @ Fri, 15 Feb 2019 09:17:30: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:17:30: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:17:31: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:17:31: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:17:31: #4 Write output xls file... ERX1420509.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:17:31: #4 Write peak in narrowPeak format file... ERX1420509.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:17:31: #4 Write summits bed file... ERX1420509.10_summits.bed INFO @ Fri, 15 Feb 2019 09:17:31: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (255 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:17:31: #4 Write output xls file... ERX1420509.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:17:31: #4 Write peak in narrowPeak format file... ERX1420509.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:17:31: #4 Write summits bed file... ERX1420509.20_summits.bed INFO @ Fri, 15 Feb 2019 09:17:31: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (33 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:17:31: #4 Write output xls file... ERX1420509.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:17:31: #4 Write peak in narrowPeak format file... ERX1420509.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:17:31: #4 Write summits bed file... ERX1420509.05_summits.bed INFO @ Fri, 15 Feb 2019 09:17:31: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (773 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。