Job ID = 11633820 sra ファイルのダウンロード中... Completed: 129036K bytes transferred in 4 seconds (223318K 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 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420437/ERR1348913.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420437/ERR1348913.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: 00:00:43 4000000 reads; of these: 4000000 (100.00%) were unpaired; of these: 301148 (7.53%) aligned 0 times 2992589 (74.81%) aligned exactly 1 time 706263 (17.66%) aligned >1 times 92.47% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 867822 / 3698852 = 0.2346 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 09:15:14: # Command line: callpeak -t ERX1420437.bam -f BAM -g 12100000 -n ERX1420437.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1420437.20 # format = BAM # ChIP-seq file = ['ERX1420437.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 09:15:14: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:15:14: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:15:14: # Command line: callpeak -t ERX1420437.bam -f BAM -g 12100000 -n ERX1420437.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1420437.05 # format = BAM # ChIP-seq file = ['ERX1420437.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 09:15:14: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:15:14: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:15:14: # Command line: callpeak -t ERX1420437.bam -f BAM -g 12100000 -n ERX1420437.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1420437.10 # format = BAM # ChIP-seq file = ['ERX1420437.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 09:15:14: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:15:14: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:15:21: 1000000 INFO @ Fri, 15 Feb 2019 09:15:21: 1000000 INFO @ Fri, 15 Feb 2019 09:15:22: 1000000 INFO @ Fri, 15 Feb 2019 09:15:29: 2000000 INFO @ Fri, 15 Feb 2019 09:15:29: 2000000 INFO @ Fri, 15 Feb 2019 09:15:29: 2000000 INFO @ Fri, 15 Feb 2019 09:15:35: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:15:35: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:15:35: #1 total tags in treatment: 2831030 INFO @ Fri, 15 Feb 2019 09:15:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:15:35: #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 09:15:35: #1 tags after filtering in treatment: 2831030 INFO @ Fri, 15 Feb 2019 09:15:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:15:35: #1 finished! INFO @ Fri, 15 Feb 2019 09:15:35: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:15:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:15:35: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:15:35: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:15:35: #1 total tags in treatment: 2831030 INFO @ Fri, 15 Feb 2019 09:15:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:15:35: #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 09:15:35: #1 tags after filtering in treatment: 2831030 INFO @ Fri, 15 Feb 2019 09:15:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:15:35: #1 finished! INFO @ Fri, 15 Feb 2019 09:15:35: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:15:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:15:35: #2 number of paired peaks: 171 WARNING @ Fri, 15 Feb 2019 09:15:35: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 15 Feb 2019 09:15:35: start model_add_line... INFO @ Fri, 15 Feb 2019 09:15:35: start X-correlation... INFO @ Fri, 15 Feb 2019 09:15:35: end of X-cor INFO @ Fri, 15 Feb 2019 09:15:35: #2 finished! INFO @ Fri, 15 Feb 2019 09:15:35: #2 predicted fragment length is 237 bps INFO @ Fri, 15 Feb 2019 09:15:35: #2 alternative fragment length(s) may be 1,10,206,223,237,267,285,368 bps INFO @ Fri, 15 Feb 2019 09:15:35: #2.2 Generate R script for model : ERX1420437.20_model.r INFO @ Fri, 15 Feb 2019 09:15:35: #2 number of paired peaks: 171 WARNING @ Fri, 15 Feb 2019 09:15:35: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 15 Feb 2019 09:15:35: start model_add_line... INFO @ Fri, 15 Feb 2019 09:15:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:15:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:15:35: start X-correlation... INFO @ Fri, 15 Feb 2019 09:15:35: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:15:35: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:15:35: #1 total tags in treatment: 2831030 INFO @ Fri, 15 Feb 2019 09:15:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:15:35: #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 09:15:35: end of X-cor INFO @ Fri, 15 Feb 2019 09:15:35: #2 finished! INFO @ Fri, 15 Feb 2019 09:15:35: #2 predicted fragment length is 237 bps INFO @ Fri, 15 Feb 2019 09:15:35: #2 alternative fragment length(s) may be 1,10,206,223,237,267,285,368 bps INFO @ Fri, 15 Feb 2019 09:15:35: #2.2 Generate R script for model : ERX1420437.10_model.r INFO @ Fri, 15 Feb 2019 09:15:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:15:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:15:36: #1 tags after filtering in treatment: 2831030 INFO @ Fri, 15 Feb 2019 09:15:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:15:36: #1 finished! INFO @ Fri, 15 Feb 2019 09:15:36: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:15:36: #2 number of paired peaks: 171 WARNING @ Fri, 15 Feb 2019 09:15:36: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 15 Feb 2019 09:15:36: start model_add_line... INFO @ Fri, 15 Feb 2019 09:15:36: start X-correlation... INFO @ Fri, 15 Feb 2019 09:15:36: end of X-cor INFO @ Fri, 15 Feb 2019 09:15:36: #2 finished! INFO @ Fri, 15 Feb 2019 09:15:36: #2 predicted fragment length is 237 bps INFO @ Fri, 15 Feb 2019 09:15:36: #2 alternative fragment length(s) may be 1,10,206,223,237,267,285,368 bps INFO @ Fri, 15 Feb 2019 09:15:36: #2.2 Generate R script for model : ERX1420437.05_model.r INFO @ Fri, 15 Feb 2019 09:15:36: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:15:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:15:42: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:15:42: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:15:42: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:15:45: #4 Write output xls file... ERX1420437.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:15:45: #4 Write peak in narrowPeak format file... ERX1420437.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:15:45: #4 Write summits bed file... ERX1420437.10_summits.bed INFO @ Fri, 15 Feb 2019 09:15:45: Done! INFO @ Fri, 15 Feb 2019 09:15:45: #4 Write output xls file... ERX1420437.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:15:45: #4 Write peak in narrowPeak format file... ERX1420437.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:15:45: #4 Write summits bed file... ERX1420437.20_summits.bed INFO @ Fri, 15 Feb 2019 09:15:45: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (13 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:15:45: #4 Write output xls file... ERX1420437.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:15:45: #4 Write peak in narrowPeak format file... ERX1420437.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:15:45: #4 Write summits bed file... ERX1420437.05_summits.bed INFO @ Fri, 15 Feb 2019 09:15:45: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (18 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。