Job ID = 11634002 sra ファイルのダウンロード中... Completed: 68189K bytes transferred in 4 seconds (127625K 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 2378758 spots for /home/okishinya/chipatlas/results/sacCer3/ERX2558649/ERR2540231.sra Written 2378758 spots for /home/okishinya/chipatlas/results/sacCer3/ERX2558649/ERR2540231.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: 00:00:39 2378758 reads; of these: 2378758 (100.00%) were unpaired; of these: 306613 (12.89%) aligned 0 times 1160545 (48.79%) aligned exactly 1 time 911600 (38.32%) aligned >1 times 87.11% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 858537 / 2072145 = 0.4143 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 09:20:36: # Command line: callpeak -t ERX2558649.bam -f BAM -g 12100000 -n ERX2558649.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX2558649.05 # format = BAM # ChIP-seq file = ['ERX2558649.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 09:20:36: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:20:36: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:20:36: # Command line: callpeak -t ERX2558649.bam -f BAM -g 12100000 -n ERX2558649.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX2558649.20 # format = BAM # ChIP-seq file = ['ERX2558649.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 09:20:36: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:20:36: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:20:36: # Command line: callpeak -t ERX2558649.bam -f BAM -g 12100000 -n ERX2558649.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX2558649.10 # format = BAM # ChIP-seq file = ['ERX2558649.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 09:20:36: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:20:36: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:20:43: 1000000 INFO @ Fri, 15 Feb 2019 09:20:43: 1000000 INFO @ Fri, 15 Feb 2019 09:20:43: 1000000 INFO @ Fri, 15 Feb 2019 09:20:44: #1 tag size is determined as 66 bps INFO @ Fri, 15 Feb 2019 09:20:44: #1 tag size = 66 INFO @ Fri, 15 Feb 2019 09:20:44: #1 total tags in treatment: 1213608 INFO @ Fri, 15 Feb 2019 09:20:44: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:20:44: #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 09:20:44: #1 tags after filtering in treatment: 1213608 INFO @ Fri, 15 Feb 2019 09:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:20:44: #1 finished! INFO @ Fri, 15 Feb 2019 09:20:44: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:20:44: #1 tag size is determined as 66 bps INFO @ Fri, 15 Feb 2019 09:20:44: #1 tag size = 66 INFO @ Fri, 15 Feb 2019 09:20:44: #2 number of paired peaks: 191 INFO @ Fri, 15 Feb 2019 09:20:44: #1 total tags in treatment: 1213608 WARNING @ Fri, 15 Feb 2019 09:20:44: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 15 Feb 2019 09:20:44: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:20:44: #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 09:20:44: start model_add_line... INFO @ Fri, 15 Feb 2019 09:20:44: #1 tag size is determined as 66 bps INFO @ Fri, 15 Feb 2019 09:20:44: #1 tag size = 66 INFO @ Fri, 15 Feb 2019 09:20:44: #1 total tags in treatment: 1213608 INFO @ Fri, 15 Feb 2019 09:20:44: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:20:44: #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 09:20:44: start X-correlation... INFO @ Fri, 15 Feb 2019 09:20:44: end of X-cor INFO @ Fri, 15 Feb 2019 09:20:44: #2 finished! INFO @ Fri, 15 Feb 2019 09:20:44: #2 predicted fragment length is 73 bps INFO @ Fri, 15 Feb 2019 09:20:44: #2 alternative fragment length(s) may be 3,73,597 bps INFO @ Fri, 15 Feb 2019 09:20:44: #2.2 Generate R script for model : ERX2558649.10_model.r INFO @ Fri, 15 Feb 2019 09:20:44: #1 tags after filtering in treatment: 1213608 INFO @ Fri, 15 Feb 2019 09:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:20:44: #1 finished! INFO @ Fri, 15 Feb 2019 09:20:44: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:20:44: #2 looking for paired plus/minus strand peaks... WARNING @ Fri, 15 Feb 2019 09:20:44: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 09:20:44: #2 You may need to consider one of the other alternative d(s): 3,73,597 WARNING @ Fri, 15 Feb 2019 09:20:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 09:20:44: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:20:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:20:44: #1 tags after filtering in treatment: 1213608 INFO @ Fri, 15 Feb 2019 09:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:20:44: #1 finished! INFO @ Fri, 15 Feb 2019 09:20:44: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:20:44: #2 number of paired peaks: 191 WARNING @ Fri, 15 Feb 2019 09:20:44: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 15 Feb 2019 09:20:44: start model_add_line... INFO @ Fri, 15 Feb 2019 09:20:44: #2 number of paired peaks: 191 WARNING @ Fri, 15 Feb 2019 09:20:44: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 15 Feb 2019 09:20:44: start model_add_line... INFO @ Fri, 15 Feb 2019 09:20:44: start X-correlation... INFO @ Fri, 15 Feb 2019 09:20:44: start X-correlation... INFO @ Fri, 15 Feb 2019 09:20:44: end of X-cor INFO @ Fri, 15 Feb 2019 09:20:44: #2 finished! INFO @ Fri, 15 Feb 2019 09:20:44: #2 predicted fragment length is 73 bps INFO @ Fri, 15 Feb 2019 09:20:44: #2 alternative fragment length(s) may be 3,73,597 bps INFO @ Fri, 15 Feb 2019 09:20:44: #2.2 Generate R script for model : ERX2558649.05_model.r INFO @ Fri, 15 Feb 2019 09:20:44: end of X-cor INFO @ Fri, 15 Feb 2019 09:20:44: #2 finished! INFO @ Fri, 15 Feb 2019 09:20:44: #2 predicted fragment length is 73 bps INFO @ Fri, 15 Feb 2019 09:20:44: #2 alternative fragment length(s) may be 3,73,597 bps INFO @ Fri, 15 Feb 2019 09:20:44: #2.2 Generate R script for model : ERX2558649.20_model.r WARNING @ Fri, 15 Feb 2019 09:20:44: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 09:20:44: #2 You may need to consider one of the other alternative d(s): 3,73,597 WARNING @ Fri, 15 Feb 2019 09:20:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 09:20:44: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:20:44: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 15 Feb 2019 09:20:44: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 09:20:44: #2 You may need to consider one of the other alternative d(s): 3,73,597 WARNING @ Fri, 15 Feb 2019 09:20:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 09:20:44: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:20:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:20:47: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:20:47: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:20:47: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:20:49: #4 Write output xls file... ERX2558649.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:20:49: #4 Write peak in narrowPeak format file... ERX2558649.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:20:49: #4 Write summits bed file... ERX2558649.10_summits.bed INFO @ Fri, 15 Feb 2019 09:20:49: Done! pass1 - making usageList (17 chroms): 4 millis pass2 - checking and writing primary data (94 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:20:49: #4 Write output xls file... ERX2558649.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:20:49: #4 Write peak in narrowPeak format file... ERX2558649.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:20:49: #4 Write summits bed file... ERX2558649.20_summits.bed INFO @ Fri, 15 Feb 2019 09:20:49: Done! INFO @ Fri, 15 Feb 2019 09:20:49: #4 Write output xls file... ERX2558649.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:20:49: #4 Write peak in narrowPeak format file... ERX2558649.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:20:49: #4 Write summits bed file... ERX2558649.05_summits.bed INFO @ Fri, 15 Feb 2019 09:20:49: Done! pass1 - making usageList (16 chroms): 7 millis pass2 - checking and writing primary data (63 records, 4 fields): 20 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 6 millis pass2 - checking and writing primary data (137 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。