Job ID = 11634006 sra ファイルのダウンロード中... Completed: 70575K bytes transferred in 3 seconds (148184K 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 2469170 spots for /home/okishinya/chipatlas/results/sacCer3/ERX2558653/ERR2540235.sra Written 2469170 spots for /home/okishinya/chipatlas/results/sacCer3/ERX2558653/ERR2540235.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 2469170 reads; of these: 2469170 (100.00%) were unpaired; of these: 364517 (14.76%) aligned 0 times 1169292 (47.36%) aligned exactly 1 time 935361 (37.88%) aligned >1 times 85.24% 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] 862835 / 2104653 = 0.4100 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 09:21:08: # Command line: callpeak -t ERX2558653.bam -f BAM -g 12100000 -n ERX2558653.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX2558653.10 # format = BAM # ChIP-seq file = ['ERX2558653.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 09:21:08: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:21:08: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:21:09: # Command line: callpeak -t ERX2558653.bam -f BAM -g 12100000 -n ERX2558653.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX2558653.20 # format = BAM # ChIP-seq file = ['ERX2558653.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 09:21:09: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:21:09: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:21:09: # Command line: callpeak -t ERX2558653.bam -f BAM -g 12100000 -n ERX2558653.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX2558653.05 # format = BAM # ChIP-seq file = ['ERX2558653.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 09:21:09: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:21:09: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:21:15: 1000000 INFO @ Fri, 15 Feb 2019 09:21:15: 1000000 INFO @ Fri, 15 Feb 2019 09:21:16: 1000000 INFO @ Fri, 15 Feb 2019 09:21:17: #1 tag size is determined as 66 bps INFO @ Fri, 15 Feb 2019 09:21:17: #1 tag size = 66 INFO @ Fri, 15 Feb 2019 09:21:17: #1 total tags in treatment: 1241818 INFO @ Fri, 15 Feb 2019 09:21:17: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:21:17: #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 09:21:17: #1 tags after filtering in treatment: 1241818 INFO @ Fri, 15 Feb 2019 09:21:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:21:17: #1 finished! INFO @ Fri, 15 Feb 2019 09:21:17: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:21:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:21:17: #1 tag size is determined as 66 bps INFO @ Fri, 15 Feb 2019 09:21:17: #1 tag size = 66 INFO @ Fri, 15 Feb 2019 09:21:17: #1 total tags in treatment: 1241818 INFO @ Fri, 15 Feb 2019 09:21:17: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:21:17: #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 09:21:17: #1 tags after filtering in treatment: 1241818 INFO @ Fri, 15 Feb 2019 09:21:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:21:17: #1 finished! INFO @ Fri, 15 Feb 2019 09:21:17: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:21:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:21:17: #2 number of paired peaks: 168 WARNING @ Fri, 15 Feb 2019 09:21:17: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 15 Feb 2019 09:21:17: start model_add_line... INFO @ Fri, 15 Feb 2019 09:21:17: start X-correlation... INFO @ Fri, 15 Feb 2019 09:21:17: end of X-cor INFO @ Fri, 15 Feb 2019 09:21:17: #2 finished! INFO @ Fri, 15 Feb 2019 09:21:17: #2 predicted fragment length is 67 bps INFO @ Fri, 15 Feb 2019 09:21:17: #2 alternative fragment length(s) may be 2,67,597 bps INFO @ Fri, 15 Feb 2019 09:21:17: #2.2 Generate R script for model : ERX2558653.20_model.r WARNING @ Fri, 15 Feb 2019 09:21:17: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 09:21:17: #2 You may need to consider one of the other alternative d(s): 2,67,597 WARNING @ Fri, 15 Feb 2019 09:21:17: #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 09:21:17: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:21:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:21:17: #2 number of paired peaks: 168 WARNING @ Fri, 15 Feb 2019 09:21:17: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 15 Feb 2019 09:21:17: start model_add_line... INFO @ Fri, 15 Feb 2019 09:21:17: start X-correlation... INFO @ Fri, 15 Feb 2019 09:21:17: end of X-cor INFO @ Fri, 15 Feb 2019 09:21:17: #2 finished! INFO @ Fri, 15 Feb 2019 09:21:17: #2 predicted fragment length is 67 bps INFO @ Fri, 15 Feb 2019 09:21:17: #2 alternative fragment length(s) may be 2,67,597 bps INFO @ Fri, 15 Feb 2019 09:21:17: #2.2 Generate R script for model : ERX2558653.05_model.r WARNING @ Fri, 15 Feb 2019 09:21:17: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 09:21:17: #2 You may need to consider one of the other alternative d(s): 2,67,597 WARNING @ Fri, 15 Feb 2019 09:21:17: #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 09:21:17: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:21:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:21:17: #1 tag size is determined as 66 bps INFO @ Fri, 15 Feb 2019 09:21:17: #1 tag size = 66 INFO @ Fri, 15 Feb 2019 09:21:17: #1 total tags in treatment: 1241818 INFO @ Fri, 15 Feb 2019 09:21:17: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:21:17: #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 09:21:17: #1 tags after filtering in treatment: 1241818 INFO @ Fri, 15 Feb 2019 09:21:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:21:17: #1 finished! INFO @ Fri, 15 Feb 2019 09:21:17: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:21:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:21:17: #2 number of paired peaks: 168 WARNING @ Fri, 15 Feb 2019 09:21:17: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 15 Feb 2019 09:21:17: start model_add_line... INFO @ Fri, 15 Feb 2019 09:21:17: start X-correlation... INFO @ Fri, 15 Feb 2019 09:21:17: end of X-cor INFO @ Fri, 15 Feb 2019 09:21:17: #2 finished! INFO @ Fri, 15 Feb 2019 09:21:17: #2 predicted fragment length is 67 bps INFO @ Fri, 15 Feb 2019 09:21:17: #2 alternative fragment length(s) may be 2,67,597 bps INFO @ Fri, 15 Feb 2019 09:21:17: #2.2 Generate R script for model : ERX2558653.10_model.r WARNING @ Fri, 15 Feb 2019 09:21:17: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 09:21:17: #2 You may need to consider one of the other alternative d(s): 2,67,597 WARNING @ Fri, 15 Feb 2019 09:21:17: #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 09:21:17: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:21:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:21:20: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:21:20: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:21:21: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:21:21: #4 Write output xls file... ERX2558653.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:21:21: #4 Write peak in narrowPeak format file... ERX2558653.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:21:21: #4 Write summits bed file... ERX2558653.20_summits.bed INFO @ Fri, 15 Feb 2019 09:21:21: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:21:21: #4 Write output xls file... ERX2558653.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:21:21: #4 Write peak in narrowPeak format file... ERX2558653.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:21:22: #4 Write summits bed file... ERX2558653.05_summits.bed INFO @ Fri, 15 Feb 2019 09:21:22: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:21:22: #4 Write output xls file... ERX2558653.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:21:22: #4 Write peak in narrowPeak format file... ERX2558653.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:21:22: #4 Write summits bed file... ERX2558653.10_summits.bed INFO @ Fri, 15 Feb 2019 09:21:22: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (86 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。