Job ID = 10937757 sra ファイルのダウンロード中... Completed: 109146K bytes transferred in 7 seconds (119720K 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 1813280 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3697534/SRR6724151.sra Written 1813280 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3697534/SRR6724151.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: 00:00:58 1813280 reads; of these: 1813280 (100.00%) were unpaired; of these: 232604 (12.83%) aligned 0 times 998840 (55.08%) aligned exactly 1 time 581836 (32.09%) aligned >1 times 87.17% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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] 526263 / 1580676 = 0.3329 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, 10 Aug 2018 03:05:14: # Command line: callpeak -t SRX3697534.bam -f BAM -g 12100000 -n SRX3697534.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3697534.05 # format = BAM # ChIP-seq file = ['SRX3697534.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, 10 Aug 2018 03:05:14: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:05:14: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:05:14: # Command line: callpeak -t SRX3697534.bam -f BAM -g 12100000 -n SRX3697534.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3697534.10 # format = BAM # ChIP-seq file = ['SRX3697534.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, 10 Aug 2018 03:05:14: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:05:14: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:05:14: # Command line: callpeak -t SRX3697534.bam -f BAM -g 12100000 -n SRX3697534.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3697534.20 # format = BAM # ChIP-seq file = ['SRX3697534.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, 10 Aug 2018 03:05:14: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:05:14: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:05:27: 1000000 INFO @ Fri, 10 Aug 2018 03:05:27: 1000000 INFO @ Fri, 10 Aug 2018 03:05:27: 1000000 INFO @ Fri, 10 Aug 2018 03:05:27: #1 tag size is determined as 150 bps INFO @ Fri, 10 Aug 2018 03:05:27: #1 tag size = 150 INFO @ Fri, 10 Aug 2018 03:05:27: #1 total tags in treatment: 1054413 INFO @ Fri, 10 Aug 2018 03:05:27: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:05:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 03:05:27: #1 tag size is determined as 150 bps INFO @ Fri, 10 Aug 2018 03:05:27: #1 tag size = 150 INFO @ Fri, 10 Aug 2018 03:05:27: #1 total tags in treatment: 1054413 INFO @ Fri, 10 Aug 2018 03:05:27: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:05:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 03:05:27: #1 tags after filtering in treatment: 1054413 INFO @ Fri, 10 Aug 2018 03:05:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 03:05:27: #1 finished! INFO @ Fri, 10 Aug 2018 03:05:27: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:05:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:05:27: #1 tags after filtering in treatment: 1054413 INFO @ Fri, 10 Aug 2018 03:05:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 03:05:27: #1 finished! INFO @ Fri, 10 Aug 2018 03:05:27: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:05:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:05:27: #2 number of paired peaks: 132 WARNING @ Fri, 10 Aug 2018 03:05:27: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 10 Aug 2018 03:05:27: start model_add_line... INFO @ Fri, 10 Aug 2018 03:05:27: #2 number of paired peaks: 132 WARNING @ Fri, 10 Aug 2018 03:05:27: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 10 Aug 2018 03:05:27: start model_add_line... INFO @ Fri, 10 Aug 2018 03:05:27: start X-correlation... INFO @ Fri, 10 Aug 2018 03:05:27: start X-correlation... INFO @ Fri, 10 Aug 2018 03:05:27: end of X-cor INFO @ Fri, 10 Aug 2018 03:05:27: #2 finished! INFO @ Fri, 10 Aug 2018 03:05:27: #2 predicted fragment length is 238 bps INFO @ Fri, 10 Aug 2018 03:05:27: #2 alternative fragment length(s) may be 1,19,57,83,114,152,180,214,238,257,284,393,564,584 bps INFO @ Fri, 10 Aug 2018 03:05:27: #2.2 Generate R script for model : SRX3697534.10_model.r INFO @ Fri, 10 Aug 2018 03:05:27: end of X-cor INFO @ Fri, 10 Aug 2018 03:05:27: #2 finished! INFO @ Fri, 10 Aug 2018 03:05:27: #2 predicted fragment length is 238 bps INFO @ Fri, 10 Aug 2018 03:05:27: #2 alternative fragment length(s) may be 1,19,57,83,114,152,180,214,238,257,284,393,564,584 bps INFO @ Fri, 10 Aug 2018 03:05:27: #2.2 Generate R script for model : SRX3697534.05_model.r WARNING @ Fri, 10 Aug 2018 03:05:27: #2 Since the d (238) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 03:05:27: #2 You may need to consider one of the other alternative d(s): 1,19,57,83,114,152,180,214,238,257,284,393,564,584 WARNING @ Fri, 10 Aug 2018 03:05:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 03:05:27: #3 Call peaks... INFO @ Fri, 10 Aug 2018 03:05:27: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 10 Aug 2018 03:05:27: #2 Since the d (238) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 03:05:27: #2 You may need to consider one of the other alternative d(s): 1,19,57,83,114,152,180,214,238,257,284,393,564,584 WARNING @ Fri, 10 Aug 2018 03:05:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 03:05:27: #3 Call peaks... INFO @ Fri, 10 Aug 2018 03:05:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 03:05:27: #1 tag size is determined as 150 bps INFO @ Fri, 10 Aug 2018 03:05:27: #1 tag size = 150 INFO @ Fri, 10 Aug 2018 03:05:27: #1 total tags in treatment: 1054413 INFO @ Fri, 10 Aug 2018 03:05:27: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:05:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 03:05:27: #1 tags after filtering in treatment: 1054413 INFO @ Fri, 10 Aug 2018 03:05:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 03:05:27: #1 finished! INFO @ Fri, 10 Aug 2018 03:05:27: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:05:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:05:28: #2 number of paired peaks: 132 WARNING @ Fri, 10 Aug 2018 03:05:28: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 10 Aug 2018 03:05:28: start model_add_line... INFO @ Fri, 10 Aug 2018 03:05:28: start X-correlation... INFO @ Fri, 10 Aug 2018 03:05:28: end of X-cor INFO @ Fri, 10 Aug 2018 03:05:28: #2 finished! INFO @ Fri, 10 Aug 2018 03:05:28: #2 predicted fragment length is 238 bps INFO @ Fri, 10 Aug 2018 03:05:28: #2 alternative fragment length(s) may be 1,19,57,83,114,152,180,214,238,257,284,393,564,584 bps INFO @ Fri, 10 Aug 2018 03:05:28: #2.2 Generate R script for model : SRX3697534.20_model.r WARNING @ Fri, 10 Aug 2018 03:05:28: #2 Since the d (238) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 03:05:28: #2 You may need to consider one of the other alternative d(s): 1,19,57,83,114,152,180,214,238,257,284,393,564,584 WARNING @ Fri, 10 Aug 2018 03:05:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 03:05:28: #3 Call peaks... INFO @ Fri, 10 Aug 2018 03:05:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 03:05:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 03:05:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 03:05:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 03:05:33: #4 Write output xls file... SRX3697534.05_peaks.xls INFO @ Fri, 10 Aug 2018 03:05:33: #4 Write peak in narrowPeak format file... SRX3697534.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 03:05:33: #4 Write summits bed file... SRX3697534.05_summits.bed INFO @ Fri, 10 Aug 2018 03:05:33: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (228 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 03:05:33: #4 Write output xls file... SRX3697534.10_peaks.xls INFO @ Fri, 10 Aug 2018 03:05:33: #4 Write peak in narrowPeak format file... SRX3697534.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 03:05:33: #4 Write summits bed file... SRX3697534.10_summits.bed INFO @ Fri, 10 Aug 2018 03:05:33: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (77 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 03:05:33: #4 Write output xls file... SRX3697534.20_peaks.xls INFO @ Fri, 10 Aug 2018 03:05:33: #4 Write peak in narrowPeak format file... SRX3697534.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 03:05:33: #4 Write summits bed file... SRX3697534.20_summits.bed INFO @ Fri, 10 Aug 2018 03:05:33: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (24 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。