Job ID = 11244844 sra ファイルのダウンロード中... Completed: 55610K bytes transferred in 3 seconds (125004K bits/sec), in 1 file. Completed: 166308K bytes transferred in 4 seconds (279270K 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 1853098 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732403/SRR6759910.sra Written 1853098 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732403/SRR6759910.sra Read 5492961 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732403/SRR6759911.sra Written 5492961 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732403/SRR6759911.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 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: 00:01:06 7346059 reads; of these: 7346059 (100.00%) were unpaired; of these: 3963576 (53.96%) aligned 0 times 2844477 (38.72%) aligned exactly 1 time 538006 (7.32%) aligned >1 times 46.04% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 1561582 / 3382483 = 0.4617 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 @ Tue, 09 Oct 2018 22:06:31: # Command line: callpeak -t SRX3732403.bam -f BAM -g 12100000 -n SRX3732403.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3732403.20 # format = BAM # ChIP-seq file = ['SRX3732403.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 @ Tue, 09 Oct 2018 22:06:31: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:06:31: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:06:31: # Command line: callpeak -t SRX3732403.bam -f BAM -g 12100000 -n SRX3732403.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3732403.10 # format = BAM # ChIP-seq file = ['SRX3732403.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 @ Tue, 09 Oct 2018 22:06:31: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:06:31: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:06:31: # Command line: callpeak -t SRX3732403.bam -f BAM -g 12100000 -n SRX3732403.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3732403.05 # format = BAM # ChIP-seq file = ['SRX3732403.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 @ Tue, 09 Oct 2018 22:06:31: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:06:31: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:06:39: 1000000 INFO @ Tue, 09 Oct 2018 22:06:40: 1000000 INFO @ Tue, 09 Oct 2018 22:06:40: 1000000 INFO @ Tue, 09 Oct 2018 22:06:45: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:06:45: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:06:45: #1 total tags in treatment: 1820901 INFO @ Tue, 09 Oct 2018 22:06:45: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:06:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:06:45: #1 tags after filtering in treatment: 1820901 INFO @ Tue, 09 Oct 2018 22:06:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:06:45: #1 finished! INFO @ Tue, 09 Oct 2018 22:06:45: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:06:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:06:45: #2 number of paired peaks: 192 WARNING @ Tue, 09 Oct 2018 22:06:45: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 09 Oct 2018 22:06:45: start model_add_line... INFO @ Tue, 09 Oct 2018 22:06:45: start X-correlation... INFO @ Tue, 09 Oct 2018 22:06:45: end of X-cor INFO @ Tue, 09 Oct 2018 22:06:45: #2 finished! INFO @ Tue, 09 Oct 2018 22:06:45: #2 predicted fragment length is 34 bps INFO @ Tue, 09 Oct 2018 22:06:45: #2 alternative fragment length(s) may be 0,34,136,169,374,447,467,481,516,525,572 bps INFO @ Tue, 09 Oct 2018 22:06:45: #2.2 Generate R script for model : SRX3732403.10_model.r WARNING @ Tue, 09 Oct 2018 22:06:45: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:06:45: #2 You may need to consider one of the other alternative d(s): 0,34,136,169,374,447,467,481,516,525,572 WARNING @ Tue, 09 Oct 2018 22:06:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:06:45: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:06:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:06:47: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:06:47: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:06:47: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:06:47: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:06:47: #1 total tags in treatment: 1820901 INFO @ Tue, 09 Oct 2018 22:06:47: #1 total tags in treatment: 1820901 INFO @ Tue, 09 Oct 2018 22:06:47: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:06:47: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:06:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:06:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:06:47: #1 tags after filtering in treatment: 1820901 INFO @ Tue, 09 Oct 2018 22:06:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:06:47: #1 tags after filtering in treatment: 1820901 INFO @ Tue, 09 Oct 2018 22:06:47: #1 finished! INFO @ Tue, 09 Oct 2018 22:06:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:06:47: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:06:47: #1 finished! INFO @ Tue, 09 Oct 2018 22:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:06:47: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:06:47: #2 number of paired peaks: 192 WARNING @ Tue, 09 Oct 2018 22:06:47: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 09 Oct 2018 22:06:47: start model_add_line... INFO @ Tue, 09 Oct 2018 22:06:47: #2 number of paired peaks: 192 WARNING @ Tue, 09 Oct 2018 22:06:47: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Tue, 09 Oct 2018 22:06:47: start model_add_line... INFO @ Tue, 09 Oct 2018 22:06:47: start X-correlation... INFO @ Tue, 09 Oct 2018 22:06:47: start X-correlation... INFO @ Tue, 09 Oct 2018 22:06:47: end of X-cor INFO @ Tue, 09 Oct 2018 22:06:47: end of X-cor INFO @ Tue, 09 Oct 2018 22:06:47: #2 finished! INFO @ Tue, 09 Oct 2018 22:06:47: #2 finished! INFO @ Tue, 09 Oct 2018 22:06:47: #2 predicted fragment length is 34 bps INFO @ Tue, 09 Oct 2018 22:06:47: #2 predicted fragment length is 34 bps INFO @ Tue, 09 Oct 2018 22:06:47: #2 alternative fragment length(s) may be 0,34,136,169,374,447,467,481,516,525,572 bps INFO @ Tue, 09 Oct 2018 22:06:47: #2 alternative fragment length(s) may be 0,34,136,169,374,447,467,481,516,525,572 bps INFO @ Tue, 09 Oct 2018 22:06:47: #2.2 Generate R script for model : SRX3732403.05_model.r INFO @ Tue, 09 Oct 2018 22:06:47: #2.2 Generate R script for model : SRX3732403.20_model.r WARNING @ Tue, 09 Oct 2018 22:06:47: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:06:47: #2 You may need to consider one of the other alternative d(s): 0,34,136,169,374,447,467,481,516,525,572 WARNING @ Tue, 09 Oct 2018 22:06:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:06:47: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:06:47: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 09 Oct 2018 22:06:47: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:06:47: #2 You may need to consider one of the other alternative d(s): 0,34,136,169,374,447,467,481,516,525,572 WARNING @ Tue, 09 Oct 2018 22:06:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:06:47: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:06:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:06:49: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:06:51: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:06:51: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:06:51: #4 Write output xls file... SRX3732403.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:06:51: #4 Write peak in narrowPeak format file... SRX3732403.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:06:51: #4 Write summits bed file... SRX3732403.10_summits.bed INFO @ Tue, 09 Oct 2018 22:06:51: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:06:53: #4 Write output xls file... SRX3732403.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:06:53: #4 Write peak in narrowPeak format file... SRX3732403.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:06:53: #4 Write summits bed file... SRX3732403.05_summits.bed INFO @ Tue, 09 Oct 2018 22:06:53: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (69 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:06:53: #4 Write output xls file... SRX3732403.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:06:53: #4 Write peak in narrowPeak format file... SRX3732403.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:06:53: #4 Write summits bed file... SRX3732403.20_summits.bed INFO @ Tue, 09 Oct 2018 22:06:53: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (10 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。