Job ID = 11244847 sra ファイルのダウンロード中... Completed: 94816K bytes transferred in 4 seconds (175904K bits/sec), in 1 file. Completed: 165774K bytes transferred in 4 seconds (273988K 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 3231611 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732406/SRR6759916.sra Written 3231611 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732406/SRR6759916.sra Read 5547977 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732406/SRR6759917.sra Written 5547977 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732406/SRR6759917.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: 00:01:21 8779588 reads; of these: 8779588 (100.00%) were unpaired; of these: 4077301 (46.44%) aligned 0 times 3886113 (44.26%) aligned exactly 1 time 816174 (9.30%) aligned >1 times 53.56% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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] 2652194 / 4702287 = 0.5640 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 22:08:01: # Command line: callpeak -t SRX3732406.bam -f BAM -g 12100000 -n SRX3732406.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3732406.10 # format = BAM # ChIP-seq file = ['SRX3732406.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 22:08:01: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:08:01: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:08:01: # Command line: callpeak -t SRX3732406.bam -f BAM -g 12100000 -n SRX3732406.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3732406.20 # format = BAM # ChIP-seq file = ['SRX3732406.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 22:08:01: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:08:01: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:08:01: # Command line: callpeak -t SRX3732406.bam -f BAM -g 12100000 -n SRX3732406.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3732406.05 # format = BAM # ChIP-seq file = ['SRX3732406.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 22:08:01: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:08:01: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:08:07: 1000000 INFO @ Tue, 09 Oct 2018 22:08:07: 1000000 INFO @ Tue, 09 Oct 2018 22:08:07: 1000000 INFO @ Tue, 09 Oct 2018 22:08:13: 2000000 INFO @ Tue, 09 Oct 2018 22:08:13: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:08:13: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:08:13: #1 total tags in treatment: 2050093 INFO @ Tue, 09 Oct 2018 22:08:13: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:08:13: #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 22:08:13: #1 tags after filtering in treatment: 2050093 INFO @ Tue, 09 Oct 2018 22:08:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:08:13: #1 finished! INFO @ Tue, 09 Oct 2018 22:08:13: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:08:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:08:13: #2 number of paired peaks: 179 WARNING @ Tue, 09 Oct 2018 22:08:13: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Tue, 09 Oct 2018 22:08:13: start model_add_line... INFO @ Tue, 09 Oct 2018 22:08:13: start X-correlation... INFO @ Tue, 09 Oct 2018 22:08:13: end of X-cor INFO @ Tue, 09 Oct 2018 22:08:13: #2 finished! INFO @ Tue, 09 Oct 2018 22:08:13: #2 predicted fragment length is 40 bps INFO @ Tue, 09 Oct 2018 22:08:13: #2 alternative fragment length(s) may be 1,40,119,150,217,260,334,348,379,466,522 bps INFO @ Tue, 09 Oct 2018 22:08:13: #2.2 Generate R script for model : SRX3732406.10_model.r WARNING @ Tue, 09 Oct 2018 22:08:13: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:08:13: #2 You may need to consider one of the other alternative d(s): 1,40,119,150,217,260,334,348,379,466,522 WARNING @ Tue, 09 Oct 2018 22:08:13: #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 22:08:13: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:08:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:08:14: 2000000 INFO @ Tue, 09 Oct 2018 22:08:14: 2000000 INFO @ Tue, 09 Oct 2018 22:08:15: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:08:15: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:08:15: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:08:15: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:08:15: #1 total tags in treatment: 2050093 INFO @ Tue, 09 Oct 2018 22:08:15: #1 total tags in treatment: 2050093 INFO @ Tue, 09 Oct 2018 22:08:15: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:08:15: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:08:15: #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 22:08:15: #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 22:08:15: #1 tags after filtering in treatment: 2050093 INFO @ Tue, 09 Oct 2018 22:08:15: #1 tags after filtering in treatment: 2050093 INFO @ Tue, 09 Oct 2018 22:08:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:08:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:08:15: #1 finished! INFO @ Tue, 09 Oct 2018 22:08:15: #1 finished! INFO @ Tue, 09 Oct 2018 22:08:15: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:08:15: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:08:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:08:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:08:15: #2 number of paired peaks: 179 WARNING @ Tue, 09 Oct 2018 22:08:15: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Tue, 09 Oct 2018 22:08:15: start model_add_line... INFO @ Tue, 09 Oct 2018 22:08:15: #2 number of paired peaks: 179 WARNING @ Tue, 09 Oct 2018 22:08:15: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Tue, 09 Oct 2018 22:08:15: start model_add_line... INFO @ Tue, 09 Oct 2018 22:08:15: start X-correlation... INFO @ Tue, 09 Oct 2018 22:08:15: start X-correlation... INFO @ Tue, 09 Oct 2018 22:08:15: end of X-cor INFO @ Tue, 09 Oct 2018 22:08:15: end of X-cor INFO @ Tue, 09 Oct 2018 22:08:15: #2 finished! INFO @ Tue, 09 Oct 2018 22:08:15: #2 finished! INFO @ Tue, 09 Oct 2018 22:08:15: #2 predicted fragment length is 40 bps INFO @ Tue, 09 Oct 2018 22:08:15: #2 predicted fragment length is 40 bps INFO @ Tue, 09 Oct 2018 22:08:15: #2 alternative fragment length(s) may be 1,40,119,150,217,260,334,348,379,466,522 bps INFO @ Tue, 09 Oct 2018 22:08:15: #2 alternative fragment length(s) may be 1,40,119,150,217,260,334,348,379,466,522 bps INFO @ Tue, 09 Oct 2018 22:08:15: #2.2 Generate R script for model : SRX3732406.20_model.r INFO @ Tue, 09 Oct 2018 22:08:15: #2.2 Generate R script for model : SRX3732406.05_model.r WARNING @ Tue, 09 Oct 2018 22:08:15: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:08:15: #2 You may need to consider one of the other alternative d(s): 1,40,119,150,217,260,334,348,379,466,522 WARNING @ Tue, 09 Oct 2018 22:08:15: #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 22:08:15: #3 Call peaks... WARNING @ Tue, 09 Oct 2018 22:08:15: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Tue, 09 Oct 2018 22:08:15: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 09 Oct 2018 22:08:15: #2 You may need to consider one of the other alternative d(s): 1,40,119,150,217,260,334,348,379,466,522 WARNING @ Tue, 09 Oct 2018 22:08:15: #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 22:08:15: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:08:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:08:18: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:08:19: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:08:19: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:08:19: #4 Write output xls file... SRX3732406.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:08:19: #4 Write peak in narrowPeak format file... SRX3732406.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:08:19: #4 Write summits bed file... SRX3732406.10_summits.bed INFO @ Tue, 09 Oct 2018 22:08:19: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (27 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:08:21: #4 Write output xls file... SRX3732406.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:08:21: #4 Write peak in narrowPeak format file... SRX3732406.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:08:21: #4 Write summits bed file... SRX3732406.05_summits.bed INFO @ Tue, 09 Oct 2018 22:08:21: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (74 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:08:21: #4 Write output xls file... SRX3732406.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:08:21: #4 Write peak in narrowPeak format file... SRX3732406.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:08:21: #4 Write summits bed file... SRX3732406.20_summits.bed INFO @ Tue, 09 Oct 2018 22:08:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (7 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。