Job ID = 11244813 sra ファイルのダウンロード中... Completed: 102911K bytes transferred in 3 seconds (213295K bits/sec), in 1 file. Completed: 195919K bytes transferred in 4 seconds (341967K 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 3501402 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732398/SRR6759900.sra Written 3501402 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732398/SRR6759900.sra Read 6537868 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732398/SRR6759901.sra Written 6537868 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732398/SRR6759901.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: 00:01:52 10039270 reads; of these: 10039270 (100.00%) were unpaired; of these: 2943889 (29.32%) aligned 0 times 5854582 (58.32%) aligned exactly 1 time 1240799 (12.36%) aligned >1 times 70.68% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 3721401 / 7095381 = 0.5245 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 22:03:00: # Command line: callpeak -t SRX3732398.bam -f BAM -g 12100000 -n SRX3732398.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3732398.05 # format = BAM # ChIP-seq file = ['SRX3732398.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 22:03:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:03:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:03:00: # Command line: callpeak -t SRX3732398.bam -f BAM -g 12100000 -n SRX3732398.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3732398.20 # format = BAM # ChIP-seq file = ['SRX3732398.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 22:03:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:03:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:03:00: # Command line: callpeak -t SRX3732398.bam -f BAM -g 12100000 -n SRX3732398.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3732398.10 # format = BAM # ChIP-seq file = ['SRX3732398.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 22:03:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:03:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:03:09: 1000000 INFO @ Tue, 09 Oct 2018 22:03:09: 1000000 INFO @ Tue, 09 Oct 2018 22:03:09: 1000000 INFO @ Tue, 09 Oct 2018 22:03:17: 2000000 INFO @ Tue, 09 Oct 2018 22:03:17: 2000000 INFO @ Tue, 09 Oct 2018 22:03:17: 2000000 INFO @ Tue, 09 Oct 2018 22:03:25: 3000000 INFO @ Tue, 09 Oct 2018 22:03:26: 3000000 INFO @ Tue, 09 Oct 2018 22:03:26: 3000000 INFO @ Tue, 09 Oct 2018 22:03:28: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:03:28: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:03:28: #1 total tags in treatment: 3373980 INFO @ Tue, 09 Oct 2018 22:03:28: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:03:28: #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 22:03:28: #1 tags after filtering in treatment: 3373980 INFO @ Tue, 09 Oct 2018 22:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:03:28: #1 finished! INFO @ Tue, 09 Oct 2018 22:03:28: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:03:28: #2 number of paired peaks: 124 WARNING @ Tue, 09 Oct 2018 22:03:28: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 09 Oct 2018 22:03:28: start model_add_line... INFO @ Tue, 09 Oct 2018 22:03:28: start X-correlation... INFO @ Tue, 09 Oct 2018 22:03:28: end of X-cor INFO @ Tue, 09 Oct 2018 22:03:28: #2 finished! INFO @ Tue, 09 Oct 2018 22:03:28: #2 predicted fragment length is 1 bps INFO @ Tue, 09 Oct 2018 22:03:28: #2 alternative fragment length(s) may be 1,16,52,109,111,468,501,545,598 bps INFO @ Tue, 09 Oct 2018 22:03:28: #2.2 Generate R script for model : SRX3732398.10_model.r WARNING @ Tue, 09 Oct 2018 22:03:28: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:03:28: #2 You may need to consider one of the other alternative d(s): 1,16,52,109,111,468,501,545,598 WARNING @ Tue, 09 Oct 2018 22:03:28: #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 22:03:28: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:03:29: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:03:29: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:03:29: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:03:29: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:03:29: #1 total tags in treatment: 3373980 INFO @ Tue, 09 Oct 2018 22:03:29: #1 total tags in treatment: 3373980 INFO @ Tue, 09 Oct 2018 22:03:29: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:03:29: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:03:29: #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 22:03:29: #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 22:03:29: #1 tags after filtering in treatment: 3373980 INFO @ Tue, 09 Oct 2018 22:03:29: #1 tags after filtering in treatment: 3373980 INFO @ Tue, 09 Oct 2018 22:03:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:03:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:03:29: #1 finished! INFO @ Tue, 09 Oct 2018 22:03:29: #1 finished! INFO @ Tue, 09 Oct 2018 22:03:29: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:03:29: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:03:29: #2 number of paired peaks: 124 WARNING @ Tue, 09 Oct 2018 22:03:29: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 09 Oct 2018 22:03:29: start model_add_line... INFO @ Tue, 09 Oct 2018 22:03:29: start X-correlation... INFO @ Tue, 09 Oct 2018 22:03:29: end of X-cor INFO @ Tue, 09 Oct 2018 22:03:29: #2 finished! INFO @ Tue, 09 Oct 2018 22:03:29: #2 predicted fragment length is 1 bps INFO @ Tue, 09 Oct 2018 22:03:29: #2 alternative fragment length(s) may be 1,16,52,109,111,468,501,545,598 bps INFO @ Tue, 09 Oct 2018 22:03:29: #2.2 Generate R script for model : SRX3732398.05_model.r WARNING @ Tue, 09 Oct 2018 22:03:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:03:29: #2 You may need to consider one of the other alternative d(s): 1,16,52,109,111,468,501,545,598 WARNING @ Tue, 09 Oct 2018 22:03:29: #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 22:03:29: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:03:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:03:29: #2 number of paired peaks: 124 WARNING @ Tue, 09 Oct 2018 22:03:29: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 09 Oct 2018 22:03:29: start model_add_line... INFO @ Tue, 09 Oct 2018 22:03:29: start X-correlation... INFO @ Tue, 09 Oct 2018 22:03:29: end of X-cor INFO @ Tue, 09 Oct 2018 22:03:29: #2 finished! INFO @ Tue, 09 Oct 2018 22:03:29: #2 predicted fragment length is 1 bps INFO @ Tue, 09 Oct 2018 22:03:29: #2 alternative fragment length(s) may be 1,16,52,109,111,468,501,545,598 bps INFO @ Tue, 09 Oct 2018 22:03:29: #2.2 Generate R script for model : SRX3732398.20_model.r WARNING @ Tue, 09 Oct 2018 22:03:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:03:29: #2 You may need to consider one of the other alternative d(s): 1,16,52,109,111,468,501,545,598 WARNING @ Tue, 09 Oct 2018 22:03:29: #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 22:03:29: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:03:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:03:33: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:03:34: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:03:34: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:03:36: #4 Write output xls file... SRX3732398.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:03:36: #4 Write peak in narrowPeak format file... SRX3732398.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:03:36: #4 Write summits bed file... SRX3732398.10_summits.bed INFO @ Tue, 09 Oct 2018 22:03:36: Done! INFO @ Tue, 09 Oct 2018 22:03:36: #4 Write output xls file... SRX3732398.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:03:36: #4 Write peak in narrowPeak format file... SRX3732398.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:03:36: #4 Write summits bed file... SRX3732398.05_summits.bed INFO @ Tue, 09 Oct 2018 22:03:36: Done! pass1 - making usageList (0 chroms): 6 millis pass1 - making usageList (0 chroms): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184)needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:03:36: #4 Write output xls file... SRX3732398.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:03:36: #4 Write peak in narrowPeak format file... SRX3732398.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:03:36: #4 Write summits bed file... SRX3732398.20_summits.bed INFO @ Tue, 09 Oct 2018 22:03:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。