Job ID = 11245249 sra ファイルのダウンロード中... Completed: 238678K bytes transferred in 5 seconds (348841K 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 5557586 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4733459/SRR7896014.sra Written 5557586 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4733459/SRR7896014.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: 00:00:44 5557586 reads; of these: 5557586 (100.00%) were unpaired; of these: 5028920 (90.49%) aligned 0 times 300165 (5.40%) aligned exactly 1 time 228501 (4.11%) aligned >1 times 9.51% overall alignment rate Time searching: 00:00:44 Overall time: 00:00:44 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] 209799 / 528666 = 0.3968 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 @ Wed, 10 Oct 2018 00:04:11: # Command line: callpeak -t SRX4733459.bam -f BAM -g 12100000 -n SRX4733459.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4733459.05 # format = BAM # ChIP-seq file = ['SRX4733459.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 @ Wed, 10 Oct 2018 00:04:11: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:04:11: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:04:11: # Command line: callpeak -t SRX4733459.bam -f BAM -g 12100000 -n SRX4733459.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4733459.20 # format = BAM # ChIP-seq file = ['SRX4733459.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 @ Wed, 10 Oct 2018 00:04:11: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:04:11: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:04:11: # Command line: callpeak -t SRX4733459.bam -f BAM -g 12100000 -n SRX4733459.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4733459.10 # format = BAM # ChIP-seq file = ['SRX4733459.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 @ Wed, 10 Oct 2018 00:04:11: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:04:11: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:04:14: #1 tag size is determined as 101 bps INFO @ Wed, 10 Oct 2018 00:04:14: #1 tag size = 101 INFO @ Wed, 10 Oct 2018 00:04:14: #1 total tags in treatment: 318867 INFO @ Wed, 10 Oct 2018 00:04:14: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:04:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:04:14: #1 tags after filtering in treatment: 318867 INFO @ Wed, 10 Oct 2018 00:04:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:04:14: #1 finished! INFO @ Wed, 10 Oct 2018 00:04:14: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:04:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:04:14: #2 number of paired peaks: 111 WARNING @ Wed, 10 Oct 2018 00:04:14: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 10 Oct 2018 00:04:14: start model_add_line... INFO @ Wed, 10 Oct 2018 00:04:14: start X-correlation... INFO @ Wed, 10 Oct 2018 00:04:14: end of X-cor INFO @ Wed, 10 Oct 2018 00:04:14: #2 finished! INFO @ Wed, 10 Oct 2018 00:04:14: #2 predicted fragment length is 200 bps INFO @ Wed, 10 Oct 2018 00:04:14: #2 alternative fragment length(s) may be 200 bps INFO @ Wed, 10 Oct 2018 00:04:14: #2.2 Generate R script for model : SRX4733459.05_model.r WARNING @ Wed, 10 Oct 2018 00:04:14: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 10 Oct 2018 00:04:14: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Wed, 10 Oct 2018 00:04:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 10 Oct 2018 00:04:14: #3 Call peaks... INFO @ Wed, 10 Oct 2018 00:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 10 Oct 2018 00:04:14: #1 tag size is determined as 101 bps INFO @ Wed, 10 Oct 2018 00:04:14: #1 tag size = 101 INFO @ Wed, 10 Oct 2018 00:04:14: #1 total tags in treatment: 318867 INFO @ Wed, 10 Oct 2018 00:04:14: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:04:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:04:14: #1 tags after filtering in treatment: 318867 INFO @ Wed, 10 Oct 2018 00:04:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:04:14: #1 finished! INFO @ Wed, 10 Oct 2018 00:04:14: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:04:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:04:14: #1 tag size is determined as 101 bps INFO @ Wed, 10 Oct 2018 00:04:14: #1 tag size = 101 INFO @ Wed, 10 Oct 2018 00:04:14: #1 total tags in treatment: 318867 INFO @ Wed, 10 Oct 2018 00:04:14: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:04:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:04:14: #1 tags after filtering in treatment: 318867 INFO @ Wed, 10 Oct 2018 00:04:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:04:14: #1 finished! INFO @ Wed, 10 Oct 2018 00:04:14: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:04:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:04:14: #2 number of paired peaks: 111 WARNING @ Wed, 10 Oct 2018 00:04:14: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 10 Oct 2018 00:04:14: start model_add_line... INFO @ Wed, 10 Oct 2018 00:04:14: start X-correlation... INFO @ Wed, 10 Oct 2018 00:04:14: end of X-cor INFO @ Wed, 10 Oct 2018 00:04:14: #2 finished! INFO @ Wed, 10 Oct 2018 00:04:14: #2 predicted fragment length is 200 bps INFO @ Wed, 10 Oct 2018 00:04:14: #2 alternative fragment length(s) may be 200 bps INFO @ Wed, 10 Oct 2018 00:04:14: #2.2 Generate R script for model : SRX4733459.20_model.r INFO @ Wed, 10 Oct 2018 00:04:14: #2 number of paired peaks: 111 WARNING @ Wed, 10 Oct 2018 00:04:14: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 10 Oct 2018 00:04:14: start model_add_line... INFO @ Wed, 10 Oct 2018 00:04:14: start X-correlation... WARNING @ Wed, 10 Oct 2018 00:04:14: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 10 Oct 2018 00:04:14: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Wed, 10 Oct 2018 00:04:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 10 Oct 2018 00:04:14: #3 Call peaks... INFO @ Wed, 10 Oct 2018 00:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 10 Oct 2018 00:04:14: end of X-cor INFO @ Wed, 10 Oct 2018 00:04:14: #2 finished! INFO @ Wed, 10 Oct 2018 00:04:14: #2 predicted fragment length is 200 bps INFO @ Wed, 10 Oct 2018 00:04:14: #2 alternative fragment length(s) may be 200 bps INFO @ Wed, 10 Oct 2018 00:04:14: #2.2 Generate R script for model : SRX4733459.10_model.r WARNING @ Wed, 10 Oct 2018 00:04:14: #2 Since the d (200) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 10 Oct 2018 00:04:14: #2 You may need to consider one of the other alternative d(s): 200 WARNING @ Wed, 10 Oct 2018 00:04:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 10 Oct 2018 00:04:14: #3 Call peaks... INFO @ Wed, 10 Oct 2018 00:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 10 Oct 2018 00:04:15: #3 Call peaks for each chromosome... INFO @ Wed, 10 Oct 2018 00:04:15: #3 Call peaks for each chromosome... INFO @ Wed, 10 Oct 2018 00:04:15: #3 Call peaks for each chromosome... INFO @ Wed, 10 Oct 2018 00:04:15: #4 Write output xls file... SRX4733459.05_peaks.xls INFO @ Wed, 10 Oct 2018 00:04:15: #4 Write peak in narrowPeak format file... SRX4733459.05_peaks.narrowPeak INFO @ Wed, 10 Oct 2018 00:04:15: #4 Write summits bed file... SRX4733459.05_summits.bed INFO @ Wed, 10 Oct 2018 00:04:15: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 10 Oct 2018 00:04:16: #4 Write output xls file... SRX4733459.20_peaks.xls INFO @ Wed, 10 Oct 2018 00:04:16: #4 Write peak in narrowPeak format file... SRX4733459.20_peaks.narrowPeak INFO @ Wed, 10 Oct 2018 00:04:16: #4 Write summits bed file... SRX4733459.20_summits.bed INFO @ Wed, 10 Oct 2018 00:04:16: Done! INFO @ Wed, 10 Oct 2018 00:04:16: #4 Write output xls file... SRX4733459.10_peaks.xls INFO @ Wed, 10 Oct 2018 00:04:16: #4 Write peak in narrowPeak format file... SRX4733459.10_peaks.narrowPeak pass1 - making usageList (2 chroms): 1 millis INFO @ Wed, 10 Oct 2018 00:04:16: #4 Write summits bed file... SRX4733459.10_summits.bed pass2 - checking and writing primary data (9 records, 4 fields): 1 millis INFO @ Wed, 10 Oct 2018 00:04:16: Done! CompletedMACS2peakCalling pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (23 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。