Job ID = 11245248 sra ファイルのダウンロード中... Completed: 212396K bytes transferred in 5 seconds (332884K 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 4989287 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4733458/SRR7896013.sra Written 4989287 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4733458/SRR7896013.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: 00:01:17 4989287 reads; of these: 4989287 (100.00%) were unpaired; of these: 644415 (12.92%) aligned 0 times 1556257 (31.19%) aligned exactly 1 time 2788615 (55.89%) aligned >1 times 87.08% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 3212049 / 4344872 = 0.7393 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 00:05:24: # Command line: callpeak -t SRX4733458.bam -f BAM -g 12100000 -n SRX4733458.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4733458.20 # format = BAM # ChIP-seq file = ['SRX4733458.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 00:05:24: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:05:24: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:05:24: # Command line: callpeak -t SRX4733458.bam -f BAM -g 12100000 -n SRX4733458.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4733458.05 # format = BAM # ChIP-seq file = ['SRX4733458.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 00:05:24: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:05:24: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:05:24: # Command line: callpeak -t SRX4733458.bam -f BAM -g 12100000 -n SRX4733458.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4733458.10 # format = BAM # ChIP-seq file = ['SRX4733458.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 00:05:24: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:05:24: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:05:35: 1000000 INFO @ Wed, 10 Oct 2018 00:05:35: 1000000 INFO @ Wed, 10 Oct 2018 00:05:35: 1000000 INFO @ Wed, 10 Oct 2018 00:05:36: #1 tag size is determined as 101 bps INFO @ Wed, 10 Oct 2018 00:05:36: #1 tag size = 101 INFO @ Wed, 10 Oct 2018 00:05:36: #1 total tags in treatment: 1132823 INFO @ Wed, 10 Oct 2018 00:05:36: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:05:36: #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 00:05:36: #1 tag size is determined as 101 bps INFO @ Wed, 10 Oct 2018 00:05:36: #1 tag size = 101 INFO @ Wed, 10 Oct 2018 00:05:36: #1 total tags in treatment: 1132823 INFO @ Wed, 10 Oct 2018 00:05:36: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:05:36: #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 00:05:36: #1 tag size is determined as 101 bps INFO @ Wed, 10 Oct 2018 00:05:36: #1 tag size = 101 INFO @ Wed, 10 Oct 2018 00:05:36: #1 total tags in treatment: 1132823 INFO @ Wed, 10 Oct 2018 00:05:36: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:05:36: #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 00:05:36: #1 tags after filtering in treatment: 1132823 INFO @ Wed, 10 Oct 2018 00:05:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:05:36: #1 finished! INFO @ Wed, 10 Oct 2018 00:05:36: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:05:36: #1 tags after filtering in treatment: 1132823 INFO @ Wed, 10 Oct 2018 00:05:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:05:36: #1 finished! INFO @ Wed, 10 Oct 2018 00:05:36: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:05:36: #1 tags after filtering in treatment: 1132823 INFO @ Wed, 10 Oct 2018 00:05:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:05:36: #1 finished! INFO @ Wed, 10 Oct 2018 00:05:36: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:05:36: #2 number of paired peaks: 154 WARNING @ Wed, 10 Oct 2018 00:05:36: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Wed, 10 Oct 2018 00:05:36: start model_add_line... INFO @ Wed, 10 Oct 2018 00:05:36: #2 number of paired peaks: 154 WARNING @ Wed, 10 Oct 2018 00:05:36: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Wed, 10 Oct 2018 00:05:36: start model_add_line... INFO @ Wed, 10 Oct 2018 00:05:36: start X-correlation... INFO @ Wed, 10 Oct 2018 00:05:36: #2 number of paired peaks: 154 WARNING @ Wed, 10 Oct 2018 00:05:36: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Wed, 10 Oct 2018 00:05:36: start X-correlation... INFO @ Wed, 10 Oct 2018 00:05:36: start model_add_line... INFO @ Wed, 10 Oct 2018 00:05:36: end of X-cor INFO @ Wed, 10 Oct 2018 00:05:36: #2 finished! INFO @ Wed, 10 Oct 2018 00:05:36: #2 predicted fragment length is 169 bps INFO @ Wed, 10 Oct 2018 00:05:36: #2 alternative fragment length(s) may be 3,159,169,581 bps INFO @ Wed, 10 Oct 2018 00:05:36: #2.2 Generate R script for model : SRX4733458.20_model.r INFO @ Wed, 10 Oct 2018 00:05:36: end of X-cor INFO @ Wed, 10 Oct 2018 00:05:36: #2 finished! INFO @ Wed, 10 Oct 2018 00:05:36: #2 predicted fragment length is 169 bps INFO @ Wed, 10 Oct 2018 00:05:36: #2 alternative fragment length(s) may be 3,159,169,581 bps INFO @ Wed, 10 Oct 2018 00:05:36: #2.2 Generate R script for model : SRX4733458.10_model.r INFO @ Wed, 10 Oct 2018 00:05:36: start X-correlation... WARNING @ Wed, 10 Oct 2018 00:05:36: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 10 Oct 2018 00:05:36: #2 You may need to consider one of the other alternative d(s): 3,159,169,581 WARNING @ Wed, 10 Oct 2018 00:05:36: #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 00:05:36: #3 Call peaks... INFO @ Wed, 10 Oct 2018 00:05:36: end of X-cor INFO @ Wed, 10 Oct 2018 00:05:36: #2 finished! INFO @ Wed, 10 Oct 2018 00:05:36: #2 predicted fragment length is 169 bps INFO @ Wed, 10 Oct 2018 00:05:36: #2 alternative fragment length(s) may be 3,159,169,581 bps INFO @ Wed, 10 Oct 2018 00:05:36: #2.2 Generate R script for model : SRX4733458.05_model.r WARNING @ Wed, 10 Oct 2018 00:05:36: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 10 Oct 2018 00:05:36: #2 You may need to consider one of the other alternative d(s): 3,159,169,581 WARNING @ Wed, 10 Oct 2018 00:05:36: #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 00:05:36: #3 Call peaks... INFO @ Wed, 10 Oct 2018 00:05:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 10 Oct 2018 00:05:36: #3 Pre-compute pvalue-qvalue table... WARNING @ Wed, 10 Oct 2018 00:05:36: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 10 Oct 2018 00:05:36: #2 You may need to consider one of the other alternative d(s): 3,159,169,581 WARNING @ Wed, 10 Oct 2018 00:05:36: #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 00:05:36: #3 Call peaks... INFO @ Wed, 10 Oct 2018 00:05:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 10 Oct 2018 00:05:39: #3 Call peaks for each chromosome... INFO @ Wed, 10 Oct 2018 00:05:40: #3 Call peaks for each chromosome... INFO @ Wed, 10 Oct 2018 00:05:40: #3 Call peaks for each chromosome... INFO @ Wed, 10 Oct 2018 00:05:41: #4 Write output xls file... SRX4733458.10_peaks.xls INFO @ Wed, 10 Oct 2018 00:05:41: #4 Write peak in narrowPeak format file... SRX4733458.10_peaks.narrowPeak INFO @ Wed, 10 Oct 2018 00:05:41: #4 Write summits bed file... SRX4733458.10_summits.bed INFO @ Wed, 10 Oct 2018 00:05:41: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (30 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Wed, 10 Oct 2018 00:05:41: #4 Write output xls file... SRX4733458.05_peaks.xls INFO @ Wed, 10 Oct 2018 00:05:41: #4 Write peak in narrowPeak format file... SRX4733458.05_peaks.narrowPeak INFO @ Wed, 10 Oct 2018 00:05:41: #4 Write summits bed file... SRX4733458.05_summits.bed INFO @ Wed, 10 Oct 2018 00:05:41: Done! INFO @ Wed, 10 Oct 2018 00:05:41: #4 Write output xls file... SRX4733458.20_peaks.xls INFO @ Wed, 10 Oct 2018 00:05:41: #4 Write peak in narrowPeak format file... SRX4733458.20_peaks.narrowPeak INFO @ Wed, 10 Oct 2018 00:05:41: #4 Write summits bed file... SRX4733458.20_summits.bed pass1 - making usageList (12 chroms): 1 millis INFO @ Wed, 10 Oct 2018 00:05:41: Done! pass2 - checking and writing primary data (57 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 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。