Job ID = 9157209 sra ファイルのダウンロード中... Completed: 434972K bytes transferred in 6 seconds (517748K bits/sec), in 1 file, 2 directories. 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... Written 10290698 spots for /home/okishinya/chipatlas/results/ce10/SRX2350719/SRR5024028.sra Written 10290698 spots total 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: 00:00:01 Multiseed full-index search: 00:02:40 10290698 reads; of these: 10290698 (100.00%) were unpaired; of these: 539422 (5.24%) aligned 0 times 7192186 (69.89%) aligned exactly 1 time 2559090 (24.87%) aligned >1 times 94.76% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1305661 / 9751276 = 0.1339 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, 27 Jun 2017 11:07:40: # Command line: callpeak -t SRX2350719.bam -f BAM -g ce -n SRX2350719.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350719.05 # format = BAM # ChIP-seq file = ['SRX2350719.bam'] # control file = None # effective genome size = 9.00e+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, 27 Jun 2017 11:07:40: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:07:40: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:07:40: # Command line: callpeak -t SRX2350719.bam -f BAM -g ce -n SRX2350719.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350719.10 # format = BAM # ChIP-seq file = ['SRX2350719.bam'] # control file = None # effective genome size = 9.00e+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, 27 Jun 2017 11:07:40: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:07:40: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:07:40: # Command line: callpeak -t SRX2350719.bam -f BAM -g ce -n SRX2350719.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350719.20 # format = BAM # ChIP-seq file = ['SRX2350719.bam'] # control file = None # effective genome size = 9.00e+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, 27 Jun 2017 11:07:40: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:07:40: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:07:48: 1000000 INFO @ Tue, 27 Jun 2017 11:07:48: 1000000 INFO @ Tue, 27 Jun 2017 11:07:49: 1000000 INFO @ Tue, 27 Jun 2017 11:07:56: 2000000 INFO @ Tue, 27 Jun 2017 11:07:57: 2000000 INFO @ Tue, 27 Jun 2017 11:07:58: 2000000 INFO @ Tue, 27 Jun 2017 11:08:05: 3000000 INFO @ Tue, 27 Jun 2017 11:08:05: 3000000 INFO @ Tue, 27 Jun 2017 11:08:07: 3000000 INFO @ Tue, 27 Jun 2017 11:08:13: 4000000 INFO @ Tue, 27 Jun 2017 11:08:14: 4000000 INFO @ Tue, 27 Jun 2017 11:08:16: 4000000 INFO @ Tue, 27 Jun 2017 11:08:21: 5000000 INFO @ Tue, 27 Jun 2017 11:08:22: 5000000 INFO @ Tue, 27 Jun 2017 11:08:24: 5000000 INFO @ Tue, 27 Jun 2017 11:08:29: 6000000 INFO @ Tue, 27 Jun 2017 11:08:31: 6000000 INFO @ Tue, 27 Jun 2017 11:08:33: 6000000 INFO @ Tue, 27 Jun 2017 11:08:38: 7000000 INFO @ Tue, 27 Jun 2017 11:08:40: 7000000 INFO @ Tue, 27 Jun 2017 11:08:42: 7000000 INFO @ Tue, 27 Jun 2017 11:08:46: 8000000 INFO @ Tue, 27 Jun 2017 11:08:49: 8000000 INFO @ Tue, 27 Jun 2017 11:08:50: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:08:50: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:08:50: #1 total tags in treatment: 8445615 INFO @ Tue, 27 Jun 2017 11:08:50: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:08:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:08:50: #1 tags after filtering in treatment: 8445615 INFO @ Tue, 27 Jun 2017 11:08:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:08:50: #1 finished! INFO @ Tue, 27 Jun 2017 11:08:50: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:08:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:08:51: 8000000 INFO @ Tue, 27 Jun 2017 11:08:51: #2 number of paired peaks: 654 WARNING @ Tue, 27 Jun 2017 11:08:51: Fewer paired peaks (654) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 654 pairs to build model! INFO @ Tue, 27 Jun 2017 11:08:51: start model_add_line... INFO @ Tue, 27 Jun 2017 11:08:51: start X-correlation... INFO @ Tue, 27 Jun 2017 11:08:51: end of X-cor INFO @ Tue, 27 Jun 2017 11:08:51: #2 finished! INFO @ Tue, 27 Jun 2017 11:08:51: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 11:08:51: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 27 Jun 2017 11:08:51: #2.2 Generate R script for model : SRX2350719.05_model.r WARNING @ Tue, 27 Jun 2017 11:08:51: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:08:51: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 27 Jun 2017 11:08:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:08:51: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:08:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:08:53: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:08:53: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:08:53: #1 total tags in treatment: 8445615 INFO @ Tue, 27 Jun 2017 11:08:53: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:08:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:08:53: #1 tags after filtering in treatment: 8445615 INFO @ Tue, 27 Jun 2017 11:08:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:08:53: #1 finished! INFO @ Tue, 27 Jun 2017 11:08:53: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:08:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:08:53: #2 number of paired peaks: 654 WARNING @ Tue, 27 Jun 2017 11:08:53: Fewer paired peaks (654) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 654 pairs to build model! INFO @ Tue, 27 Jun 2017 11:08:53: start model_add_line... INFO @ Tue, 27 Jun 2017 11:08:54: start X-correlation... INFO @ Tue, 27 Jun 2017 11:08:54: end of X-cor INFO @ Tue, 27 Jun 2017 11:08:54: #2 finished! INFO @ Tue, 27 Jun 2017 11:08:54: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 11:08:54: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 27 Jun 2017 11:08:54: #2.2 Generate R script for model : SRX2350719.20_model.r WARNING @ Tue, 27 Jun 2017 11:08:54: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:08:54: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 27 Jun 2017 11:08:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:08:54: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:08:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:08:54: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:08:54: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:08:54: #1 total tags in treatment: 8445615 INFO @ Tue, 27 Jun 2017 11:08:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:08:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:08:54: #1 tags after filtering in treatment: 8445615 INFO @ Tue, 27 Jun 2017 11:08:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:08:54: #1 finished! INFO @ Tue, 27 Jun 2017 11:08:54: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:08:55: #2 number of paired peaks: 654 WARNING @ Tue, 27 Jun 2017 11:08:55: Fewer paired peaks (654) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 654 pairs to build model! INFO @ Tue, 27 Jun 2017 11:08:55: start model_add_line... INFO @ Tue, 27 Jun 2017 11:08:55: start X-correlation... INFO @ Tue, 27 Jun 2017 11:08:55: end of X-cor INFO @ Tue, 27 Jun 2017 11:08:55: #2 finished! INFO @ Tue, 27 Jun 2017 11:08:55: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 11:08:55: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 27 Jun 2017 11:08:55: #2.2 Generate R script for model : SRX2350719.10_model.r WARNING @ Tue, 27 Jun 2017 11:08:55: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:08:55: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 27 Jun 2017 11:08:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:08:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:08:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:09:10: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:09:12: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:09:14: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:09:21: #4 Write output xls file... SRX2350719.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:09:21: #4 Write peak in narrowPeak format file... SRX2350719.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:09:21: #4 Write summits bed file... SRX2350719.05_summits.bed INFO @ Tue, 27 Jun 2017 11:09:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (778 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:09:22: #4 Write output xls file... SRX2350719.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:09:22: #4 Write peak in narrowPeak format file... SRX2350719.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:09:22: #4 Write summits bed file... SRX2350719.20_summits.bed INFO @ Tue, 27 Jun 2017 11:09:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (199 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:09:24: #4 Write output xls file... SRX2350719.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:09:24: #4 Write peak in narrowPeak format file... SRX2350719.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:09:24: #4 Write summits bed file... SRX2350719.10_summits.bed INFO @ Tue, 27 Jun 2017 11:09:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (481 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。