Job ID = 9157226 sra ファイルのダウンロード中... Completed: 537108K bytes transferred in 6 seconds (679835K 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 11837376 spots for /home/okishinya/chipatlas/results/ce10/SRX2350730/SRR5024039.sra Written 11837376 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: 00:00:00 Multiseed full-index search: 00:03:38 11837376 reads; of these: 11837376 (100.00%) were unpaired; of these: 210819 (1.78%) aligned 0 times 9325222 (78.78%) aligned exactly 1 time 2301335 (19.44%) aligned >1 times 98.22% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1323683 / 11626557 = 0.1138 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 11:13:12: # Command line: callpeak -t SRX2350730.bam -f BAM -g ce -n SRX2350730.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350730.10 # format = BAM # ChIP-seq file = ['SRX2350730.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 11:13:12: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:13:12: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:13:12: # Command line: callpeak -t SRX2350730.bam -f BAM -g ce -n SRX2350730.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350730.05 # format = BAM # ChIP-seq file = ['SRX2350730.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 11:13:12: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:13:12: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:13:12: # Command line: callpeak -t SRX2350730.bam -f BAM -g ce -n SRX2350730.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350730.20 # format = BAM # ChIP-seq file = ['SRX2350730.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 11:13:12: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:13:12: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:13:20: 1000000 INFO @ Tue, 27 Jun 2017 11:13:22: 1000000 INFO @ Tue, 27 Jun 2017 11:13:22: 1000000 INFO @ Tue, 27 Jun 2017 11:13:28: 2000000 INFO @ Tue, 27 Jun 2017 11:13:32: 2000000 INFO @ Tue, 27 Jun 2017 11:13:32: 2000000 INFO @ Tue, 27 Jun 2017 11:13:37: 3000000 INFO @ Tue, 27 Jun 2017 11:13:43: 3000000 INFO @ Tue, 27 Jun 2017 11:13:43: 3000000 INFO @ Tue, 27 Jun 2017 11:13:45: 4000000 INFO @ Tue, 27 Jun 2017 11:13:53: 4000000 INFO @ Tue, 27 Jun 2017 11:13:53: 4000000 INFO @ Tue, 27 Jun 2017 11:13:53: 5000000 INFO @ Tue, 27 Jun 2017 11:14:02: 6000000 INFO @ Tue, 27 Jun 2017 11:14:03: 5000000 INFO @ Tue, 27 Jun 2017 11:14:03: 5000000 INFO @ Tue, 27 Jun 2017 11:14:10: 7000000 INFO @ Tue, 27 Jun 2017 11:14:13: 6000000 INFO @ Tue, 27 Jun 2017 11:14:13: 6000000 INFO @ Tue, 27 Jun 2017 11:14:18: 8000000 INFO @ Tue, 27 Jun 2017 11:14:23: 7000000 INFO @ Tue, 27 Jun 2017 11:14:23: 7000000 INFO @ Tue, 27 Jun 2017 11:14:26: 9000000 INFO @ Tue, 27 Jun 2017 11:14:32: 8000000 INFO @ Tue, 27 Jun 2017 11:14:32: 8000000 INFO @ Tue, 27 Jun 2017 11:14:33: 10000000 INFO @ Tue, 27 Jun 2017 11:14:36: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:14:36: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:14:36: #1 total tags in treatment: 10302874 INFO @ Tue, 27 Jun 2017 11:14:36: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:14:36: #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 11:14:36: #1 tags after filtering in treatment: 10302874 INFO @ Tue, 27 Jun 2017 11:14:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:14:36: #1 finished! INFO @ Tue, 27 Jun 2017 11:14:36: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:14:37: #2 number of paired peaks: 364 WARNING @ Tue, 27 Jun 2017 11:14:37: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Tue, 27 Jun 2017 11:14:37: start model_add_line... INFO @ Tue, 27 Jun 2017 11:14:37: start X-correlation... INFO @ Tue, 27 Jun 2017 11:14:37: end of X-cor INFO @ Tue, 27 Jun 2017 11:14:37: #2 finished! INFO @ Tue, 27 Jun 2017 11:14:37: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 11:14:37: #2 alternative fragment length(s) may be 2,48,580 bps INFO @ Tue, 27 Jun 2017 11:14:37: #2.2 Generate R script for model : SRX2350730.10_model.r WARNING @ Tue, 27 Jun 2017 11:14:37: #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 11:14:37: #2 You may need to consider one of the other alternative d(s): 2,48,580 WARNING @ Tue, 27 Jun 2017 11:14:37: #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 11:14:37: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:14:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:14:41: 9000000 INFO @ Tue, 27 Jun 2017 11:14:41: 9000000 INFO @ Tue, 27 Jun 2017 11:14:50: 10000000 INFO @ Tue, 27 Jun 2017 11:14:50: 10000000 INFO @ Tue, 27 Jun 2017 11:14:53: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:14:53: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:14:53: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:14:53: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:14:53: #1 total tags in treatment: 10302874 INFO @ Tue, 27 Jun 2017 11:14:53: #1 total tags in treatment: 10302874 INFO @ Tue, 27 Jun 2017 11:14:53: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:14:53: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:14:53: #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 11:14:53: #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 11:14:53: #1 tags after filtering in treatment: 10302874 INFO @ Tue, 27 Jun 2017 11:14:53: #1 tags after filtering in treatment: 10302874 INFO @ Tue, 27 Jun 2017 11:14:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:14:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:14:53: #1 finished! INFO @ Tue, 27 Jun 2017 11:14:53: #1 finished! INFO @ Tue, 27 Jun 2017 11:14:53: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:14:53: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:14:54: #2 number of paired peaks: 364 WARNING @ Tue, 27 Jun 2017 11:14:54: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Tue, 27 Jun 2017 11:14:54: start model_add_line... INFO @ Tue, 27 Jun 2017 11:14:54: #2 number of paired peaks: 364 WARNING @ Tue, 27 Jun 2017 11:14:54: Fewer paired peaks (364) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 364 pairs to build model! INFO @ Tue, 27 Jun 2017 11:14:54: start model_add_line... INFO @ Tue, 27 Jun 2017 11:14:54: start X-correlation... INFO @ Tue, 27 Jun 2017 11:14:54: end of X-cor INFO @ Tue, 27 Jun 2017 11:14:54: #2 finished! INFO @ Tue, 27 Jun 2017 11:14:54: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 11:14:54: #2 alternative fragment length(s) may be 2,48,580 bps INFO @ Tue, 27 Jun 2017 11:14:54: #2.2 Generate R script for model : SRX2350730.20_model.r WARNING @ Tue, 27 Jun 2017 11:14:54: #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 11:14:54: #2 You may need to consider one of the other alternative d(s): 2,48,580 WARNING @ Tue, 27 Jun 2017 11:14:54: #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 11:14:54: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:14:54: start X-correlation... INFO @ Tue, 27 Jun 2017 11:14:54: end of X-cor INFO @ Tue, 27 Jun 2017 11:14:54: #2 finished! INFO @ Tue, 27 Jun 2017 11:14:54: #2 predicted fragment length is 48 bps INFO @ Tue, 27 Jun 2017 11:14:54: #2 alternative fragment length(s) may be 2,48,580 bps INFO @ Tue, 27 Jun 2017 11:14:54: #2.2 Generate R script for model : SRX2350730.05_model.r WARNING @ Tue, 27 Jun 2017 11:14:54: #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 11:14:54: #2 You may need to consider one of the other alternative d(s): 2,48,580 WARNING @ Tue, 27 Jun 2017 11:14:54: #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 11:14:54: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:14:59: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:15:11: #4 Write output xls file... SRX2350730.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:15:11: #4 Write peak in narrowPeak format file... SRX2350730.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:15:11: #4 Write summits bed file... SRX2350730.10_summits.bed INFO @ Tue, 27 Jun 2017 11:15:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (430 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:15:15: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:15:15: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:15:26: #4 Write output xls file... SRX2350730.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:15:26: #4 Write peak in narrowPeak format file... SRX2350730.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:15:26: #4 Write summits bed file... SRX2350730.20_summits.bed INFO @ Tue, 27 Jun 2017 11:15:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:15:29: #4 Write output xls file... SRX2350730.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:15:29: #4 Write peak in narrowPeak format file... SRX2350730.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:15:29: #4 Write summits bed file... SRX2350730.05_summits.bed INFO @ Tue, 27 Jun 2017 11:15:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (707 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。