Job ID = 9157215 sra ファイルのダウンロード中... Completed: 656134K bytes transferred in 8 seconds (615526K 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 15486368 spots for /home/okishinya/chipatlas/results/ce10/SRX2350723/SRR5024032.sra Written 15486368 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: 00:04:18 15486368 reads; of these: 15486368 (100.00%) were unpaired; of these: 558836 (3.61%) aligned 0 times 10872169 (70.20%) aligned exactly 1 time 4055363 (26.19%) aligned >1 times 96.39% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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] 3431156 / 14927532 = 0.2299 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 11:12:17: # Command line: callpeak -t SRX2350723.bam -f BAM -g ce -n SRX2350723.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350723.10 # format = BAM # ChIP-seq file = ['SRX2350723.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 11:12:17: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:12:17: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:12:17: # Command line: callpeak -t SRX2350723.bam -f BAM -g ce -n SRX2350723.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350723.05 # format = BAM # ChIP-seq file = ['SRX2350723.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 11:12:17: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:12:17: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:12:17: # Command line: callpeak -t SRX2350723.bam -f BAM -g ce -n SRX2350723.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350723.20 # format = BAM # ChIP-seq file = ['SRX2350723.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 11:12:17: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:12:17: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:12:25: 1000000 INFO @ Tue, 27 Jun 2017 11:12:26: 1000000 INFO @ Tue, 27 Jun 2017 11:12:26: 1000000 INFO @ Tue, 27 Jun 2017 11:12:33: 2000000 INFO @ Tue, 27 Jun 2017 11:12:35: 2000000 INFO @ Tue, 27 Jun 2017 11:12:35: 2000000 INFO @ Tue, 27 Jun 2017 11:12:41: 3000000 INFO @ Tue, 27 Jun 2017 11:12:44: 3000000 INFO @ Tue, 27 Jun 2017 11:12:44: 3000000 INFO @ Tue, 27 Jun 2017 11:12:50: 4000000 INFO @ Tue, 27 Jun 2017 11:12:53: 4000000 INFO @ Tue, 27 Jun 2017 11:12:53: 4000000 INFO @ Tue, 27 Jun 2017 11:12:58: 5000000 INFO @ Tue, 27 Jun 2017 11:13:02: 5000000 INFO @ Tue, 27 Jun 2017 11:13:02: 5000000 INFO @ Tue, 27 Jun 2017 11:13:05: 6000000 INFO @ Tue, 27 Jun 2017 11:13:10: 6000000 INFO @ Tue, 27 Jun 2017 11:13:10: 6000000 INFO @ Tue, 27 Jun 2017 11:13:12: 7000000 INFO @ Tue, 27 Jun 2017 11:13:18: 7000000 INFO @ Tue, 27 Jun 2017 11:13:18: 7000000 INFO @ Tue, 27 Jun 2017 11:13:20: 8000000 INFO @ Tue, 27 Jun 2017 11:13:26: 8000000 INFO @ Tue, 27 Jun 2017 11:13:26: 8000000 INFO @ Tue, 27 Jun 2017 11:13:27: 9000000 INFO @ Tue, 27 Jun 2017 11:13:34: 10000000 INFO @ Tue, 27 Jun 2017 11:13:35: 9000000 INFO @ Tue, 27 Jun 2017 11:13:35: 9000000 INFO @ Tue, 27 Jun 2017 11:13:41: 11000000 INFO @ Tue, 27 Jun 2017 11:13:43: 10000000 INFO @ Tue, 27 Jun 2017 11:13:43: 10000000 INFO @ Tue, 27 Jun 2017 11:13:45: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:13:45: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:13:45: #1 total tags in treatment: 11496376 INFO @ Tue, 27 Jun 2017 11:13:45: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:13:45: #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 11:13:45: #1 tags after filtering in treatment: 11496376 INFO @ Tue, 27 Jun 2017 11:13:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:13:45: #1 finished! INFO @ Tue, 27 Jun 2017 11:13:45: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:13:46: #2 number of paired peaks: 612 WARNING @ Tue, 27 Jun 2017 11:13:46: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Tue, 27 Jun 2017 11:13:46: start model_add_line... INFO @ Tue, 27 Jun 2017 11:13:46: start X-correlation... INFO @ Tue, 27 Jun 2017 11:13:46: end of X-cor INFO @ Tue, 27 Jun 2017 11:13:46: #2 finished! INFO @ Tue, 27 Jun 2017 11:13:46: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 11:13:46: #2 alternative fragment length(s) may be 2,48,554,573 bps INFO @ Tue, 27 Jun 2017 11:13:46: #2.2 Generate R script for model : SRX2350723.10_model.r WARNING @ Tue, 27 Jun 2017 11:13:46: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:13:46: #2 You may need to consider one of the other alternative d(s): 2,48,554,573 WARNING @ Tue, 27 Jun 2017 11:13:46: #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 11:13:46: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:13:50: 11000000 INFO @ Tue, 27 Jun 2017 11:13:50: 11000000 INFO @ Tue, 27 Jun 2017 11:13:54: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:13:54: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:13:54: #1 total tags in treatment: 11496376 INFO @ Tue, 27 Jun 2017 11:13:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:13:54: #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 11:13:54: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:13:54: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:13:54: #1 total tags in treatment: 11496376 INFO @ Tue, 27 Jun 2017 11:13:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:13:54: #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 11:13:54: #1 tags after filtering in treatment: 11496376 INFO @ Tue, 27 Jun 2017 11:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:13:54: #1 finished! INFO @ Tue, 27 Jun 2017 11:13:54: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:13:54: #1 tags after filtering in treatment: 11496376 INFO @ Tue, 27 Jun 2017 11:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:13:54: #1 finished! INFO @ Tue, 27 Jun 2017 11:13:54: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:13:55: #2 number of paired peaks: 612 WARNING @ Tue, 27 Jun 2017 11:13:55: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Tue, 27 Jun 2017 11:13:55: start model_add_line... INFO @ Tue, 27 Jun 2017 11:13:55: #2 number of paired peaks: 612 WARNING @ Tue, 27 Jun 2017 11:13:55: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Tue, 27 Jun 2017 11:13:55: start model_add_line... INFO @ Tue, 27 Jun 2017 11:13:55: start X-correlation... INFO @ Tue, 27 Jun 2017 11:13:55: end of X-cor INFO @ Tue, 27 Jun 2017 11:13:55: #2 finished! INFO @ Tue, 27 Jun 2017 11:13:55: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 11:13:55: #2 alternative fragment length(s) may be 2,48,554,573 bps INFO @ Tue, 27 Jun 2017 11:13:55: #2.2 Generate R script for model : SRX2350723.05_model.r INFO @ Tue, 27 Jun 2017 11:13:55: start X-correlation... WARNING @ Tue, 27 Jun 2017 11:13:55: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:13:55: #2 You may need to consider one of the other alternative d(s): 2,48,554,573 WARNING @ Tue, 27 Jun 2017 11:13:55: #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 11:13:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:13:55: end of X-cor INFO @ Tue, 27 Jun 2017 11:13:55: #2 finished! INFO @ Tue, 27 Jun 2017 11:13:55: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 11:13:55: #2 alternative fragment length(s) may be 2,48,554,573 bps INFO @ Tue, 27 Jun 2017 11:13:55: #2.2 Generate R script for model : SRX2350723.20_model.r WARNING @ Tue, 27 Jun 2017 11:13:55: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:13:55: #2 You may need to consider one of the other alternative d(s): 2,48,554,573 WARNING @ Tue, 27 Jun 2017 11:13:55: #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 11:13:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:14:09: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:14:15: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:14:16: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:14:20: #4 Write output xls file... SRX2350723.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:14:20: #4 Write peak in narrowPeak format file... SRX2350723.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:14:20: #4 Write summits bed file... SRX2350723.10_summits.bed INFO @ Tue, 27 Jun 2017 11:14:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:14:28: #4 Write output xls file... SRX2350723.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:14:28: #4 Write peak in narrowPeak format file... SRX2350723.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:14:28: #4 Write summits bed file... SRX2350723.05_summits.bed INFO @ Tue, 27 Jun 2017 11:14:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:14:29: #4 Write output xls file... SRX2350723.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:14:29: #4 Write peak in narrowPeak format file... SRX2350723.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:14:29: #4 Write summits bed file... SRX2350723.20_summits.bed INFO @ Tue, 27 Jun 2017 11:14:29: 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。