Job ID = 9157223 sra ファイルのダウンロード中... Completed: 707110K bytes transferred in 9 seconds (615194K 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 16441458 spots for /home/okishinya/chipatlas/results/ce10/SRX2350728/SRR5024037.sra Written 16441458 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: 00:04:22 16441458 reads; of these: 16441458 (100.00%) were unpaired; of these: 203769 (1.24%) aligned 0 times 13295282 (80.86%) aligned exactly 1 time 2942407 (17.90%) aligned >1 times 98.76% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 1359379 / 16237689 = 0.0837 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 11:14:31: # Command line: callpeak -t SRX2350728.bam -f BAM -g ce -n SRX2350728.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350728.05 # format = BAM # ChIP-seq file = ['SRX2350728.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 11:14:31: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:14:31: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:14:31: # Command line: callpeak -t SRX2350728.bam -f BAM -g ce -n SRX2350728.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350728.20 # format = BAM # ChIP-seq file = ['SRX2350728.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 11:14:31: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:14:31: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:14:31: # Command line: callpeak -t SRX2350728.bam -f BAM -g ce -n SRX2350728.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350728.10 # format = BAM # ChIP-seq file = ['SRX2350728.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 11:14:31: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:14:31: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:14:38: 1000000 INFO @ Tue, 27 Jun 2017 11:14:38: 1000000 INFO @ Tue, 27 Jun 2017 11:14:38: 1000000 INFO @ Tue, 27 Jun 2017 11:14:45: 2000000 INFO @ Tue, 27 Jun 2017 11:14:45: 2000000 INFO @ Tue, 27 Jun 2017 11:14:45: 2000000 INFO @ Tue, 27 Jun 2017 11:14:52: 3000000 INFO @ Tue, 27 Jun 2017 11:14:52: 3000000 INFO @ Tue, 27 Jun 2017 11:14:52: 3000000 INFO @ Tue, 27 Jun 2017 11:14:59: 4000000 INFO @ Tue, 27 Jun 2017 11:14:59: 4000000 INFO @ Tue, 27 Jun 2017 11:14:59: 4000000 INFO @ Tue, 27 Jun 2017 11:15:06: 5000000 INFO @ Tue, 27 Jun 2017 11:15:06: 5000000 INFO @ Tue, 27 Jun 2017 11:15:06: 5000000 INFO @ Tue, 27 Jun 2017 11:15:13: 6000000 INFO @ Tue, 27 Jun 2017 11:15:13: 6000000 INFO @ Tue, 27 Jun 2017 11:15:13: 6000000 INFO @ Tue, 27 Jun 2017 11:15:20: 7000000 INFO @ Tue, 27 Jun 2017 11:15:20: 7000000 INFO @ Tue, 27 Jun 2017 11:15:20: 7000000 INFO @ Tue, 27 Jun 2017 11:15:27: 8000000 INFO @ Tue, 27 Jun 2017 11:15:27: 8000000 INFO @ Tue, 27 Jun 2017 11:15:27: 8000000 INFO @ Tue, 27 Jun 2017 11:15:34: 9000000 INFO @ Tue, 27 Jun 2017 11:15:34: 9000000 INFO @ Tue, 27 Jun 2017 11:15:34: 9000000 INFO @ Tue, 27 Jun 2017 11:15:41: 10000000 INFO @ Tue, 27 Jun 2017 11:15:41: 10000000 INFO @ Tue, 27 Jun 2017 11:15:41: 10000000 INFO @ Tue, 27 Jun 2017 11:15:47: 11000000 INFO @ Tue, 27 Jun 2017 11:15:48: 11000000 INFO @ Tue, 27 Jun 2017 11:15:48: 11000000 INFO @ Tue, 27 Jun 2017 11:15:54: 12000000 INFO @ Tue, 27 Jun 2017 11:15:55: 12000000 INFO @ Tue, 27 Jun 2017 11:15:55: 12000000 INFO @ Tue, 27 Jun 2017 11:16:01: 13000000 INFO @ Tue, 27 Jun 2017 11:16:02: 13000000 INFO @ Tue, 27 Jun 2017 11:16:02: 13000000 INFO @ Tue, 27 Jun 2017 11:16:08: 14000000 INFO @ Tue, 27 Jun 2017 11:16:09: 14000000 INFO @ Tue, 27 Jun 2017 11:16:09: 14000000 INFO @ Tue, 27 Jun 2017 11:16:14: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:16:14: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:16:14: #1 total tags in treatment: 14878310 INFO @ Tue, 27 Jun 2017 11:16:14: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:16:14: #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 11:16:15: #1 tags after filtering in treatment: 14878310 INFO @ Tue, 27 Jun 2017 11:16:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:16:15: #1 finished! INFO @ Tue, 27 Jun 2017 11:16:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:16:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:16:15: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:16:15: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:16:15: #1 total tags in treatment: 14878310 INFO @ Tue, 27 Jun 2017 11:16:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:16:15: #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 11:16:15: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:16:15: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:16:15: #1 total tags in treatment: 14878310 INFO @ Tue, 27 Jun 2017 11:16:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:16:15: #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 11:16:15: #1 tags after filtering in treatment: 14878310 INFO @ Tue, 27 Jun 2017 11:16:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:16:15: #1 finished! INFO @ Tue, 27 Jun 2017 11:16:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:16:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:16:15: #1 tags after filtering in treatment: 14878310 INFO @ Tue, 27 Jun 2017 11:16:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:16:15: #1 finished! INFO @ Tue, 27 Jun 2017 11:16:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:16:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:16:16: #2 number of paired peaks: 289 WARNING @ Tue, 27 Jun 2017 11:16:16: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 27 Jun 2017 11:16:16: start model_add_line... INFO @ Tue, 27 Jun 2017 11:16:16: start X-correlation... INFO @ Tue, 27 Jun 2017 11:16:16: end of X-cor INFO @ Tue, 27 Jun 2017 11:16:16: #2 finished! INFO @ Tue, 27 Jun 2017 11:16:16: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 11:16:16: #2 alternative fragment length(s) may be 2,30,50 bps INFO @ Tue, 27 Jun 2017 11:16:16: #2.2 Generate R script for model : SRX2350728.10_model.r WARNING @ Tue, 27 Jun 2017 11:16:16: #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 11:16:16: #2 You may need to consider one of the other alternative d(s): 2,30,50 WARNING @ Tue, 27 Jun 2017 11:16:16: #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 11:16:16: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:16:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:16:16: #2 number of paired peaks: 289 WARNING @ Tue, 27 Jun 2017 11:16:16: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 27 Jun 2017 11:16:16: start model_add_line... INFO @ Tue, 27 Jun 2017 11:16:17: #2 number of paired peaks: 289 WARNING @ Tue, 27 Jun 2017 11:16:17: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 27 Jun 2017 11:16:17: start model_add_line... INFO @ Tue, 27 Jun 2017 11:16:17: start X-correlation... INFO @ Tue, 27 Jun 2017 11:16:17: end of X-cor INFO @ Tue, 27 Jun 2017 11:16:17: #2 finished! INFO @ Tue, 27 Jun 2017 11:16:17: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 11:16:17: #2 alternative fragment length(s) may be 2,30,50 bps INFO @ Tue, 27 Jun 2017 11:16:17: #2.2 Generate R script for model : SRX2350728.05_model.r WARNING @ Tue, 27 Jun 2017 11:16:17: #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 11:16:17: #2 You may need to consider one of the other alternative d(s): 2,30,50 WARNING @ Tue, 27 Jun 2017 11:16:17: #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 11:16:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:16:17: start X-correlation... INFO @ Tue, 27 Jun 2017 11:16:17: end of X-cor INFO @ Tue, 27 Jun 2017 11:16:17: #2 finished! INFO @ Tue, 27 Jun 2017 11:16:17: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 11:16:17: #2 alternative fragment length(s) may be 2,30,50 bps INFO @ Tue, 27 Jun 2017 11:16:17: #2.2 Generate R script for model : SRX2350728.20_model.r WARNING @ Tue, 27 Jun 2017 11:16:17: #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 11:16:17: #2 You may need to consider one of the other alternative d(s): 2,30,50 WARNING @ Tue, 27 Jun 2017 11:16:17: #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 11:16:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:16:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:16:44: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:16:45: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:16:58: #4 Write output xls file... SRX2350728.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:16:58: #4 Write peak in narrowPeak format file... SRX2350728.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:16:58: #4 Write summits bed file... SRX2350728.20_summits.bed INFO @ Tue, 27 Jun 2017 11:16:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:16:58: #4 Write output xls file... SRX2350728.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:16:58: #4 Write peak in narrowPeak format file... SRX2350728.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:16:58: #4 Write summits bed file... SRX2350728.10_summits.bed INFO @ Tue, 27 Jun 2017 11:16:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:17:02: #4 Write output xls file... SRX2350728.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:17:02: #4 Write peak in narrowPeak format file... SRX2350728.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:17:02: #4 Write summits bed file... SRX2350728.05_summits.bed INFO @ Tue, 27 Jun 2017 11:17:02: 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。