Job ID = 9157211 sra ファイルのダウンロード中... Completed: 613334K bytes transferred in 7 seconds (707343K 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 14168528 spots for /home/okishinya/chipatlas/results/ce10/SRX2350720/SRR5024029.sra Written 14168528 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: 00:03:51 14168528 reads; of these: 14168528 (100.00%) were unpaired; of these: 435782 (3.08%) aligned 0 times 10160799 (71.71%) aligned exactly 1 time 3571947 (25.21%) aligned >1 times 96.92% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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] 2434700 / 13732746 = 0.1773 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 11:10:41: # Command line: callpeak -t SRX2350720.bam -f BAM -g ce -n SRX2350720.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2350720.05 # format = BAM # ChIP-seq file = ['SRX2350720.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 11:10:41: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:10:41: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:10:41: # Command line: callpeak -t SRX2350720.bam -f BAM -g ce -n SRX2350720.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2350720.20 # format = BAM # ChIP-seq file = ['SRX2350720.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 11:10:41: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:10:41: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:10:41: # Command line: callpeak -t SRX2350720.bam -f BAM -g ce -n SRX2350720.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2350720.10 # format = BAM # ChIP-seq file = ['SRX2350720.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 11:10:41: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:10:41: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:10:49: 1000000 INFO @ Tue, 27 Jun 2017 11:10:50: 1000000 INFO @ Tue, 27 Jun 2017 11:10:50: 1000000 INFO @ Tue, 27 Jun 2017 11:10:56: 2000000 INFO @ Tue, 27 Jun 2017 11:10:59: 2000000 INFO @ Tue, 27 Jun 2017 11:10:59: 2000000 INFO @ Tue, 27 Jun 2017 11:11:04: 3000000 INFO @ Tue, 27 Jun 2017 11:11:07: 3000000 INFO @ Tue, 27 Jun 2017 11:11:07: 3000000 INFO @ Tue, 27 Jun 2017 11:11:11: 4000000 INFO @ Tue, 27 Jun 2017 11:11:15: 4000000 INFO @ Tue, 27 Jun 2017 11:11:15: 4000000 INFO @ Tue, 27 Jun 2017 11:11:19: 5000000 INFO @ Tue, 27 Jun 2017 11:11:24: 5000000 INFO @ Tue, 27 Jun 2017 11:11:24: 5000000 INFO @ Tue, 27 Jun 2017 11:11:27: 6000000 INFO @ Tue, 27 Jun 2017 11:11:32: 6000000 INFO @ Tue, 27 Jun 2017 11:11:32: 6000000 INFO @ Tue, 27 Jun 2017 11:11:34: 7000000 INFO @ Tue, 27 Jun 2017 11:11:41: 7000000 INFO @ Tue, 27 Jun 2017 11:11:41: 7000000 INFO @ Tue, 27 Jun 2017 11:11:42: 8000000 INFO @ Tue, 27 Jun 2017 11:11:49: 9000000 INFO @ Tue, 27 Jun 2017 11:11:49: 8000000 INFO @ Tue, 27 Jun 2017 11:11:49: 8000000 INFO @ Tue, 27 Jun 2017 11:11:57: 10000000 INFO @ Tue, 27 Jun 2017 11:11:58: 9000000 INFO @ Tue, 27 Jun 2017 11:11:58: 9000000 INFO @ Tue, 27 Jun 2017 11:12:04: 11000000 INFO @ Tue, 27 Jun 2017 11:12:06: 10000000 INFO @ Tue, 27 Jun 2017 11:12:06: 10000000 INFO @ Tue, 27 Jun 2017 11:12:06: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:12:06: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:12:06: #1 total tags in treatment: 11298046 INFO @ Tue, 27 Jun 2017 11:12:06: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:12:06: #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 11:12:07: #1 tags after filtering in treatment: 11298046 INFO @ Tue, 27 Jun 2017 11:12:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:12:07: #1 finished! INFO @ Tue, 27 Jun 2017 11:12:07: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:12:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:12:07: #2 number of paired peaks: 509 WARNING @ Tue, 27 Jun 2017 11:12:07: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 27 Jun 2017 11:12:07: start model_add_line... INFO @ Tue, 27 Jun 2017 11:12:08: start X-correlation... INFO @ Tue, 27 Jun 2017 11:12:08: end of X-cor INFO @ Tue, 27 Jun 2017 11:12:08: #2 finished! INFO @ Tue, 27 Jun 2017 11:12:08: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 11:12:08: #2 alternative fragment length(s) may be 2,31,45 bps INFO @ Tue, 27 Jun 2017 11:12:08: #2.2 Generate R script for model : SRX2350720.05_model.r WARNING @ Tue, 27 Jun 2017 11:12:08: #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 11:12:08: #2 You may need to consider one of the other alternative d(s): 2,31,45 WARNING @ Tue, 27 Jun 2017 11:12:08: #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 11:12:08: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:12:14: 11000000 INFO @ Tue, 27 Jun 2017 11:12:14: 11000000 INFO @ Tue, 27 Jun 2017 11:12:17: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:12:17: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:12:17: #1 total tags in treatment: 11298046 INFO @ Tue, 27 Jun 2017 11:12:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:12:17: #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 11:12:17: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:12:17: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:12:17: #1 total tags in treatment: 11298046 INFO @ Tue, 27 Jun 2017 11:12:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:12:17: #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 11:12:17: #1 tags after filtering in treatment: 11298046 INFO @ Tue, 27 Jun 2017 11:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:12:17: #1 finished! INFO @ Tue, 27 Jun 2017 11:12:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:12:17: #1 tags after filtering in treatment: 11298046 INFO @ Tue, 27 Jun 2017 11:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:12:17: #1 finished! INFO @ Tue, 27 Jun 2017 11:12:17: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:12:18: #2 number of paired peaks: 509 WARNING @ Tue, 27 Jun 2017 11:12:18: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 27 Jun 2017 11:12:18: start model_add_line... INFO @ Tue, 27 Jun 2017 11:12:18: #2 number of paired peaks: 509 WARNING @ Tue, 27 Jun 2017 11:12:18: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 27 Jun 2017 11:12:18: start model_add_line... INFO @ Tue, 27 Jun 2017 11:12:18: start X-correlation... INFO @ Tue, 27 Jun 2017 11:12:18: end of X-cor INFO @ Tue, 27 Jun 2017 11:12:18: #2 finished! INFO @ Tue, 27 Jun 2017 11:12:18: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 11:12:18: #2 alternative fragment length(s) may be 2,31,45 bps INFO @ Tue, 27 Jun 2017 11:12:18: #2.2 Generate R script for model : SRX2350720.10_model.r WARNING @ Tue, 27 Jun 2017 11:12:18: #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 11:12:18: #2 You may need to consider one of the other alternative d(s): 2,31,45 WARNING @ Tue, 27 Jun 2017 11:12:18: #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 11:12:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:12:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:12:18: start X-correlation... INFO @ Tue, 27 Jun 2017 11:12:18: end of X-cor INFO @ Tue, 27 Jun 2017 11:12:18: #2 finished! INFO @ Tue, 27 Jun 2017 11:12:18: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 11:12:18: #2 alternative fragment length(s) may be 2,31,45 bps INFO @ Tue, 27 Jun 2017 11:12:18: #2.2 Generate R script for model : SRX2350720.20_model.r WARNING @ Tue, 27 Jun 2017 11:12:18: #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 11:12:18: #2 You may need to consider one of the other alternative d(s): 2,31,45 WARNING @ Tue, 27 Jun 2017 11:12:18: #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 11:12:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:12:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:12:29: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:12:38: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:12:39: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:12:40: #4 Write output xls file... SRX2350720.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:12:40: #4 Write peak in narrowPeak format file... SRX2350720.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:12:40: #4 Write summits bed file... SRX2350720.05_summits.bed INFO @ Tue, 27 Jun 2017 11:12:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:12:50: #4 Write output xls file... SRX2350720.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:12:50: #4 Write peak in narrowPeak format file... SRX2350720.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:12:50: #4 Write summits bed file... SRX2350720.20_summits.bed INFO @ Tue, 27 Jun 2017 11:12:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:12:50: #4 Write output xls file... SRX2350720.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:12:50: #4 Write peak in narrowPeak format file... SRX2350720.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:12:50: #4 Write summits bed file... SRX2350720.10_summits.bed INFO @ Tue, 27 Jun 2017 11:12:50: 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。