Job ID = 9157788 sra ファイルのダウンロード中... Completed: 557985K bytes transferred in 7 seconds (581071K 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 18464702 spots for /home/okishinya/chipatlas/results/ce10/SRX982090/SRR1956577.sra Written 18464702 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: 00:04:45 18464702 reads; of these: 18464702 (100.00%) were unpaired; of these: 180996 (0.98%) aligned 0 times 15063952 (81.58%) aligned exactly 1 time 3219754 (17.44%) aligned >1 times 99.02% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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] 1792389 / 18283706 = 0.0980 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 13:45:01: # Command line: callpeak -t SRX982090.bam -f BAM -g ce -n SRX982090.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982090.10 # format = BAM # ChIP-seq file = ['SRX982090.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 13:45:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 13:45:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 13:45:01: # Command line: callpeak -t SRX982090.bam -f BAM -g ce -n SRX982090.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982090.05 # format = BAM # ChIP-seq file = ['SRX982090.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 13:45:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 13:45:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 13:45:01: # Command line: callpeak -t SRX982090.bam -f BAM -g ce -n SRX982090.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982090.20 # format = BAM # ChIP-seq file = ['SRX982090.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 13:45:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 13:45:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 13:45:10: 1000000 INFO @ Tue, 27 Jun 2017 13:45:10: 1000000 INFO @ Tue, 27 Jun 2017 13:45:10: 1000000 INFO @ Tue, 27 Jun 2017 13:45:17: 2000000 INFO @ Tue, 27 Jun 2017 13:45:17: 2000000 INFO @ Tue, 27 Jun 2017 13:45:17: 2000000 INFO @ Tue, 27 Jun 2017 13:45:25: 3000000 INFO @ Tue, 27 Jun 2017 13:45:25: 3000000 INFO @ Tue, 27 Jun 2017 13:45:25: 3000000 INFO @ Tue, 27 Jun 2017 13:45:33: 4000000 INFO @ Tue, 27 Jun 2017 13:45:33: 4000000 INFO @ Tue, 27 Jun 2017 13:45:33: 4000000 INFO @ Tue, 27 Jun 2017 13:45:40: 5000000 INFO @ Tue, 27 Jun 2017 13:45:41: 5000000 INFO @ Tue, 27 Jun 2017 13:45:41: 5000000 INFO @ Tue, 27 Jun 2017 13:45:47: 6000000 INFO @ Tue, 27 Jun 2017 13:45:48: 6000000 INFO @ Tue, 27 Jun 2017 13:45:48: 6000000 INFO @ Tue, 27 Jun 2017 13:45:55: 7000000 INFO @ Tue, 27 Jun 2017 13:45:57: 7000000 INFO @ Tue, 27 Jun 2017 13:45:57: 7000000 INFO @ Tue, 27 Jun 2017 13:46:02: 8000000 INFO @ Tue, 27 Jun 2017 13:46:04: 8000000 INFO @ Tue, 27 Jun 2017 13:46:04: 8000000 INFO @ Tue, 27 Jun 2017 13:46:09: 9000000 INFO @ Tue, 27 Jun 2017 13:46:12: 9000000 INFO @ Tue, 27 Jun 2017 13:46:12: 9000000 INFO @ Tue, 27 Jun 2017 13:46:16: 10000000 INFO @ Tue, 27 Jun 2017 13:46:19: 10000000 INFO @ Tue, 27 Jun 2017 13:46:19: 10000000 INFO @ Tue, 27 Jun 2017 13:46:24: 11000000 INFO @ Tue, 27 Jun 2017 13:46:27: 11000000 INFO @ Tue, 27 Jun 2017 13:46:27: 11000000 INFO @ Tue, 27 Jun 2017 13:46:32: 12000000 INFO @ Tue, 27 Jun 2017 13:46:35: 12000000 INFO @ Tue, 27 Jun 2017 13:46:35: 12000000 INFO @ Tue, 27 Jun 2017 13:46:39: 13000000 INFO @ Tue, 27 Jun 2017 13:46:42: 13000000 INFO @ Tue, 27 Jun 2017 13:46:42: 13000000 INFO @ Tue, 27 Jun 2017 13:46:46: 14000000 INFO @ Tue, 27 Jun 2017 13:46:50: 14000000 INFO @ Tue, 27 Jun 2017 13:46:50: 14000000 INFO @ Tue, 27 Jun 2017 13:46:54: 15000000 INFO @ Tue, 27 Jun 2017 13:46:58: 15000000 INFO @ Tue, 27 Jun 2017 13:46:58: 15000000 INFO @ Tue, 27 Jun 2017 13:47:01: 16000000 INFO @ Tue, 27 Jun 2017 13:47:04: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 13:47:04: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 13:47:04: #1 total tags in treatment: 16491317 INFO @ Tue, 27 Jun 2017 13:47:04: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 13:47:04: #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 13:47:05: #1 tags after filtering in treatment: 16491317 INFO @ Tue, 27 Jun 2017 13:47:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 13:47:05: #1 finished! INFO @ Tue, 27 Jun 2017 13:47:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 13:47:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 13:47:05: 16000000 INFO @ Tue, 27 Jun 2017 13:47:05: 16000000 INFO @ Tue, 27 Jun 2017 13:47:06: #2 number of paired peaks: 272 WARNING @ Tue, 27 Jun 2017 13:47:06: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Tue, 27 Jun 2017 13:47:06: start model_add_line... INFO @ Tue, 27 Jun 2017 13:47:06: start X-correlation... INFO @ Tue, 27 Jun 2017 13:47:06: end of X-cor INFO @ Tue, 27 Jun 2017 13:47:06: #2 finished! INFO @ Tue, 27 Jun 2017 13:47:06: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 13:47:06: #2 alternative fragment length(s) may be 2,30,556,586 bps INFO @ Tue, 27 Jun 2017 13:47:06: #2.2 Generate R script for model : SRX982090.20_model.r WARNING @ Tue, 27 Jun 2017 13:47:06: #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 13:47:06: #2 You may need to consider one of the other alternative d(s): 2,30,556,586 WARNING @ Tue, 27 Jun 2017 13:47:06: #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 13:47:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 13:47:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 13:47:09: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 13:47:09: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 13:47:09: #1 total tags in treatment: 16491317 INFO @ Tue, 27 Jun 2017 13:47:09: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 13:47:09: #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 13:47:09: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 13:47:09: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 13:47:09: #1 total tags in treatment: 16491317 INFO @ Tue, 27 Jun 2017 13:47:09: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 13:47:09: #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 13:47:09: #1 tags after filtering in treatment: 16491317 INFO @ Tue, 27 Jun 2017 13:47:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 13:47:09: #1 finished! INFO @ Tue, 27 Jun 2017 13:47:09: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 13:47:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 13:47:09: #1 tags after filtering in treatment: 16491317 INFO @ Tue, 27 Jun 2017 13:47:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 13:47:09: #1 finished! INFO @ Tue, 27 Jun 2017 13:47:09: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 13:47:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 13:47:10: #2 number of paired peaks: 272 WARNING @ Tue, 27 Jun 2017 13:47:10: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Tue, 27 Jun 2017 13:47:10: start model_add_line... INFO @ Tue, 27 Jun 2017 13:47:11: #2 number of paired peaks: 272 WARNING @ Tue, 27 Jun 2017 13:47:11: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Tue, 27 Jun 2017 13:47:11: start model_add_line... INFO @ Tue, 27 Jun 2017 13:47:11: start X-correlation... INFO @ Tue, 27 Jun 2017 13:47:11: end of X-cor INFO @ Tue, 27 Jun 2017 13:47:11: #2 finished! INFO @ Tue, 27 Jun 2017 13:47:11: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 13:47:11: #2 alternative fragment length(s) may be 2,30,556,586 bps INFO @ Tue, 27 Jun 2017 13:47:11: #2.2 Generate R script for model : SRX982090.05_model.r WARNING @ Tue, 27 Jun 2017 13:47:11: #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 13:47:11: #2 You may need to consider one of the other alternative d(s): 2,30,556,586 WARNING @ Tue, 27 Jun 2017 13:47:11: #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 13:47:11: #3 Call peaks... INFO @ Tue, 27 Jun 2017 13:47:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 13:47:11: start X-correlation... INFO @ Tue, 27 Jun 2017 13:47:11: end of X-cor INFO @ Tue, 27 Jun 2017 13:47:11: #2 finished! INFO @ Tue, 27 Jun 2017 13:47:11: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 13:47:11: #2 alternative fragment length(s) may be 2,30,556,586 bps INFO @ Tue, 27 Jun 2017 13:47:11: #2.2 Generate R script for model : SRX982090.10_model.r WARNING @ Tue, 27 Jun 2017 13:47:11: #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 13:47:11: #2 You may need to consider one of the other alternative d(s): 2,30,556,586 WARNING @ Tue, 27 Jun 2017 13:47:11: #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 13:47:11: #3 Call peaks... INFO @ Tue, 27 Jun 2017 13:47:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 13:47:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 13:47:40: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 13:47:41: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 13:47:50: #4 Write output xls file... SRX982090.20_peaks.xls INFO @ Tue, 27 Jun 2017 13:47:50: #4 Write peak in narrowPeak format file... SRX982090.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 13:47:50: #4 Write summits bed file... SRX982090.20_summits.bed INFO @ Tue, 27 Jun 2017 13:47:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 13:47:55: #4 Write output xls file... SRX982090.10_peaks.xls INFO @ Tue, 27 Jun 2017 13:47:55: #4 Write peak in narrowPeak format file... SRX982090.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 13:47:55: #4 Write summits bed file... SRX982090.10_summits.bed INFO @ Tue, 27 Jun 2017 13:47:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 13:47:55: #4 Write output xls file... SRX982090.05_peaks.xls INFO @ Tue, 27 Jun 2017 13:47:55: #4 Write peak in narrowPeak format file... SRX982090.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 13:47:55: #4 Write summits bed file... SRX982090.05_summits.bed INFO @ Tue, 27 Jun 2017 13:47:55: 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。