Job ID = 9157356 sra ファイルのダウンロード中... Completed: 369026K bytes transferred in 7 seconds (379537K 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 24337237 spots for /home/okishinya/chipatlas/results/ce10/SRX063961/SRR210889.sra Written 24337237 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: 00:05:47 24337237 reads; of these: 24337237 (100.00%) were unpaired; of these: 256190 (1.05%) aligned 0 times 18598611 (76.42%) aligned exactly 1 time 5482436 (22.53%) aligned >1 times 98.95% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 4524321 / 24081047 = 0.1879 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 11:37:01: # Command line: callpeak -t SRX063961.bam -f BAM -g ce -n SRX063961.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX063961.20 # format = BAM # ChIP-seq file = ['SRX063961.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 11:37:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:37:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:37:01: # Command line: callpeak -t SRX063961.bam -f BAM -g ce -n SRX063961.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX063961.10 # format = BAM # ChIP-seq file = ['SRX063961.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 11:37:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:37:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:37:01: # Command line: callpeak -t SRX063961.bam -f BAM -g ce -n SRX063961.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX063961.05 # format = BAM # ChIP-seq file = ['SRX063961.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 11:37:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:37:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:37:08: 1000000 INFO @ Tue, 27 Jun 2017 11:37:08: 1000000 INFO @ Tue, 27 Jun 2017 11:37:08: 1000000 INFO @ Tue, 27 Jun 2017 11:37:14: 2000000 INFO @ Tue, 27 Jun 2017 11:37:15: 2000000 INFO @ Tue, 27 Jun 2017 11:37:15: 2000000 INFO @ Tue, 27 Jun 2017 11:37:20: 3000000 INFO @ Tue, 27 Jun 2017 11:37:22: 3000000 INFO @ Tue, 27 Jun 2017 11:37:22: 3000000 INFO @ Tue, 27 Jun 2017 11:37:26: 4000000 INFO @ Tue, 27 Jun 2017 11:37:29: 4000000 INFO @ Tue, 27 Jun 2017 11:37:29: 4000000 INFO @ Tue, 27 Jun 2017 11:37:32: 5000000 INFO @ Tue, 27 Jun 2017 11:37:35: 5000000 INFO @ Tue, 27 Jun 2017 11:37:35: 5000000 INFO @ Tue, 27 Jun 2017 11:37:38: 6000000 INFO @ Tue, 27 Jun 2017 11:37:42: 6000000 INFO @ Tue, 27 Jun 2017 11:37:42: 6000000 INFO @ Tue, 27 Jun 2017 11:37:43: 7000000 INFO @ Tue, 27 Jun 2017 11:37:49: 7000000 INFO @ Tue, 27 Jun 2017 11:37:49: 7000000 INFO @ Tue, 27 Jun 2017 11:37:49: 8000000 INFO @ Tue, 27 Jun 2017 11:37:55: 8000000 INFO @ Tue, 27 Jun 2017 11:37:55: 8000000 INFO @ Tue, 27 Jun 2017 11:37:55: 9000000 INFO @ Tue, 27 Jun 2017 11:38:01: 10000000 INFO @ Tue, 27 Jun 2017 11:38:02: 9000000 INFO @ Tue, 27 Jun 2017 11:38:02: 9000000 INFO @ Tue, 27 Jun 2017 11:38:07: 11000000 INFO @ Tue, 27 Jun 2017 11:38:08: 10000000 INFO @ Tue, 27 Jun 2017 11:38:08: 10000000 INFO @ Tue, 27 Jun 2017 11:38:13: 12000000 INFO @ Tue, 27 Jun 2017 11:38:15: 11000000 INFO @ Tue, 27 Jun 2017 11:38:15: 11000000 INFO @ Tue, 27 Jun 2017 11:38:19: 13000000 INFO @ Tue, 27 Jun 2017 11:38:22: 12000000 INFO @ Tue, 27 Jun 2017 11:38:22: 12000000 INFO @ Tue, 27 Jun 2017 11:38:25: 14000000 INFO @ Tue, 27 Jun 2017 11:38:28: 13000000 INFO @ Tue, 27 Jun 2017 11:38:28: 13000000 INFO @ Tue, 27 Jun 2017 11:38:31: 15000000 INFO @ Tue, 27 Jun 2017 11:38:35: 14000000 INFO @ Tue, 27 Jun 2017 11:38:35: 14000000 INFO @ Tue, 27 Jun 2017 11:38:37: 16000000 INFO @ Tue, 27 Jun 2017 11:38:41: 15000000 INFO @ Tue, 27 Jun 2017 11:38:41: 15000000 INFO @ Tue, 27 Jun 2017 11:38:43: 17000000 INFO @ Tue, 27 Jun 2017 11:38:49: 16000000 INFO @ Tue, 27 Jun 2017 11:38:49: 16000000 INFO @ Tue, 27 Jun 2017 11:38:50: 18000000 INFO @ Tue, 27 Jun 2017 11:38:56: 17000000 INFO @ Tue, 27 Jun 2017 11:38:56: 17000000 INFO @ Tue, 27 Jun 2017 11:38:57: 19000000 INFO @ Tue, 27 Jun 2017 11:39:01: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 11:39:01: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 11:39:01: #1 total tags in treatment: 19556726 INFO @ Tue, 27 Jun 2017 11:39:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:39:01: #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 11:39:01: #1 tags after filtering in treatment: 19556726 INFO @ Tue, 27 Jun 2017 11:39:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:39:01: #1 finished! INFO @ Tue, 27 Jun 2017 11:39:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:39:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:39:02: #2 number of paired peaks: 305 WARNING @ Tue, 27 Jun 2017 11:39:02: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Tue, 27 Jun 2017 11:39:02: start model_add_line... INFO @ Tue, 27 Jun 2017 11:39:03: start X-correlation... INFO @ Tue, 27 Jun 2017 11:39:03: end of X-cor INFO @ Tue, 27 Jun 2017 11:39:03: #2 finished! INFO @ Tue, 27 Jun 2017 11:39:03: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:39:03: #2 alternative fragment length(s) may be 1,31,557,577 bps INFO @ Tue, 27 Jun 2017 11:39:03: #2.2 Generate R script for model : SRX063961.20_model.r WARNING @ Tue, 27 Jun 2017 11:39:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:39:03: #2 You may need to consider one of the other alternative d(s): 1,31,557,577 WARNING @ Tue, 27 Jun 2017 11:39:03: #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 11:39:03: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:39:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:39:04: 18000000 INFO @ Tue, 27 Jun 2017 11:39:04: 18000000 INFO @ Tue, 27 Jun 2017 11:39:12: 19000000 INFO @ Tue, 27 Jun 2017 11:39:12: 19000000 INFO @ Tue, 27 Jun 2017 11:39:16: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 11:39:16: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 11:39:16: #1 total tags in treatment: 19556726 INFO @ Tue, 27 Jun 2017 11:39:16: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:39:16: #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 11:39:16: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 11:39:16: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 11:39:16: #1 total tags in treatment: 19556726 INFO @ Tue, 27 Jun 2017 11:39:16: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:39:16: #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 11:39:16: #1 tags after filtering in treatment: 19556726 INFO @ Tue, 27 Jun 2017 11:39:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:39:16: #1 finished! INFO @ Tue, 27 Jun 2017 11:39:16: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:39:16: #1 tags after filtering in treatment: 19556726 INFO @ Tue, 27 Jun 2017 11:39:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:39:16: #1 finished! INFO @ Tue, 27 Jun 2017 11:39:16: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:39:18: #2 number of paired peaks: 305 WARNING @ Tue, 27 Jun 2017 11:39:18: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Tue, 27 Jun 2017 11:39:18: start model_add_line... INFO @ Tue, 27 Jun 2017 11:39:18: #2 number of paired peaks: 305 WARNING @ Tue, 27 Jun 2017 11:39:18: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Tue, 27 Jun 2017 11:39:18: start model_add_line... INFO @ Tue, 27 Jun 2017 11:39:18: start X-correlation... INFO @ Tue, 27 Jun 2017 11:39:18: end of X-cor INFO @ Tue, 27 Jun 2017 11:39:18: #2 finished! INFO @ Tue, 27 Jun 2017 11:39:18: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:39:18: #2 alternative fragment length(s) may be 1,31,557,577 bps INFO @ Tue, 27 Jun 2017 11:39:18: #2.2 Generate R script for model : SRX063961.10_model.r WARNING @ Tue, 27 Jun 2017 11:39:18: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:39:18: #2 You may need to consider one of the other alternative d(s): 1,31,557,577 WARNING @ Tue, 27 Jun 2017 11:39:18: #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 11:39:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:39:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:39:18: start X-correlation... INFO @ Tue, 27 Jun 2017 11:39:18: end of X-cor INFO @ Tue, 27 Jun 2017 11:39:18: #2 finished! INFO @ Tue, 27 Jun 2017 11:39:18: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:39:18: #2 alternative fragment length(s) may be 1,31,557,577 bps INFO @ Tue, 27 Jun 2017 11:39:18: #2.2 Generate R script for model : SRX063961.05_model.r WARNING @ Tue, 27 Jun 2017 11:39:18: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:39:18: #2 You may need to consider one of the other alternative d(s): 1,31,557,577 WARNING @ Tue, 27 Jun 2017 11:39:18: #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 11:39:18: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:39:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:39:35: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:39:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:39:51: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:39:51: #4 Write output xls file... SRX063961.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:39:51: #4 Write peak in narrowPeak format file... SRX063961.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:39:51: #4 Write summits bed file... SRX063961.20_summits.bed INFO @ Tue, 27 Jun 2017 11:39:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:40:07: #4 Write output xls file... SRX063961.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:40:07: #4 Write peak in narrowPeak format file... SRX063961.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:40:07: #4 Write summits bed file... SRX063961.05_summits.bed INFO @ Tue, 27 Jun 2017 11:40:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:40:08: #4 Write output xls file... SRX063961.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:40:08: #4 Write peak in narrowPeak format file... SRX063961.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:40:08: #4 Write summits bed file... SRX063961.10_summits.bed INFO @ Tue, 27 Jun 2017 11:40:08: Done! pass1 - making usageList (0 chroms): 0 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。