Job ID = 9157400 sra ファイルのダウンロード中... Completed: 488708K bytes transferred in 7 seconds (560561K 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 20859731 spots for /home/okishinya/chipatlas/results/ce10/SRX1949398/SRR3922838.sra Written 20859731 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: 00:05:22 20859731 reads; of these: 20859731 (100.00%) were unpaired; of these: 208949 (1.00%) aligned 0 times 17280153 (82.84%) aligned exactly 1 time 3370629 (16.16%) aligned >1 times 99.00% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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 12 files... [bam_rmdupse_core] 2035333 / 20650782 = 0.0986 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 11:53:39: # Command line: callpeak -t SRX1949398.bam -f BAM -g ce -n SRX1949398.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1949398.20 # format = BAM # ChIP-seq file = ['SRX1949398.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 11:53:39: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:39: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:39: # Command line: callpeak -t SRX1949398.bam -f BAM -g ce -n SRX1949398.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1949398.05 # format = BAM # ChIP-seq file = ['SRX1949398.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 11:53:39: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:39: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:39: # Command line: callpeak -t SRX1949398.bam -f BAM -g ce -n SRX1949398.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1949398.10 # format = BAM # ChIP-seq file = ['SRX1949398.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 11:53:39: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:53:39: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:53:46: 1000000 INFO @ Tue, 27 Jun 2017 11:53:46: 1000000 INFO @ Tue, 27 Jun 2017 11:53:46: 1000000 INFO @ Tue, 27 Jun 2017 11:53:52: 2000000 INFO @ Tue, 27 Jun 2017 11:53:52: 2000000 INFO @ Tue, 27 Jun 2017 11:53:53: 2000000 INFO @ Tue, 27 Jun 2017 11:53:58: 3000000 INFO @ Tue, 27 Jun 2017 11:53:59: 3000000 INFO @ Tue, 27 Jun 2017 11:54:00: 3000000 INFO @ Tue, 27 Jun 2017 11:54:05: 4000000 INFO @ Tue, 27 Jun 2017 11:54:06: 4000000 INFO @ Tue, 27 Jun 2017 11:54:07: 4000000 INFO @ Tue, 27 Jun 2017 11:54:11: 5000000 INFO @ Tue, 27 Jun 2017 11:54:12: 5000000 INFO @ Tue, 27 Jun 2017 11:54:14: 5000000 INFO @ Tue, 27 Jun 2017 11:54:17: 6000000 INFO @ Tue, 27 Jun 2017 11:54:19: 6000000 INFO @ Tue, 27 Jun 2017 11:54:22: 6000000 INFO @ Tue, 27 Jun 2017 11:54:23: 7000000 INFO @ Tue, 27 Jun 2017 11:54:26: 7000000 INFO @ Tue, 27 Jun 2017 11:54:29: 7000000 INFO @ Tue, 27 Jun 2017 11:54:29: 8000000 INFO @ Tue, 27 Jun 2017 11:54:32: 8000000 INFO @ Tue, 27 Jun 2017 11:54:35: 9000000 INFO @ Tue, 27 Jun 2017 11:54:36: 8000000 INFO @ Tue, 27 Jun 2017 11:54:39: 9000000 INFO @ Tue, 27 Jun 2017 11:54:43: 10000000 INFO @ Tue, 27 Jun 2017 11:54:44: 9000000 INFO @ Tue, 27 Jun 2017 11:54:46: 10000000 INFO @ Tue, 27 Jun 2017 11:54:52: 11000000 INFO @ Tue, 27 Jun 2017 11:54:52: 10000000 INFO @ Tue, 27 Jun 2017 11:54:54: 11000000 INFO @ Tue, 27 Jun 2017 11:55:00: 12000000 INFO @ Tue, 27 Jun 2017 11:55:01: 11000000 INFO @ Tue, 27 Jun 2017 11:55:01: 12000000 INFO @ Tue, 27 Jun 2017 11:55:08: 13000000 INFO @ Tue, 27 Jun 2017 11:55:08: 13000000 INFO @ Tue, 27 Jun 2017 11:55:09: 12000000 INFO @ Tue, 27 Jun 2017 11:55:16: 14000000 INFO @ Tue, 27 Jun 2017 11:55:16: 14000000 INFO @ Tue, 27 Jun 2017 11:55:17: 13000000 INFO @ Tue, 27 Jun 2017 11:55:23: 15000000 INFO @ Tue, 27 Jun 2017 11:55:24: 15000000 INFO @ Tue, 27 Jun 2017 11:55:26: 14000000 INFO @ Tue, 27 Jun 2017 11:55:30: 16000000 INFO @ Tue, 27 Jun 2017 11:55:31: 16000000 INFO @ Tue, 27 Jun 2017 11:55:32: 15000000 INFO @ Tue, 27 Jun 2017 11:55:36: 17000000 INFO @ Tue, 27 Jun 2017 11:55:37: 17000000 INFO @ Tue, 27 Jun 2017 11:55:39: 16000000 INFO @ Tue, 27 Jun 2017 11:55:43: 18000000 INFO @ Tue, 27 Jun 2017 11:55:43: 18000000 INFO @ Tue, 27 Jun 2017 11:55:46: 17000000 INFO @ Tue, 27 Jun 2017 11:55:47: #1 tag size is determined as 49 bps INFO @ Tue, 27 Jun 2017 11:55:47: #1 tag size = 49 INFO @ Tue, 27 Jun 2017 11:55:47: #1 total tags in treatment: 18615449 INFO @ Tue, 27 Jun 2017 11:55:47: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:47: #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 11:55:47: #1 tag size is determined as 49 bps INFO @ Tue, 27 Jun 2017 11:55:47: #1 tag size = 49 INFO @ Tue, 27 Jun 2017 11:55:47: #1 total tags in treatment: 18615449 INFO @ Tue, 27 Jun 2017 11:55:47: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:47: #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 11:55:47: #1 tags after filtering in treatment: 18615449 INFO @ Tue, 27 Jun 2017 11:55:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:47: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:47: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:48: #1 tags after filtering in treatment: 18615449 INFO @ Tue, 27 Jun 2017 11:55:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:48: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:48: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:49: #2 number of paired peaks: 210 WARNING @ Tue, 27 Jun 2017 11:55:49: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 27 Jun 2017 11:55:49: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:49: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:49: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:49: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:49: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:55:49: #2 alternative fragment length(s) may be 1,44,565 bps INFO @ Tue, 27 Jun 2017 11:55:49: #2.2 Generate R script for model : SRX1949398.10_model.r WARNING @ Tue, 27 Jun 2017 11:55:49: #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 11:55:49: #2 You may need to consider one of the other alternative d(s): 1,44,565 WARNING @ Tue, 27 Jun 2017 11:55:49: #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 11:55:49: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:49: #2 number of paired peaks: 210 WARNING @ Tue, 27 Jun 2017 11:55:49: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 27 Jun 2017 11:55:49: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:49: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:49: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:49: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:49: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:55:49: #2 alternative fragment length(s) may be 1,44,565 bps INFO @ Tue, 27 Jun 2017 11:55:49: #2.2 Generate R script for model : SRX1949398.05_model.r WARNING @ Tue, 27 Jun 2017 11:55:49: #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 11:55:49: #2 You may need to consider one of the other alternative d(s): 1,44,565 WARNING @ Tue, 27 Jun 2017 11:55:49: #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 11:55:49: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:55:53: 18000000 INFO @ Tue, 27 Jun 2017 11:55:57: #1 tag size is determined as 49 bps INFO @ Tue, 27 Jun 2017 11:55:57: #1 tag size = 49 INFO @ Tue, 27 Jun 2017 11:55:57: #1 total tags in treatment: 18615449 INFO @ Tue, 27 Jun 2017 11:55:57: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:55:57: #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 11:55:57: #1 tags after filtering in treatment: 18615449 INFO @ Tue, 27 Jun 2017 11:55:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:55:57: #1 finished! INFO @ Tue, 27 Jun 2017 11:55:57: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:55:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:55:58: #2 number of paired peaks: 210 WARNING @ Tue, 27 Jun 2017 11:55:58: Fewer paired peaks (210) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 210 pairs to build model! INFO @ Tue, 27 Jun 2017 11:55:58: start model_add_line... INFO @ Tue, 27 Jun 2017 11:55:59: start X-correlation... INFO @ Tue, 27 Jun 2017 11:55:59: end of X-cor INFO @ Tue, 27 Jun 2017 11:55:59: #2 finished! INFO @ Tue, 27 Jun 2017 11:55:59: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 11:55:59: #2 alternative fragment length(s) may be 1,44,565 bps INFO @ Tue, 27 Jun 2017 11:55:59: #2.2 Generate R script for model : SRX1949398.20_model.r WARNING @ Tue, 27 Jun 2017 11:55:59: #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 11:55:59: #2 You may need to consider one of the other alternative d(s): 1,44,565 WARNING @ Tue, 27 Jun 2017 11:55:59: #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 11:55:59: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:55:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:56:21: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:56:22: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:56:34: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:56:38: #4 Write output xls file... SRX1949398.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:56:38: #4 Write peak in narrowPeak format file... SRX1949398.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:56:38: #4 Write summits bed file... SRX1949398.05_summits.bed INFO @ Tue, 27 Jun 2017 11:56:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:56:38: #4 Write output xls file... SRX1949398.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:56:38: #4 Write peak in narrowPeak format file... SRX1949398.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:56:38: #4 Write summits bed file... SRX1949398.10_summits.bed INFO @ Tue, 27 Jun 2017 11:56:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:56:50: #4 Write output xls file... SRX1949398.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:56:50: #4 Write peak in narrowPeak format file... SRX1949398.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:56:50: #4 Write summits bed file... SRX1949398.20_summits.bed INFO @ Tue, 27 Jun 2017 11:56:50: 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。