Job ID = 9163553 sra ファイルのダウンロード中... Completed: 339511K bytes transferred in 6 seconds (411211K 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 12332224 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876304/SRR1802407.sra Written 12332224 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: 00:01:44 12332224 reads; of these: 12332224 (100.00%) were unpaired; of these: 2277937 (18.47%) aligned 0 times 7927615 (64.28%) aligned exactly 1 time 2126672 (17.24%) aligned >1 times 81.53% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 8823068 / 10054287 = 0.8775 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 @ Wed, 28 Jun 2017 10:56:28: # Command line: callpeak -t SRX876304.bam -f BAM -g 12100000 -n SRX876304.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX876304.20 # format = BAM # ChIP-seq file = ['SRX876304.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 28 Jun 2017 10:56:28: #1 read tag files... INFO @ Wed, 28 Jun 2017 10:56:28: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 10:56:28: # Command line: callpeak -t SRX876304.bam -f BAM -g 12100000 -n SRX876304.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX876304.05 # format = BAM # ChIP-seq file = ['SRX876304.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 28 Jun 2017 10:56:28: #1 read tag files... INFO @ Wed, 28 Jun 2017 10:56:28: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 10:56:28: # Command line: callpeak -t SRX876304.bam -f BAM -g 12100000 -n SRX876304.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX876304.10 # format = BAM # ChIP-seq file = ['SRX876304.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 28 Jun 2017 10:56:28: #1 read tag files... INFO @ Wed, 28 Jun 2017 10:56:28: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 10:56:34: 1000000 INFO @ Wed, 28 Jun 2017 10:56:34: 1000000 INFO @ Wed, 28 Jun 2017 10:56:34: 1000000 INFO @ Wed, 28 Jun 2017 10:56:35: #1 tag size is determined as 40 bps INFO @ Wed, 28 Jun 2017 10:56:35: #1 tag size is determined as 40 bps INFO @ Wed, 28 Jun 2017 10:56:35: #1 tag size = 40 INFO @ Wed, 28 Jun 2017 10:56:35: #1 tag size = 40 INFO @ Wed, 28 Jun 2017 10:56:35: #1 total tags in treatment: 1231219 INFO @ Wed, 28 Jun 2017 10:56:35: #1 total tags in treatment: 1231219 INFO @ Wed, 28 Jun 2017 10:56:35: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 10:56:35: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 10:56:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 10:56:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 10:56:35: #1 tags after filtering in treatment: 1231219 INFO @ Wed, 28 Jun 2017 10:56:35: #1 tags after filtering in treatment: 1231219 INFO @ Wed, 28 Jun 2017 10:56:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 10:56:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 10:56:35: #1 finished! INFO @ Wed, 28 Jun 2017 10:56:35: #1 finished! INFO @ Wed, 28 Jun 2017 10:56:35: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 10:56:35: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 10:56:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 10:56:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 10:56:36: #2 number of paired peaks: 260 WARNING @ Wed, 28 Jun 2017 10:56:36: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Wed, 28 Jun 2017 10:56:36: start model_add_line... INFO @ Wed, 28 Jun 2017 10:56:36: #2 number of paired peaks: 260 WARNING @ Wed, 28 Jun 2017 10:56:36: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Wed, 28 Jun 2017 10:56:36: start model_add_line... INFO @ Wed, 28 Jun 2017 10:56:36: start X-correlation... INFO @ Wed, 28 Jun 2017 10:56:36: start X-correlation... INFO @ Wed, 28 Jun 2017 10:56:36: end of X-cor INFO @ Wed, 28 Jun 2017 10:56:36: end of X-cor INFO @ Wed, 28 Jun 2017 10:56:36: #2 finished! INFO @ Wed, 28 Jun 2017 10:56:36: #2 finished! INFO @ Wed, 28 Jun 2017 10:56:36: #2 predicted fragment length is 2 bps INFO @ Wed, 28 Jun 2017 10:56:36: #2 predicted fragment length is 2 bps INFO @ Wed, 28 Jun 2017 10:56:36: #2 alternative fragment length(s) may be 2,10,35,75,96,152,159,178,183,222,237,254,295,320,341,348,372,387,412,438,479,496,508,572 bps INFO @ Wed, 28 Jun 2017 10:56:36: #2 alternative fragment length(s) may be 2,10,35,75,96,152,159,178,183,222,237,254,295,320,341,348,372,387,412,438,479,496,508,572 bps INFO @ Wed, 28 Jun 2017 10:56:36: #2.2 Generate R script for model : SRX876304.20_model.r INFO @ Wed, 28 Jun 2017 10:56:36: #2.2 Generate R script for model : SRX876304.05_model.r WARNING @ Wed, 28 Jun 2017 10:56:36: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 10:56:36: #2 You may need to consider one of the other alternative d(s): 2,10,35,75,96,152,159,178,183,222,237,254,295,320,341,348,372,387,412,438,479,496,508,572 WARNING @ Wed, 28 Jun 2017 10:56:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 10:56:36: #3 Call peaks... WARNING @ Wed, 28 Jun 2017 10:56:36: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 10:56:36: #2 You may need to consider one of the other alternative d(s): 2,10,35,75,96,152,159,178,183,222,237,254,295,320,341,348,372,387,412,438,479,496,508,572 WARNING @ Wed, 28 Jun 2017 10:56:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 10:56:36: #3 Call peaks... INFO @ Wed, 28 Jun 2017 10:56:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 10:56:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 10:56:36: #1 tag size is determined as 40 bps INFO @ Wed, 28 Jun 2017 10:56:36: #1 tag size = 40 INFO @ Wed, 28 Jun 2017 10:56:36: #1 total tags in treatment: 1231219 INFO @ Wed, 28 Jun 2017 10:56:36: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 10:56:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 10:56:36: #1 tags after filtering in treatment: 1231219 INFO @ Wed, 28 Jun 2017 10:56:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 10:56:36: #1 finished! INFO @ Wed, 28 Jun 2017 10:56:36: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 10:56:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 10:56:36: #2 number of paired peaks: 260 WARNING @ Wed, 28 Jun 2017 10:56:36: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Wed, 28 Jun 2017 10:56:36: start model_add_line... INFO @ Wed, 28 Jun 2017 10:56:36: start X-correlation... INFO @ Wed, 28 Jun 2017 10:56:36: end of X-cor INFO @ Wed, 28 Jun 2017 10:56:36: #2 finished! INFO @ Wed, 28 Jun 2017 10:56:36: #2 predicted fragment length is 2 bps INFO @ Wed, 28 Jun 2017 10:56:36: #2 alternative fragment length(s) may be 2,10,35,75,96,152,159,178,183,222,237,254,295,320,341,348,372,387,412,438,479,496,508,572 bps INFO @ Wed, 28 Jun 2017 10:56:36: #2.2 Generate R script for model : SRX876304.10_model.r WARNING @ Wed, 28 Jun 2017 10:56:36: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 10:56:36: #2 You may need to consider one of the other alternative d(s): 2,10,35,75,96,152,159,178,183,222,237,254,295,320,341,348,372,387,412,438,479,496,508,572 WARNING @ Wed, 28 Jun 2017 10:56:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 10:56:36: #3 Call peaks... INFO @ Wed, 28 Jun 2017 10:56:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 10:56:38: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 10:56:38: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 10:56:38: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 10:56:39: #4 Write output xls file... SRX876304.20_peaks.xls INFO @ Wed, 28 Jun 2017 10:56:39: #4 Write peak in narrowPeak format file... SRX876304.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 10:56:39: #4 Write summits bed file... SRX876304.20_summits.bed INFO @ Wed, 28 Jun 2017 10:56:39: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 10:56:39: #4 Write output xls file... SRX876304.05_peaks.xls INFO @ Wed, 28 Jun 2017 10:56:40: #4 Write peak in narrowPeak format file... SRX876304.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 10:56:40: #4 Write summits bed file... SRX876304.05_summits.bed INFO @ Wed, 28 Jun 2017 10:56:40: Done! INFO @ Wed, 28 Jun 2017 10:56:40: #4 Write output xls file... SRX876304.10_peaks.xls INFO @ Wed, 28 Jun 2017 10:56:40: #4 Write peak in narrowPeak format file... SRX876304.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 10:56:40: #4 Write summits bed file... SRX876304.10_summits.bed INFO @ Wed, 28 Jun 2017 10:56:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling 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。