Job ID = 9157617 sra ファイルのダウンロード中... Completed: 682651K bytes transferred in 8 seconds (642966K 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 19590984 spots for /home/okishinya/chipatlas/results/ce10/SRX330987/SRR947192.sra Written 19590984 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: 00:06:07 19590984 reads; of these: 19590984 (100.00%) were unpaired; of these: 935003 (4.77%) aligned 0 times 12581355 (64.22%) aligned exactly 1 time 6074626 (31.01%) aligned >1 times 95.23% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 4946919 / 18655981 = 0.2652 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 12:34:34: # Command line: callpeak -t SRX330987.bam -f BAM -g ce -n SRX330987.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX330987.10 # format = BAM # ChIP-seq file = ['SRX330987.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 12:34:34: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:34:34: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:34:34: # Command line: callpeak -t SRX330987.bam -f BAM -g ce -n SRX330987.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX330987.20 # format = BAM # ChIP-seq file = ['SRX330987.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 12:34:34: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:34:34: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:34:34: # Command line: callpeak -t SRX330987.bam -f BAM -g ce -n SRX330987.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX330987.05 # format = BAM # ChIP-seq file = ['SRX330987.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 12:34:34: #1 read tag files... INFO @ Tue, 27 Jun 2017 12:34:34: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 12:34:42: 1000000 INFO @ Tue, 27 Jun 2017 12:34:42: 1000000 INFO @ Tue, 27 Jun 2017 12:34:42: 1000000 INFO @ Tue, 27 Jun 2017 12:34:50: 2000000 INFO @ Tue, 27 Jun 2017 12:34:50: 2000000 INFO @ Tue, 27 Jun 2017 12:34:50: 2000000 INFO @ Tue, 27 Jun 2017 12:34:59: 3000000 INFO @ Tue, 27 Jun 2017 12:34:59: 3000000 INFO @ Tue, 27 Jun 2017 12:34:59: 3000000 INFO @ Tue, 27 Jun 2017 12:35:07: 4000000 INFO @ Tue, 27 Jun 2017 12:35:07: 4000000 INFO @ Tue, 27 Jun 2017 12:35:07: 4000000 INFO @ Tue, 27 Jun 2017 12:35:15: 5000000 INFO @ Tue, 27 Jun 2017 12:35:15: 5000000 INFO @ Tue, 27 Jun 2017 12:35:15: 5000000 INFO @ Tue, 27 Jun 2017 12:35:22: 6000000 INFO @ Tue, 27 Jun 2017 12:35:22: 6000000 INFO @ Tue, 27 Jun 2017 12:35:22: 6000000 INFO @ Tue, 27 Jun 2017 12:35:30: 7000000 INFO @ Tue, 27 Jun 2017 12:35:30: 7000000 INFO @ Tue, 27 Jun 2017 12:35:30: 7000000 INFO @ Tue, 27 Jun 2017 12:35:38: 8000000 INFO @ Tue, 27 Jun 2017 12:35:38: 8000000 INFO @ Tue, 27 Jun 2017 12:35:38: 8000000 INFO @ Tue, 27 Jun 2017 12:35:46: 9000000 INFO @ Tue, 27 Jun 2017 12:35:46: 9000000 INFO @ Tue, 27 Jun 2017 12:35:46: 9000000 INFO @ Tue, 27 Jun 2017 12:35:54: 10000000 INFO @ Tue, 27 Jun 2017 12:35:54: 10000000 INFO @ Tue, 27 Jun 2017 12:35:54: 10000000 INFO @ Tue, 27 Jun 2017 12:36:01: 11000000 INFO @ Tue, 27 Jun 2017 12:36:01: 11000000 INFO @ Tue, 27 Jun 2017 12:36:01: 11000000 INFO @ Tue, 27 Jun 2017 12:36:09: 12000000 INFO @ Tue, 27 Jun 2017 12:36:09: 12000000 INFO @ Tue, 27 Jun 2017 12:36:09: 12000000 INFO @ Tue, 27 Jun 2017 12:36:17: 13000000 INFO @ Tue, 27 Jun 2017 12:36:17: 13000000 INFO @ Tue, 27 Jun 2017 12:36:17: 13000000 INFO @ Tue, 27 Jun 2017 12:36:23: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 12:36:23: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 12:36:23: #1 total tags in treatment: 13709062 INFO @ Tue, 27 Jun 2017 12:36:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:36:23: #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 12:36:23: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 12:36:23: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 12:36:23: #1 total tags in treatment: 13709062 INFO @ Tue, 27 Jun 2017 12:36:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:36:23: #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 12:36:23: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 12:36:23: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 12:36:23: #1 total tags in treatment: 13709062 INFO @ Tue, 27 Jun 2017 12:36:23: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 12:36:23: #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 12:36:23: #1 tags after filtering in treatment: 13709062 INFO @ Tue, 27 Jun 2017 12:36:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:36:23: #1 finished! INFO @ Tue, 27 Jun 2017 12:36:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:36:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:36:23: #1 tags after filtering in treatment: 13709062 INFO @ Tue, 27 Jun 2017 12:36:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:36:23: #1 finished! INFO @ Tue, 27 Jun 2017 12:36:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:36:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:36:23: #1 tags after filtering in treatment: 13709062 INFO @ Tue, 27 Jun 2017 12:36:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 12:36:23: #1 finished! INFO @ Tue, 27 Jun 2017 12:36:23: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 12:36:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 12:36:24: #2 number of paired peaks: 907 WARNING @ Tue, 27 Jun 2017 12:36:24: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Tue, 27 Jun 2017 12:36:24: #2 number of paired peaks: 907 INFO @ Tue, 27 Jun 2017 12:36:24: start model_add_line... WARNING @ Tue, 27 Jun 2017 12:36:24: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Tue, 27 Jun 2017 12:36:24: start model_add_line... INFO @ Tue, 27 Jun 2017 12:36:24: #2 number of paired peaks: 907 WARNING @ Tue, 27 Jun 2017 12:36:24: Fewer paired peaks (907) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 907 pairs to build model! INFO @ Tue, 27 Jun 2017 12:36:24: start model_add_line... INFO @ Tue, 27 Jun 2017 12:36:24: start X-correlation... INFO @ Tue, 27 Jun 2017 12:36:24: start X-correlation... INFO @ Tue, 27 Jun 2017 12:36:24: end of X-cor INFO @ Tue, 27 Jun 2017 12:36:24: end of X-cor INFO @ Tue, 27 Jun 2017 12:36:24: #2 finished! INFO @ Tue, 27 Jun 2017 12:36:24: #2 finished! INFO @ Tue, 27 Jun 2017 12:36:24: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:36:24: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:36:24: #2 alternative fragment length(s) may be 1,16,35,573,590 bps INFO @ Tue, 27 Jun 2017 12:36:24: #2 alternative fragment length(s) may be 1,16,35,573,590 bps INFO @ Tue, 27 Jun 2017 12:36:24: #2.2 Generate R script for model : SRX330987.05_model.r INFO @ Tue, 27 Jun 2017 12:36:24: #2.2 Generate R script for model : SRX330987.20_model.r WARNING @ Tue, 27 Jun 2017 12:36:24: #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 12:36:24: #2 You may need to consider one of the other alternative d(s): 1,16,35,573,590 WARNING @ Tue, 27 Jun 2017 12:36:24: #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 12:36:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Tue, 27 Jun 2017 12:36:24: #2 You may need to consider one of the other alternative d(s): 1,16,35,573,590 INFO @ Tue, 27 Jun 2017 12:36:24: #3 Call peaks... WARNING @ Tue, 27 Jun 2017 12:36:24: #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 12:36:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:36:24: start X-correlation... INFO @ Tue, 27 Jun 2017 12:36:24: end of X-cor INFO @ Tue, 27 Jun 2017 12:36:24: #2 finished! INFO @ Tue, 27 Jun 2017 12:36:24: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 12:36:24: #2 alternative fragment length(s) may be 1,16,35,573,590 bps INFO @ Tue, 27 Jun 2017 12:36:24: #2.2 Generate R script for model : SRX330987.10_model.r WARNING @ Tue, 27 Jun 2017 12:36:24: #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 12:36:24: #2 You may need to consider one of the other alternative d(s): 1,16,35,573,590 WARNING @ Tue, 27 Jun 2017 12:36:24: #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 12:36:24: #3 Call peaks... INFO @ Tue, 27 Jun 2017 12:36:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:36:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:36:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 12:36:48: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:36:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:36:50: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 12:37:01: #4 Write output xls file... SRX330987.05_peaks.xls INFO @ Tue, 27 Jun 2017 12:37:01: #4 Write peak in narrowPeak format file... SRX330987.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:37:01: #4 Write summits bed file... SRX330987.05_summits.bed INFO @ Tue, 27 Jun 2017 12:37:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:37:03: #4 Write output xls file... SRX330987.10_peaks.xls INFO @ Tue, 27 Jun 2017 12:37:03: #4 Write peak in narrowPeak format file... SRX330987.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:37:03: #4 Write summits bed file... SRX330987.10_summits.bed INFO @ Tue, 27 Jun 2017 12:37:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 12:37:05: #4 Write output xls file... SRX330987.20_peaks.xls INFO @ Tue, 27 Jun 2017 12:37:05: #4 Write peak in narrowPeak format file... SRX330987.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 12:37:05: #4 Write summits bed file... SRX330987.20_summits.bed INFO @ Tue, 27 Jun 2017 12:37:05: 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。