Job ID = 9157410 sra ファイルのダウンロード中... Completed: 311611K bytes transferred in 5 seconds (456792K 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 11387508 spots for /home/okishinya/chipatlas/results/ce10/SRX208776/SRR628910.sra Written 11387508 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: 00:04:08 11387508 reads; of these: 11387508 (100.00%) were unpaired; of these: 1211670 (10.64%) aligned 0 times 8803291 (77.31%) aligned exactly 1 time 1372547 (12.05%) aligned >1 times 89.36% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 5782714 / 10175838 = 0.5683 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 11:54:04: # Command line: callpeak -t SRX208776.bam -f BAM -g ce -n SRX208776.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208776.10 # format = BAM # ChIP-seq file = ['SRX208776.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 11:54:04: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:54:04: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:54:04: # Command line: callpeak -t SRX208776.bam -f BAM -g ce -n SRX208776.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208776.20 # format = BAM # ChIP-seq file = ['SRX208776.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 11:54:04: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:54:04: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:54:04: # Command line: callpeak -t SRX208776.bam -f BAM -g ce -n SRX208776.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208776.05 # format = BAM # ChIP-seq file = ['SRX208776.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 11:54:04: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:54:04: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:54:11: 1000000 INFO @ Tue, 27 Jun 2017 11:54:11: 1000000 INFO @ Tue, 27 Jun 2017 11:54:11: 1000000 INFO @ Tue, 27 Jun 2017 11:54:18: 2000000 INFO @ Tue, 27 Jun 2017 11:54:18: 2000000 INFO @ Tue, 27 Jun 2017 11:54:18: 2000000 INFO @ Tue, 27 Jun 2017 11:54:25: 3000000 INFO @ Tue, 27 Jun 2017 11:54:25: 3000000 INFO @ Tue, 27 Jun 2017 11:54:26: 3000000 INFO @ Tue, 27 Jun 2017 11:54:32: 4000000 INFO @ Tue, 27 Jun 2017 11:54:33: 4000000 INFO @ Tue, 27 Jun 2017 11:54:34: 4000000 INFO @ Tue, 27 Jun 2017 11:54:34: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:54:34: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:54:34: #1 total tags in treatment: 4393124 INFO @ Tue, 27 Jun 2017 11:54:34: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:54:34: #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 11:54:35: #1 tags after filtering in treatment: 4393124 INFO @ Tue, 27 Jun 2017 11:54:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:54:35: #1 finished! INFO @ Tue, 27 Jun 2017 11:54:35: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:54:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:54:35: #2 number of paired peaks: 341 WARNING @ Tue, 27 Jun 2017 11:54:35: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Tue, 27 Jun 2017 11:54:35: start model_add_line... INFO @ Tue, 27 Jun 2017 11:54:35: start X-correlation... INFO @ Tue, 27 Jun 2017 11:54:35: end of X-cor INFO @ Tue, 27 Jun 2017 11:54:35: #2 finished! INFO @ Tue, 27 Jun 2017 11:54:35: #2 predicted fragment length is 211 bps INFO @ Tue, 27 Jun 2017 11:54:35: #2 alternative fragment length(s) may be 211 bps INFO @ Tue, 27 Jun 2017 11:54:35: #2.2 Generate R script for model : SRX208776.05_model.r INFO @ Tue, 27 Jun 2017 11:54:35: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:54:36: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:54:36: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:54:36: #1 total tags in treatment: 4393124 INFO @ Tue, 27 Jun 2017 11:54:36: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:54:36: #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 11:54:36: #1 tags after filtering in treatment: 4393124 INFO @ Tue, 27 Jun 2017 11:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:54:36: #1 finished! INFO @ Tue, 27 Jun 2017 11:54:36: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:54:36: #2 number of paired peaks: 341 WARNING @ Tue, 27 Jun 2017 11:54:36: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Tue, 27 Jun 2017 11:54:36: start model_add_line... INFO @ Tue, 27 Jun 2017 11:54:36: start X-correlation... INFO @ Tue, 27 Jun 2017 11:54:36: end of X-cor INFO @ Tue, 27 Jun 2017 11:54:36: #2 finished! INFO @ Tue, 27 Jun 2017 11:54:36: #2 predicted fragment length is 211 bps INFO @ Tue, 27 Jun 2017 11:54:36: #2 alternative fragment length(s) may be 211 bps INFO @ Tue, 27 Jun 2017 11:54:36: #2.2 Generate R script for model : SRX208776.10_model.r INFO @ Tue, 27 Jun 2017 11:54:36: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:54:37: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 11:54:37: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 11:54:37: #1 total tags in treatment: 4393124 INFO @ Tue, 27 Jun 2017 11:54:37: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:54:37: #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 11:54:37: #1 tags after filtering in treatment: 4393124 INFO @ Tue, 27 Jun 2017 11:54:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:54:37: #1 finished! INFO @ Tue, 27 Jun 2017 11:54:37: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:54:37: #2 number of paired peaks: 341 WARNING @ Tue, 27 Jun 2017 11:54:37: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Tue, 27 Jun 2017 11:54:37: start model_add_line... INFO @ Tue, 27 Jun 2017 11:54:37: start X-correlation... INFO @ Tue, 27 Jun 2017 11:54:37: end of X-cor INFO @ Tue, 27 Jun 2017 11:54:37: #2 finished! INFO @ Tue, 27 Jun 2017 11:54:37: #2 predicted fragment length is 211 bps INFO @ Tue, 27 Jun 2017 11:54:37: #2 alternative fragment length(s) may be 211 bps INFO @ Tue, 27 Jun 2017 11:54:37: #2.2 Generate R script for model : SRX208776.20_model.r INFO @ Tue, 27 Jun 2017 11:54:37: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:54:46: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:54:47: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:54:48: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:54:51: #4 Write output xls file... SRX208776.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:54:51: #4 Write peak in narrowPeak format file... SRX208776.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:54:51: #4 Write summits bed file... SRX208776.05_summits.bed INFO @ Tue, 27 Jun 2017 11:54:51: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (866 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:54:53: #4 Write output xls file... SRX208776.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:54:53: #4 Write peak in narrowPeak format file... SRX208776.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:54:53: #4 Write summits bed file... SRX208776.10_summits.bed INFO @ Tue, 27 Jun 2017 11:54:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (532 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:54:54: #4 Write output xls file... SRX208776.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:54:54: #4 Write peak in narrowPeak format file... SRX208776.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:54:54: #4 Write summits bed file... SRX208776.20_summits.bed INFO @ Tue, 27 Jun 2017 11:54:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (256 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。