Job ID = 9157167 sra ファイルのダウンロード中... Completed: 145440K bytes transferred in 4 seconds (262388K 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 6864509 spots for /home/okishinya/chipatlas/results/ce10/SRX2228889/SRR4380345.sra Written 6864509 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: 00:01:43 6864509 reads; of these: 6864509 (100.00%) were unpaired; of these: 621156 (9.05%) aligned 0 times 5175801 (75.40%) aligned exactly 1 time 1067552 (15.55%) aligned >1 times 90.95% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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_rmdupse_core] 951877 / 6243353 = 0.1525 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 10:52:41: # Command line: callpeak -t SRX2228889.bam -f BAM -g ce -n SRX2228889.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228889.05 # format = BAM # ChIP-seq file = ['SRX2228889.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 10:52:41: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:52:41: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:52:41: # Command line: callpeak -t SRX2228889.bam -f BAM -g ce -n SRX2228889.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228889.10 # format = BAM # ChIP-seq file = ['SRX2228889.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 10:52:41: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:52:41: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:52:41: # Command line: callpeak -t SRX2228889.bam -f BAM -g ce -n SRX2228889.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228889.20 # format = BAM # ChIP-seq file = ['SRX2228889.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 10:52:41: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:52:41: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:52:47: 1000000 INFO @ Tue, 27 Jun 2017 10:52:48: 1000000 INFO @ Tue, 27 Jun 2017 10:52:48: 1000000 INFO @ Tue, 27 Jun 2017 10:52:54: 2000000 INFO @ Tue, 27 Jun 2017 10:52:56: 2000000 INFO @ Tue, 27 Jun 2017 10:52:56: 2000000 INFO @ Tue, 27 Jun 2017 10:53:01: 3000000 INFO @ Tue, 27 Jun 2017 10:53:03: 3000000 INFO @ Tue, 27 Jun 2017 10:53:03: 3000000 INFO @ Tue, 27 Jun 2017 10:53:08: 4000000 INFO @ Tue, 27 Jun 2017 10:53:11: 4000000 INFO @ Tue, 27 Jun 2017 10:53:11: 4000000 INFO @ Tue, 27 Jun 2017 10:53:14: 5000000 INFO @ Tue, 27 Jun 2017 10:53:16: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:53:16: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:53:16: #1 total tags in treatment: 5291476 INFO @ Tue, 27 Jun 2017 10:53:16: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:53:16: #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 10:53:16: #1 tags after filtering in treatment: 5291476 INFO @ Tue, 27 Jun 2017 10:53:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:53:16: #1 finished! INFO @ Tue, 27 Jun 2017 10:53:16: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:53:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:53:17: #2 number of paired peaks: 653 WARNING @ Tue, 27 Jun 2017 10:53:17: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Tue, 27 Jun 2017 10:53:17: start model_add_line... INFO @ Tue, 27 Jun 2017 10:53:17: start X-correlation... INFO @ Tue, 27 Jun 2017 10:53:17: end of X-cor INFO @ Tue, 27 Jun 2017 10:53:17: #2 finished! INFO @ Tue, 27 Jun 2017 10:53:17: #2 predicted fragment length is 114 bps INFO @ Tue, 27 Jun 2017 10:53:17: #2 alternative fragment length(s) may be 114 bps INFO @ Tue, 27 Jun 2017 10:53:17: #2.2 Generate R script for model : SRX2228889.05_model.r INFO @ Tue, 27 Jun 2017 10:53:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:53:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:53:18: 5000000 INFO @ Tue, 27 Jun 2017 10:53:18: 5000000 INFO @ Tue, 27 Jun 2017 10:53:20: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:53:20: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:53:20: #1 total tags in treatment: 5291476 INFO @ Tue, 27 Jun 2017 10:53:20: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:53:20: #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 10:53:20: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:53:20: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:53:20: #1 total tags in treatment: 5291476 INFO @ Tue, 27 Jun 2017 10:53:20: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:53:20: #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 10:53:20: #1 tags after filtering in treatment: 5291476 INFO @ Tue, 27 Jun 2017 10:53:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:53:20: #1 finished! INFO @ Tue, 27 Jun 2017 10:53:20: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:53:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:53:20: #1 tags after filtering in treatment: 5291476 INFO @ Tue, 27 Jun 2017 10:53:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:53:20: #1 finished! INFO @ Tue, 27 Jun 2017 10:53:20: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:53:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:53:21: #2 number of paired peaks: 653 WARNING @ Tue, 27 Jun 2017 10:53:21: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Tue, 27 Jun 2017 10:53:21: start model_add_line... INFO @ Tue, 27 Jun 2017 10:53:21: #2 number of paired peaks: 653 WARNING @ Tue, 27 Jun 2017 10:53:21: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Tue, 27 Jun 2017 10:53:21: start model_add_line... INFO @ Tue, 27 Jun 2017 10:53:21: start X-correlation... INFO @ Tue, 27 Jun 2017 10:53:21: end of X-cor INFO @ Tue, 27 Jun 2017 10:53:21: #2 finished! INFO @ Tue, 27 Jun 2017 10:53:21: #2 predicted fragment length is 114 bps INFO @ Tue, 27 Jun 2017 10:53:21: #2 alternative fragment length(s) may be 114 bps INFO @ Tue, 27 Jun 2017 10:53:21: #2.2 Generate R script for model : SRX2228889.10_model.r INFO @ Tue, 27 Jun 2017 10:53:21: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:53:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:53:21: start X-correlation... INFO @ Tue, 27 Jun 2017 10:53:21: end of X-cor INFO @ Tue, 27 Jun 2017 10:53:21: #2 finished! INFO @ Tue, 27 Jun 2017 10:53:21: #2 predicted fragment length is 114 bps INFO @ Tue, 27 Jun 2017 10:53:21: #2 alternative fragment length(s) may be 114 bps INFO @ Tue, 27 Jun 2017 10:53:21: #2.2 Generate R script for model : SRX2228889.20_model.r INFO @ Tue, 27 Jun 2017 10:53:21: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:53:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:53:30: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:53:34: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:53:34: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:53:37: #4 Write output xls file... SRX2228889.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:53:37: #4 Write peak in narrowPeak format file... SRX2228889.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:53:37: #4 Write summits bed file... SRX2228889.05_summits.bed INFO @ Tue, 27 Jun 2017 10:53:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1600 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:53:41: #4 Write output xls file... SRX2228889.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:53:41: #4 Write peak in narrowPeak format file... SRX2228889.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:53:41: #4 Write summits bed file... SRX2228889.10_summits.bed INFO @ Tue, 27 Jun 2017 10:53:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (998 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:53:42: #4 Write output xls file... SRX2228889.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:53:42: #4 Write peak in narrowPeak format file... SRX2228889.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:53:42: #4 Write summits bed file... SRX2228889.20_summits.bed INFO @ Tue, 27 Jun 2017 10:53:42: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (558 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。