Job ID = 9157150 sra ファイルのダウンロード中... Completed: 438670K bytes transferred in 6 seconds (540522K 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 19204008 spots for /home/okishinya/chipatlas/results/ce10/SRX2228879/SRR4380335.sra Written 19204008 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: 00:02:49 19204008 reads; of these: 19204008 (100.00%) were unpaired; of these: 12927682 (67.32%) aligned 0 times 5179270 (26.97%) aligned exactly 1 time 1097056 (5.71%) aligned >1 times 32.68% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 869411 / 6276326 = 0.1385 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 10:50:39: # Command line: callpeak -t SRX2228879.bam -f BAM -g ce -n SRX2228879.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228879.05 # format = BAM # ChIP-seq file = ['SRX2228879.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 10:50:39: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:50:39: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:50:39: # Command line: callpeak -t SRX2228879.bam -f BAM -g ce -n SRX2228879.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228879.20 # format = BAM # ChIP-seq file = ['SRX2228879.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 10:50:39: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:50:39: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:50:39: # Command line: callpeak -t SRX2228879.bam -f BAM -g ce -n SRX2228879.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228879.10 # format = BAM # ChIP-seq file = ['SRX2228879.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 10:50:39: #1 read tag files... INFO @ Tue, 27 Jun 2017 10:50:39: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 10:50:46: 1000000 INFO @ Tue, 27 Jun 2017 10:50:46: 1000000 INFO @ Tue, 27 Jun 2017 10:50:47: 1000000 INFO @ Tue, 27 Jun 2017 10:50:52: 2000000 INFO @ Tue, 27 Jun 2017 10:50:53: 2000000 INFO @ Tue, 27 Jun 2017 10:50:54: 2000000 INFO @ Tue, 27 Jun 2017 10:50:59: 3000000 INFO @ Tue, 27 Jun 2017 10:51:01: 3000000 INFO @ Tue, 27 Jun 2017 10:51:02: 3000000 INFO @ Tue, 27 Jun 2017 10:51:05: 4000000 INFO @ Tue, 27 Jun 2017 10:51:08: 4000000 INFO @ Tue, 27 Jun 2017 10:51:10: 4000000 INFO @ Tue, 27 Jun 2017 10:51:11: 5000000 INFO @ Tue, 27 Jun 2017 10:51:14: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:51:14: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:51:14: #1 total tags in treatment: 5406915 INFO @ Tue, 27 Jun 2017 10:51:14: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:51:14: #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 10:51:14: #1 tags after filtering in treatment: 5406915 INFO @ Tue, 27 Jun 2017 10:51:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:51:14: #1 finished! INFO @ Tue, 27 Jun 2017 10:51:14: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:51:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:51:14: #2 number of paired peaks: 756 WARNING @ Tue, 27 Jun 2017 10:51:14: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Tue, 27 Jun 2017 10:51:14: start model_add_line... INFO @ Tue, 27 Jun 2017 10:51:14: start X-correlation... INFO @ Tue, 27 Jun 2017 10:51:14: end of X-cor INFO @ Tue, 27 Jun 2017 10:51:14: #2 finished! INFO @ Tue, 27 Jun 2017 10:51:14: #2 predicted fragment length is 112 bps INFO @ Tue, 27 Jun 2017 10:51:14: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 27 Jun 2017 10:51:14: #2.2 Generate R script for model : SRX2228879.20_model.r INFO @ Tue, 27 Jun 2017 10:51:14: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:51:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:51:15: 5000000 INFO @ Tue, 27 Jun 2017 10:51:17: 5000000 INFO @ Tue, 27 Jun 2017 10:51:18: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:51:18: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:51:18: #1 total tags in treatment: 5406915 INFO @ Tue, 27 Jun 2017 10:51:18: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:51:18: #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 10:51:18: #1 tags after filtering in treatment: 5406915 INFO @ Tue, 27 Jun 2017 10:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:51:18: #1 finished! INFO @ Tue, 27 Jun 2017 10:51:18: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:51:19: #2 number of paired peaks: 756 WARNING @ Tue, 27 Jun 2017 10:51:19: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Tue, 27 Jun 2017 10:51:19: start model_add_line... INFO @ Tue, 27 Jun 2017 10:51:19: start X-correlation... INFO @ Tue, 27 Jun 2017 10:51:19: end of X-cor INFO @ Tue, 27 Jun 2017 10:51:19: #2 finished! INFO @ Tue, 27 Jun 2017 10:51:19: #2 predicted fragment length is 112 bps INFO @ Tue, 27 Jun 2017 10:51:19: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 27 Jun 2017 10:51:19: #2.2 Generate R script for model : SRX2228879.10_model.r INFO @ Tue, 27 Jun 2017 10:51:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:51:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:51:20: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 10:51:20: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 10:51:20: #1 total tags in treatment: 5406915 INFO @ Tue, 27 Jun 2017 10:51:20: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 10:51:20: #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 10:51:20: #1 tags after filtering in treatment: 5406915 INFO @ Tue, 27 Jun 2017 10:51:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 10:51:20: #1 finished! INFO @ Tue, 27 Jun 2017 10:51:20: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 10:51:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 10:51:21: #2 number of paired peaks: 756 WARNING @ Tue, 27 Jun 2017 10:51:21: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Tue, 27 Jun 2017 10:51:21: start model_add_line... INFO @ Tue, 27 Jun 2017 10:51:21: start X-correlation... INFO @ Tue, 27 Jun 2017 10:51:21: end of X-cor INFO @ Tue, 27 Jun 2017 10:51:21: #2 finished! INFO @ Tue, 27 Jun 2017 10:51:21: #2 predicted fragment length is 112 bps INFO @ Tue, 27 Jun 2017 10:51:21: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 27 Jun 2017 10:51:21: #2.2 Generate R script for model : SRX2228879.05_model.r INFO @ Tue, 27 Jun 2017 10:51:21: #3 Call peaks... INFO @ Tue, 27 Jun 2017 10:51:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 10:51:28: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:51:32: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:51:34: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 10:51:36: #4 Write output xls file... SRX2228879.20_peaks.xls INFO @ Tue, 27 Jun 2017 10:51:36: #4 Write peak in narrowPeak format file... SRX2228879.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:51:36: #4 Write summits bed file... SRX2228879.20_summits.bed INFO @ Tue, 27 Jun 2017 10:51:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (554 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:51:40: #4 Write output xls file... SRX2228879.10_peaks.xls INFO @ Tue, 27 Jun 2017 10:51:40: #4 Write peak in narrowPeak format file... SRX2228879.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:51:40: #4 Write summits bed file... SRX2228879.10_summits.bed INFO @ Tue, 27 Jun 2017 10:51:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1000 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 10:51:41: #4 Write output xls file... SRX2228879.05_peaks.xls INFO @ Tue, 27 Jun 2017 10:51:41: #4 Write peak in narrowPeak format file... SRX2228879.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 10:51:41: #4 Write summits bed file... SRX2228879.05_summits.bed INFO @ Tue, 27 Jun 2017 10:51:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1574 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。