Job ID = 10480711 sra ファイルのダウンロード中... Completed: 603821K bytes transferred in 15 seconds (312254K bits/sec), in 1 file. 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 19111552 spots for /home/okishinya/chipatlas/results/dm3/SRX3068982/SRR5907458.sra Written 19111552 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:00:01 Multiseed full-index search: 00:05:55 19111552 reads; of these: 19111552 (100.00%) were unpaired; of these: 2382764 (12.47%) aligned 0 times 14064968 (73.59%) aligned exactly 1 time 2663820 (13.94%) aligned >1 times 87.53% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5969264 / 16728788 = 0.3568 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 @ Fri, 16 Mar 2018 07:53:01: # Command line: callpeak -t SRX3068982.bam -f BAM -g dm -n SRX3068982.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068982.05 # format = BAM # ChIP-seq file = ['SRX3068982.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 16 Mar 2018 07:53:01: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:53:01: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:53:01: # Command line: callpeak -t SRX3068982.bam -f BAM -g dm -n SRX3068982.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068982.20 # format = BAM # ChIP-seq file = ['SRX3068982.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 16 Mar 2018 07:53:01: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:53:01: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:53:01: # Command line: callpeak -t SRX3068982.bam -f BAM -g dm -n SRX3068982.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068982.10 # format = BAM # ChIP-seq file = ['SRX3068982.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 16 Mar 2018 07:53:01: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:53:01: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:53:07: 1000000 INFO @ Fri, 16 Mar 2018 07:53:07: 1000000 INFO @ Fri, 16 Mar 2018 07:53:07: 1000000 INFO @ Fri, 16 Mar 2018 07:53:14: 2000000 INFO @ Fri, 16 Mar 2018 07:53:14: 2000000 INFO @ Fri, 16 Mar 2018 07:53:14: 2000000 INFO @ Fri, 16 Mar 2018 07:53:20: 3000000 INFO @ Fri, 16 Mar 2018 07:53:20: 3000000 INFO @ Fri, 16 Mar 2018 07:53:21: 3000000 INFO @ Fri, 16 Mar 2018 07:53:26: 4000000 INFO @ Fri, 16 Mar 2018 07:53:27: 4000000 INFO @ Fri, 16 Mar 2018 07:53:27: 4000000 INFO @ Fri, 16 Mar 2018 07:53:33: 5000000 INFO @ Fri, 16 Mar 2018 07:53:34: 5000000 INFO @ Fri, 16 Mar 2018 07:53:34: 5000000 INFO @ Fri, 16 Mar 2018 07:53:40: 6000000 INFO @ Fri, 16 Mar 2018 07:53:41: 6000000 INFO @ Fri, 16 Mar 2018 07:53:41: 6000000 INFO @ Fri, 16 Mar 2018 07:53:46: 7000000 INFO @ Fri, 16 Mar 2018 07:53:48: 7000000 INFO @ Fri, 16 Mar 2018 07:53:48: 7000000 INFO @ Fri, 16 Mar 2018 07:53:52: 8000000 INFO @ Fri, 16 Mar 2018 07:53:54: 8000000 INFO @ Fri, 16 Mar 2018 07:53:55: 8000000 INFO @ Fri, 16 Mar 2018 07:53:59: 9000000 INFO @ Fri, 16 Mar 2018 07:54:01: 9000000 INFO @ Fri, 16 Mar 2018 07:54:01: 9000000 INFO @ Fri, 16 Mar 2018 07:54:06: 10000000 INFO @ Fri, 16 Mar 2018 07:54:08: 10000000 INFO @ Fri, 16 Mar 2018 07:54:08: 10000000 INFO @ Fri, 16 Mar 2018 07:54:12: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:54:12: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:54:12: #1 total tags in treatment: 10759524 INFO @ Fri, 16 Mar 2018 07:54:12: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:54:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:54:12: #1 tags after filtering in treatment: 10759524 INFO @ Fri, 16 Mar 2018 07:54:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:54:12: #1 finished! INFO @ Fri, 16 Mar 2018 07:54:12: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:54:13: #2 number of paired peaks: 888 WARNING @ Fri, 16 Mar 2018 07:54:13: Fewer paired peaks (888) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 888 pairs to build model! INFO @ Fri, 16 Mar 2018 07:54:13: start model_add_line... INFO @ Fri, 16 Mar 2018 07:54:13: start X-correlation... INFO @ Fri, 16 Mar 2018 07:54:13: end of X-cor INFO @ Fri, 16 Mar 2018 07:54:13: #2 finished! INFO @ Fri, 16 Mar 2018 07:54:13: #2 predicted fragment length is 123 bps INFO @ Fri, 16 Mar 2018 07:54:13: #2 alternative fragment length(s) may be 123 bps INFO @ Fri, 16 Mar 2018 07:54:13: #2.2 Generate R script for model : SRX3068982.10_model.r INFO @ Fri, 16 Mar 2018 07:54:13: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:54:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:54:14: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:54:14: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:54:14: #1 total tags in treatment: 10759524 INFO @ Fri, 16 Mar 2018 07:54:14: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:54:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:54:14: #1 tags after filtering in treatment: 10759524 INFO @ Fri, 16 Mar 2018 07:54:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:54:14: #1 finished! INFO @ Fri, 16 Mar 2018 07:54:14: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:54:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:54:15: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:54:15: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:54:15: #1 total tags in treatment: 10759524 INFO @ Fri, 16 Mar 2018 07:54:15: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:54:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:54:15: #1 tags after filtering in treatment: 10759524 INFO @ Fri, 16 Mar 2018 07:54:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:54:15: #1 finished! INFO @ Fri, 16 Mar 2018 07:54:15: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:54:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:54:15: #2 number of paired peaks: 888 WARNING @ Fri, 16 Mar 2018 07:54:15: Fewer paired peaks (888) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 888 pairs to build model! INFO @ Fri, 16 Mar 2018 07:54:15: start model_add_line... INFO @ Fri, 16 Mar 2018 07:54:15: start X-correlation... INFO @ Fri, 16 Mar 2018 07:54:15: end of X-cor INFO @ Fri, 16 Mar 2018 07:54:15: #2 finished! INFO @ Fri, 16 Mar 2018 07:54:15: #2 predicted fragment length is 123 bps INFO @ Fri, 16 Mar 2018 07:54:15: #2 alternative fragment length(s) may be 123 bps INFO @ Fri, 16 Mar 2018 07:54:15: #2.2 Generate R script for model : SRX3068982.20_model.r INFO @ Fri, 16 Mar 2018 07:54:15: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:54:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:54:16: #2 number of paired peaks: 888 WARNING @ Fri, 16 Mar 2018 07:54:16: Fewer paired peaks (888) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 888 pairs to build model! INFO @ Fri, 16 Mar 2018 07:54:16: start model_add_line... INFO @ Fri, 16 Mar 2018 07:54:16: start X-correlation... INFO @ Fri, 16 Mar 2018 07:54:16: end of X-cor INFO @ Fri, 16 Mar 2018 07:54:16: #2 finished! INFO @ Fri, 16 Mar 2018 07:54:16: #2 predicted fragment length is 123 bps INFO @ Fri, 16 Mar 2018 07:54:16: #2 alternative fragment length(s) may be 123 bps INFO @ Fri, 16 Mar 2018 07:54:16: #2.2 Generate R script for model : SRX3068982.05_model.r INFO @ Fri, 16 Mar 2018 07:54:16: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:54:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:54:40: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:54:40: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:54:40: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:54:53: #4 Write output xls file... SRX3068982.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:54:53: #4 Write peak in narrowPeak format file... SRX3068982.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:54:53: #4 Write summits bed file... SRX3068982.20_summits.bed INFO @ Fri, 16 Mar 2018 07:54:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2911 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:54:54: #4 Write output xls file... SRX3068982.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:54:54: #4 Write peak in narrowPeak format file... SRX3068982.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:54:54: #4 Write summits bed file... SRX3068982.05_summits.bed INFO @ Fri, 16 Mar 2018 07:54:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9457 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:54:56: #4 Write output xls file... SRX3068982.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:54:56: #4 Write peak in narrowPeak format file... SRX3068982.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:54:57: #4 Write summits bed file... SRX3068982.10_summits.bed INFO @ Fri, 16 Mar 2018 07:54:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6254 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。