Job ID = 10609080 sra ファイルのダウンロード中... Completed: 57348K bytes transferred in 10 seconds (43592K 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... Read 1439839 spots for /home/okishinya/chipatlas/results/dm3/SRX2504293/SRR5188371.sra Written 1439839 spots for /home/okishinya/chipatlas/results/dm3/SRX2504293/SRR5188371.sra 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:27 1439839 reads; of these: 1439839 (100.00%) were unpaired; of these: 241 (0.02%) aligned 0 times 1364781 (94.79%) aligned exactly 1 time 74817 (5.20%) aligned >1 times 99.98% overall alignment rate Time searching: 00:00:28 Overall time: 00:00:28 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_rmdupse_core] 902 / 1439598 = 0.0006 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, 04 May 2018 07:00:28: # Command line: callpeak -t SRX2504293.bam -f BAM -g dm -n SRX2504293.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2504293.05 # format = BAM # ChIP-seq file = ['SRX2504293.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, 04 May 2018 07:00:28: #1 read tag files... INFO @ Fri, 04 May 2018 07:00:28: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:00:28: # Command line: callpeak -t SRX2504293.bam -f BAM -g dm -n SRX2504293.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2504293.20 # format = BAM # ChIP-seq file = ['SRX2504293.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, 04 May 2018 07:00:28: #1 read tag files... INFO @ Fri, 04 May 2018 07:00:28: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:00:28: # Command line: callpeak -t SRX2504293.bam -f BAM -g dm -n SRX2504293.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2504293.10 # format = BAM # ChIP-seq file = ['SRX2504293.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, 04 May 2018 07:00:28: #1 read tag files... INFO @ Fri, 04 May 2018 07:00:28: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:00:36: 1000000 INFO @ Fri, 04 May 2018 07:00:36: 1000000 INFO @ Fri, 04 May 2018 07:00:36: 1000000 INFO @ Fri, 04 May 2018 07:00:39: #1 tag size is determined as 75 bps INFO @ Fri, 04 May 2018 07:00:39: #1 tag size = 75 INFO @ Fri, 04 May 2018 07:00:39: #1 total tags in treatment: 1438696 INFO @ Fri, 04 May 2018 07:00:39: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:00:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:00:39: #1 tags after filtering in treatment: 1438696 INFO @ Fri, 04 May 2018 07:00:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:00:39: #1 finished! INFO @ Fri, 04 May 2018 07:00:39: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:00:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:00:39: #1 tag size is determined as 75 bps INFO @ Fri, 04 May 2018 07:00:39: #1 tag size = 75 INFO @ Fri, 04 May 2018 07:00:39: #1 total tags in treatment: 1438696 INFO @ Fri, 04 May 2018 07:00:39: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:00:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:00:39: #1 tags after filtering in treatment: 1438696 INFO @ Fri, 04 May 2018 07:00:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:00:39: #1 finished! INFO @ Fri, 04 May 2018 07:00:39: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:00:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:00:39: #2 number of paired peaks: 230 WARNING @ Fri, 04 May 2018 07:00:39: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Fri, 04 May 2018 07:00:39: start model_add_line... INFO @ Fri, 04 May 2018 07:00:39: start X-correlation... INFO @ Fri, 04 May 2018 07:00:39: end of X-cor INFO @ Fri, 04 May 2018 07:00:39: #2 finished! INFO @ Fri, 04 May 2018 07:00:39: #2 predicted fragment length is 180 bps INFO @ Fri, 04 May 2018 07:00:39: #2 alternative fragment length(s) may be 57,107,180,288 bps INFO @ Fri, 04 May 2018 07:00:39: #2.2 Generate R script for model : SRX2504293.20_model.r INFO @ Fri, 04 May 2018 07:00:39: #3 Call peaks... INFO @ Fri, 04 May 2018 07:00:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:00:39: #1 tag size is determined as 75 bps INFO @ Fri, 04 May 2018 07:00:39: #1 tag size = 75 INFO @ Fri, 04 May 2018 07:00:39: #1 total tags in treatment: 1438696 INFO @ Fri, 04 May 2018 07:00:39: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:00:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:00:39: #2 number of paired peaks: 230 WARNING @ Fri, 04 May 2018 07:00:39: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Fri, 04 May 2018 07:00:39: start model_add_line... INFO @ Fri, 04 May 2018 07:00:39: #1 tags after filtering in treatment: 1438696 INFO @ Fri, 04 May 2018 07:00:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:00:39: #1 finished! INFO @ Fri, 04 May 2018 07:00:39: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:00:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:00:39: start X-correlation... INFO @ Fri, 04 May 2018 07:00:39: end of X-cor INFO @ Fri, 04 May 2018 07:00:39: #2 finished! INFO @ Fri, 04 May 2018 07:00:39: #2 predicted fragment length is 180 bps INFO @ Fri, 04 May 2018 07:00:39: #2 alternative fragment length(s) may be 57,107,180,288 bps INFO @ Fri, 04 May 2018 07:00:39: #2.2 Generate R script for model : SRX2504293.05_model.r INFO @ Fri, 04 May 2018 07:00:39: #3 Call peaks... INFO @ Fri, 04 May 2018 07:00:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:00:39: #2 number of paired peaks: 230 WARNING @ Fri, 04 May 2018 07:00:39: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Fri, 04 May 2018 07:00:39: start model_add_line... INFO @ Fri, 04 May 2018 07:00:39: start X-correlation... INFO @ Fri, 04 May 2018 07:00:39: end of X-cor INFO @ Fri, 04 May 2018 07:00:39: #2 finished! INFO @ Fri, 04 May 2018 07:00:39: #2 predicted fragment length is 180 bps INFO @ Fri, 04 May 2018 07:00:39: #2 alternative fragment length(s) may be 57,107,180,288 bps INFO @ Fri, 04 May 2018 07:00:39: #2.2 Generate R script for model : SRX2504293.10_model.r INFO @ Fri, 04 May 2018 07:00:39: #3 Call peaks... INFO @ Fri, 04 May 2018 07:00:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:00:42: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:00:42: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:00:43: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:00:44: #4 Write output xls file... SRX2504293.20_peaks.xls INFO @ Fri, 04 May 2018 07:00:44: #4 Write peak in narrowPeak format file... SRX2504293.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:00:44: #4 Write summits bed file... SRX2504293.20_summits.bed INFO @ Fri, 04 May 2018 07:00:44: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:00:44: #4 Write output xls file... SRX2504293.10_peaks.xls INFO @ Fri, 04 May 2018 07:00:44: #4 Write peak in narrowPeak format file... SRX2504293.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:00:44: #4 Write summits bed file... SRX2504293.10_summits.bed INFO @ Fri, 04 May 2018 07:00:44: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (34 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:00:44: #4 Write output xls file... SRX2504293.05_peaks.xls INFO @ Fri, 04 May 2018 07:00:44: #4 Write peak in narrowPeak format file... SRX2504293.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:00:44: #4 Write summits bed file... SRX2504293.05_summits.bed INFO @ Fri, 04 May 2018 07:00:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (73 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。