Job ID = 11633519 sra ファイルのダウンロード中... Completed: 37274K bytes transferred in 3 seconds (91318K 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: PAIRED fastq に変換中... Read 529716 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236296/ERR1162889.sra Written 529716 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236296/ERR1162889.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:25 529716 reads; of these: 529716 (100.00%) were paired; of these: 44946 (8.48%) aligned concordantly 0 times 426046 (80.43%) aligned concordantly exactly 1 time 58724 (11.09%) aligned concordantly >1 times ---- 44946 pairs aligned concordantly 0 times; of these: 1121 (2.49%) aligned discordantly 1 time ---- 43825 pairs aligned 0 times concordantly or discordantly; of these: 87650 mates make up the pairs; of these: 84833 (96.79%) aligned 0 times 2181 (2.49%) aligned exactly 1 time 636 (0.73%) aligned >1 times 91.99% overall alignment rate Time searching: 00:00:25 Overall time: 00:00:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 55770 / 485659 = 0.1148 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, 15 Feb 2019 09:00:06: # Command line: callpeak -t ERX1236296.bam -f BAM -g 12100000 -n ERX1236296.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236296.10 # format = BAM # ChIP-seq file = ['ERX1236296.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 15 Feb 2019 09:00:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:00:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:00:06: # Command line: callpeak -t ERX1236296.bam -f BAM -g 12100000 -n ERX1236296.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236296.05 # format = BAM # ChIP-seq file = ['ERX1236296.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 15 Feb 2019 09:00:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:00:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:00:06: # Command line: callpeak -t ERX1236296.bam -f BAM -g 12100000 -n ERX1236296.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236296.20 # format = BAM # ChIP-seq file = ['ERX1236296.bam'] # control file = None # effective genome size = 1.21e+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 @ Fri, 15 Feb 2019 09:00:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:00:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:00:11: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:00:11: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:00:11: #1 total tags in treatment: 429045 INFO @ Fri, 15 Feb 2019 09:00:11: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:00:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:00:11: #1 tags after filtering in treatment: 412481 INFO @ Fri, 15 Feb 2019 09:00:11: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 15 Feb 2019 09:00:11: #1 finished! INFO @ Fri, 15 Feb 2019 09:00:11: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:00:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:00:12: #2 number of paired peaks: 318 WARNING @ Fri, 15 Feb 2019 09:00:12: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Fri, 15 Feb 2019 09:00:12: start model_add_line... INFO @ Fri, 15 Feb 2019 09:00:12: start X-correlation... INFO @ Fri, 15 Feb 2019 09:00:12: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:00:12: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:00:12: #1 total tags in treatment: 429045 INFO @ Fri, 15 Feb 2019 09:00:12: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:00:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:00:12: #1 tags after filtering in treatment: 412481 INFO @ Fri, 15 Feb 2019 09:00:12: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 15 Feb 2019 09:00:12: #1 finished! INFO @ Fri, 15 Feb 2019 09:00:12: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:00:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:00:12: #2 number of paired peaks: 318 WARNING @ Fri, 15 Feb 2019 09:00:12: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Fri, 15 Feb 2019 09:00:12: start model_add_line... INFO @ Fri, 15 Feb 2019 09:00:12: start X-correlation... INFO @ Fri, 15 Feb 2019 09:00:12: end of X-cor INFO @ Fri, 15 Feb 2019 09:00:12: #2 finished! INFO @ Fri, 15 Feb 2019 09:00:12: #2 predicted fragment length is 184 bps INFO @ Fri, 15 Feb 2019 09:00:12: #2 alternative fragment length(s) may be 127,162,184,214 bps INFO @ Fri, 15 Feb 2019 09:00:12: #2.2 Generate R script for model : ERX1236296.05_model.r INFO @ Fri, 15 Feb 2019 09:00:12: end of X-cor INFO @ Fri, 15 Feb 2019 09:00:12: #2 finished! INFO @ Fri, 15 Feb 2019 09:00:12: #2 predicted fragment length is 184 bps INFO @ Fri, 15 Feb 2019 09:00:12: #2 alternative fragment length(s) may be 127,162,184,214 bps INFO @ Fri, 15 Feb 2019 09:00:12: #2.2 Generate R script for model : ERX1236296.20_model.r INFO @ Fri, 15 Feb 2019 09:00:12: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:00:12: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:00:12: #1 total tags in treatment: 429045 INFO @ Fri, 15 Feb 2019 09:00:12: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:00:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:00:12: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:00:12: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:00:12: #1 tags after filtering in treatment: 412481 INFO @ Fri, 15 Feb 2019 09:00:12: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 15 Feb 2019 09:00:12: #1 finished! INFO @ Fri, 15 Feb 2019 09:00:12: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:00:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:00:12: #2 number of paired peaks: 318 WARNING @ Fri, 15 Feb 2019 09:00:12: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Fri, 15 Feb 2019 09:00:12: start model_add_line... INFO @ Fri, 15 Feb 2019 09:00:12: start X-correlation... INFO @ Fri, 15 Feb 2019 09:00:12: end of X-cor INFO @ Fri, 15 Feb 2019 09:00:12: #2 finished! INFO @ Fri, 15 Feb 2019 09:00:12: #2 predicted fragment length is 184 bps INFO @ Fri, 15 Feb 2019 09:00:12: #2 alternative fragment length(s) may be 127,162,184,214 bps INFO @ Fri, 15 Feb 2019 09:00:12: #2.2 Generate R script for model : ERX1236296.10_model.r INFO @ Fri, 15 Feb 2019 09:00:12: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:00:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:00:13: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:00:13: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:00:13: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:00:14: #4 Write output xls file... ERX1236296.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:00:14: #4 Write peak in narrowPeak format file... ERX1236296.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:00:14: #4 Write summits bed file... ERX1236296.20_summits.bed INFO @ Fri, 15 Feb 2019 09:00:14: Done! INFO @ Fri, 15 Feb 2019 09:00:14: #4 Write output xls file... ERX1236296.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:00:14: #4 Write output xls file... ERX1236296.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:00:14: #4 Write peak in narrowPeak format file... ERX1236296.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:00:14: #4 Write peak in narrowPeak format file... ERX1236296.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:00:14: #4 Write summits bed file... ERX1236296.10_summits.bed INFO @ Fri, 15 Feb 2019 09:00:14: #4 Write summits bed file... ERX1236296.05_summits.bed INFO @ Fri, 15 Feb 2019 09:00:14: Done! INFO @ Fri, 15 Feb 2019 09:00:14: Done! pass1 - making usageList (15 chroms): 12 millis pass1 - making usageList (16 chroms): 9 millis pass2 - checking and writing primary data (87 records, 4 fields)pass2 - checking and writing primary data (218 records, 4 fields): 13 millis : 8 millis pass1 - making usageList (16 chroms): 21 millis pass2 - checking and writing primary data (370 records, 4 fields): 14 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。