Job ID = 11633552 sra ファイルのダウンロード中... Completed: 84379K bytes transferred in 4 seconds (171971K 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 1273433 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236329/ERR1162922.sra Written 1273433 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236329/ERR1162922.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: 00:00:56 1273433 reads; of these: 1273433 (100.00%) were paired; of these: 192919 (15.15%) aligned concordantly 0 times 964182 (75.72%) aligned concordantly exactly 1 time 116332 (9.14%) aligned concordantly >1 times ---- 192919 pairs aligned concordantly 0 times; of these: 6229 (3.23%) aligned discordantly 1 time ---- 186690 pairs aligned 0 times concordantly or discordantly; of these: 373380 mates make up the pairs; of these: 364968 (97.75%) aligned 0 times 5913 (1.58%) aligned exactly 1 time 2499 (0.67%) aligned >1 times 85.67% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 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] 317346 / 1086289 = 0.2921 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 09:09:13: # Command line: callpeak -t ERX1236329.bam -f BAM -g 12100000 -n ERX1236329.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236329.20 # format = BAM # ChIP-seq file = ['ERX1236329.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 09:09:13: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:09:13: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:09:13: # Command line: callpeak -t ERX1236329.bam -f BAM -g 12100000 -n ERX1236329.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236329.05 # format = BAM # ChIP-seq file = ['ERX1236329.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 09:09:13: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:09:13: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:09:13: # Command line: callpeak -t ERX1236329.bam -f BAM -g 12100000 -n ERX1236329.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236329.10 # format = BAM # ChIP-seq file = ['ERX1236329.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 09:09:13: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:09:13: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:09:19: 1000000 INFO @ Fri, 15 Feb 2019 09:09:19: 1000000 INFO @ Fri, 15 Feb 2019 09:09:19: 1000000 INFO @ Fri, 15 Feb 2019 09:09:22: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:09:22: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:09:22: #1 total tags in treatment: 764136 INFO @ Fri, 15 Feb 2019 09:09:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:09:22: #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 09:09:22: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:09:22: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:09:22: #1 total tags in treatment: 764136 INFO @ Fri, 15 Feb 2019 09:09:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:09:22: #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 09:09:22: #1 tags after filtering in treatment: 720858 INFO @ Fri, 15 Feb 2019 09:09:22: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 15 Feb 2019 09:09:22: #1 finished! INFO @ Fri, 15 Feb 2019 09:09:22: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:09:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:09:22: #1 tags after filtering in treatment: 720858 INFO @ Fri, 15 Feb 2019 09:09:22: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 15 Feb 2019 09:09:22: #1 finished! INFO @ Fri, 15 Feb 2019 09:09:22: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:09:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:09:22: #2 number of paired peaks: 309 WARNING @ Fri, 15 Feb 2019 09:09:22: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 15 Feb 2019 09:09:22: start model_add_line... INFO @ Fri, 15 Feb 2019 09:09:22: start X-correlation... INFO @ Fri, 15 Feb 2019 09:09:22: end of X-cor INFO @ Fri, 15 Feb 2019 09:09:22: #2 finished! INFO @ Fri, 15 Feb 2019 09:09:22: #2 predicted fragment length is 124 bps INFO @ Fri, 15 Feb 2019 09:09:22: #2 alternative fragment length(s) may be 4,124,127,145 bps INFO @ Fri, 15 Feb 2019 09:09:22: #2 number of paired peaks: 309 INFO @ Fri, 15 Feb 2019 09:09:22: #2.2 Generate R script for model : ERX1236329.20_model.r WARNING @ Fri, 15 Feb 2019 09:09:22: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 15 Feb 2019 09:09:22: start model_add_line... INFO @ Fri, 15 Feb 2019 09:09:22: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:09:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:09:22: start X-correlation... INFO @ Fri, 15 Feb 2019 09:09:22: end of X-cor INFO @ Fri, 15 Feb 2019 09:09:22: #2 finished! INFO @ Fri, 15 Feb 2019 09:09:22: #2 predicted fragment length is 124 bps INFO @ Fri, 15 Feb 2019 09:09:22: #2 alternative fragment length(s) may be 4,124,127,145 bps INFO @ Fri, 15 Feb 2019 09:09:22: #2.2 Generate R script for model : ERX1236329.10_model.r INFO @ Fri, 15 Feb 2019 09:09:22: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:09:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:09:22: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:09:22: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:09:22: #1 total tags in treatment: 764136 INFO @ Fri, 15 Feb 2019 09:09:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:09:22: #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 09:09:22: #1 tags after filtering in treatment: 720858 INFO @ Fri, 15 Feb 2019 09:09:22: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 15 Feb 2019 09:09:22: #1 finished! INFO @ Fri, 15 Feb 2019 09:09:22: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:09:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:09:22: #2 number of paired peaks: 309 WARNING @ Fri, 15 Feb 2019 09:09:22: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 15 Feb 2019 09:09:22: start model_add_line... INFO @ Fri, 15 Feb 2019 09:09:22: start X-correlation... INFO @ Fri, 15 Feb 2019 09:09:22: end of X-cor INFO @ Fri, 15 Feb 2019 09:09:22: #2 finished! INFO @ Fri, 15 Feb 2019 09:09:22: #2 predicted fragment length is 124 bps INFO @ Fri, 15 Feb 2019 09:09:22: #2 alternative fragment length(s) may be 4,124,127,145 bps INFO @ Fri, 15 Feb 2019 09:09:22: #2.2 Generate R script for model : ERX1236329.05_model.r INFO @ Fri, 15 Feb 2019 09:09:22: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:09:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:09:24: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:09:24: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:09:24: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write output xls file... ERX1236329.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write peak in narrowPeak format file... ERX1236329.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write summits bed file... ERX1236329.20_summits.bed INFO @ Fri, 15 Feb 2019 09:09:25: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (128 records, 4 fields): 4 millis INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write output xls file... ERX1236329.10_peaks.xls CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write peak in narrowPeak format file... ERX1236329.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write summits bed file... ERX1236329.10_summits.bed INFO @ Fri, 15 Feb 2019 09:09:25: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (301 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write output xls file... ERX1236329.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write peak in narrowPeak format file... ERX1236329.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:09:25: #4 Write summits bed file... ERX1236329.05_summits.bed INFO @ Fri, 15 Feb 2019 09:09:25: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (482 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。