Job ID = 11192711 sra ファイルのダウンロード中... Completed: 10218K bytes transferred in 2 seconds (29103K 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 328899 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924789/SRR3824820.sra Written 328899 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924789/SRR3824820.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: 00:00:12 328899 reads; of these: 328899 (100.00%) were paired; of these: 102667 (31.22%) aligned concordantly 0 times 216247 (65.75%) aligned concordantly exactly 1 time 9985 (3.04%) aligned concordantly >1 times ---- 102667 pairs aligned concordantly 0 times; of these: 20660 (20.12%) aligned discordantly 1 time ---- 82007 pairs aligned 0 times concordantly or discordantly; of these: 164014 mates make up the pairs; of these: 88075 (53.70%) aligned 0 times 70078 (42.73%) aligned exactly 1 time 5861 (3.57%) aligned >1 times 86.61% overall alignment rate Time searching: 00:00:12 Overall time: 00:00:12 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 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] 115641 / 236760 = 0.4884 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 @ Sat, 15 Sep 2018 09:48:41: # Command line: callpeak -t SRX1924789.bam -f BAM -g 12100000 -n SRX1924789.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1924789.05 # format = BAM # ChIP-seq file = ['SRX1924789.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 @ Sat, 15 Sep 2018 09:48:41: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:48:41: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:48:41: # Command line: callpeak -t SRX1924789.bam -f BAM -g 12100000 -n SRX1924789.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1924789.10 # format = BAM # ChIP-seq file = ['SRX1924789.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 @ Sat, 15 Sep 2018 09:48:41: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:48:41: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:48:41: # Command line: callpeak -t SRX1924789.bam -f BAM -g 12100000 -n SRX1924789.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1924789.20 # format = BAM # ChIP-seq file = ['SRX1924789.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 @ Sat, 15 Sep 2018 09:48:41: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:48:41: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:48:43: #1 tag size is determined as 41 bps INFO @ Sat, 15 Sep 2018 09:48:43: #1 tag size = 41 INFO @ Sat, 15 Sep 2018 09:48:43: #1 total tags in treatment: 114424 INFO @ Sat, 15 Sep 2018 09:48:43: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:48:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:48:43: #1 tags after filtering in treatment: 111846 INFO @ Sat, 15 Sep 2018 09:48:43: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 15 Sep 2018 09:48:43: #1 finished! INFO @ Sat, 15 Sep 2018 09:48:43: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:48:43: #1 tag size is determined as 41 bps INFO @ Sat, 15 Sep 2018 09:48:43: #1 tag size = 41 INFO @ Sat, 15 Sep 2018 09:48:43: #1 total tags in treatment: 114424 INFO @ Sat, 15 Sep 2018 09:48:43: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:48:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:48:43: #1 tags after filtering in treatment: 111846 INFO @ Sat, 15 Sep 2018 09:48:43: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 15 Sep 2018 09:48:43: #1 finished! INFO @ Sat, 15 Sep 2018 09:48:43: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:48:43: #2 number of paired peaks: 100 WARNING @ Sat, 15 Sep 2018 09:48:43: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 15 Sep 2018 09:48:43: start model_add_line... INFO @ Sat, 15 Sep 2018 09:48:43: start X-correlation... INFO @ Sat, 15 Sep 2018 09:48:43: end of X-cor INFO @ Sat, 15 Sep 2018 09:48:43: #2 finished! INFO @ Sat, 15 Sep 2018 09:48:43: #2 predicted fragment length is 267 bps INFO @ Sat, 15 Sep 2018 09:48:43: #2 alternative fragment length(s) may be 16,39,64,131,165,181,221,267,295,341,390,413,440,493,538,568 bps INFO @ Sat, 15 Sep 2018 09:48:43: #2.2 Generate R script for model : SRX1924789.05_model.r INFO @ Sat, 15 Sep 2018 09:48:43: #2 number of paired peaks: 100 WARNING @ Sat, 15 Sep 2018 09:48:43: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 15 Sep 2018 09:48:43: start model_add_line... INFO @ Sat, 15 Sep 2018 09:48:43: start X-correlation... INFO @ Sat, 15 Sep 2018 09:48:43: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:48:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:48:43: end of X-cor INFO @ Sat, 15 Sep 2018 09:48:43: #2 finished! INFO @ Sat, 15 Sep 2018 09:48:43: #2 predicted fragment length is 267 bps INFO @ Sat, 15 Sep 2018 09:48:43: #2 alternative fragment length(s) may be 16,39,64,131,165,181,221,267,295,341,390,413,440,493,538,568 bps INFO @ Sat, 15 Sep 2018 09:48:43: #2.2 Generate R script for model : SRX1924789.10_model.r INFO @ Sat, 15 Sep 2018 09:48:43: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:48:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:48:43: #1 tag size is determined as 41 bps INFO @ Sat, 15 Sep 2018 09:48:43: #1 tag size = 41 INFO @ Sat, 15 Sep 2018 09:48:43: #1 total tags in treatment: 114424 INFO @ Sat, 15 Sep 2018 09:48:43: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:48:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:48:43: #1 tags after filtering in treatment: 111846 INFO @ Sat, 15 Sep 2018 09:48:43: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 15 Sep 2018 09:48:43: #1 finished! INFO @ Sat, 15 Sep 2018 09:48:43: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:48:43: #2 number of paired peaks: 100 WARNING @ Sat, 15 Sep 2018 09:48:43: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 15 Sep 2018 09:48:43: start model_add_line... INFO @ Sat, 15 Sep 2018 09:48:43: start X-correlation... INFO @ Sat, 15 Sep 2018 09:48:43: end of X-cor INFO @ Sat, 15 Sep 2018 09:48:43: #2 finished! INFO @ Sat, 15 Sep 2018 09:48:43: #2 predicted fragment length is 267 bps INFO @ Sat, 15 Sep 2018 09:48:43: #2 alternative fragment length(s) may be 16,39,64,131,165,181,221,267,295,341,390,413,440,493,538,568 bps INFO @ Sat, 15 Sep 2018 09:48:43: #2.2 Generate R script for model : SRX1924789.20_model.r INFO @ Sat, 15 Sep 2018 09:48:43: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:48:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:48:43: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:48:43: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:48:43: #4 Write output xls file... SRX1924789.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:48:43: #4 Write peak in narrowPeak format file... SRX1924789.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:48:43: #4 Write summits bed file... SRX1924789.05_summits.bed INFO @ Sat, 15 Sep 2018 09:48:43: Done! INFO @ Sat, 15 Sep 2018 09:48:43: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:48:43: #4 Write output xls file... SRX1924789.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:48:43: #4 Write peak in narrowPeak format file... SRX1924789.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:48:43: #4 Write summits bed file... SRX1924789.10_summits.bed pass1 - making usageList (11 chroms): 1 millis INFO @ Sat, 15 Sep 2018 09:48:43: Done! pass2 - checking and writing primary data (27 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:48:43: #4 Write output xls file... SRX1924789.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:48:43: #4 Write peak in narrowPeak format file... SRX1924789.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:48:43: #4 Write summits bed file... SRX1924789.20_summits.bed INFO @ Sat, 15 Sep 2018 09:48:43: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。