Job ID = 11633620 sra ファイルのダウンロード中... Completed: 139380K bytes transferred in 4 seconds (229175K 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 1927295 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420239/ERR1348715.sra Written 1927295 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420239/ERR1348715.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: 00:00:42 1927295 reads; of these: 1927295 (100.00%) were paired; of these: 1692330 (87.81%) aligned concordantly 0 times 215333 (11.17%) aligned concordantly exactly 1 time 19632 (1.02%) aligned concordantly >1 times ---- 1692330 pairs aligned concordantly 0 times; of these: 209359 (12.37%) aligned discordantly 1 time ---- 1482971 pairs aligned 0 times concordantly or discordantly; of these: 2965942 mates make up the pairs; of these: 2764959 (93.22%) aligned 0 times 157565 (5.31%) aligned exactly 1 time 43418 (1.46%) aligned >1 times 28.27% overall alignment rate Time searching: 00:00:42 Overall time: 00:00:42 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] 144495 / 305715 = 0.4726 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 09:11:50: # Command line: callpeak -t ERX1420239.bam -f BAM -g 12100000 -n ERX1420239.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1420239.10 # format = BAM # ChIP-seq file = ['ERX1420239.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 09:11:50: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:11:50: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:11:50: # Command line: callpeak -t ERX1420239.bam -f BAM -g 12100000 -n ERX1420239.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1420239.05 # format = BAM # ChIP-seq file = ['ERX1420239.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 09:11:50: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:11:50: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:11:50: # Command line: callpeak -t ERX1420239.bam -f BAM -g 12100000 -n ERX1420239.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1420239.20 # format = BAM # ChIP-seq file = ['ERX1420239.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 09:11:50: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:11:50: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:11:55: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:11:55: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:11:55: #1 total tags in treatment: 123480 INFO @ Fri, 15 Feb 2019 09:11:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:11:55: #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 09:11:55: #1 tags after filtering in treatment: 118536 INFO @ Fri, 15 Feb 2019 09:11:55: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 15 Feb 2019 09:11:55: #1 finished! INFO @ Fri, 15 Feb 2019 09:11:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:11:55: #2 number of paired peaks: 128 WARNING @ Fri, 15 Feb 2019 09:11:55: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 15 Feb 2019 09:11:55: start model_add_line... INFO @ Fri, 15 Feb 2019 09:11:55: start X-correlation... INFO @ Fri, 15 Feb 2019 09:11:55: end of X-cor INFO @ Fri, 15 Feb 2019 09:11:55: #2 finished! INFO @ Fri, 15 Feb 2019 09:11:55: #2 predicted fragment length is 290 bps INFO @ Fri, 15 Feb 2019 09:11:55: #2 alternative fragment length(s) may be 36,89,161,241,269,290,315,335 bps INFO @ Fri, 15 Feb 2019 09:11:55: #2.2 Generate R script for model : ERX1420239.10_model.r INFO @ Fri, 15 Feb 2019 09:11:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:11:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:11:55: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:11:55: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:11:55: #1 total tags in treatment: 123480 INFO @ Fri, 15 Feb 2019 09:11:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:11:55: #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 09:11:55: #1 tags after filtering in treatment: 118536 INFO @ Fri, 15 Feb 2019 09:11:55: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 15 Feb 2019 09:11:55: #1 finished! INFO @ Fri, 15 Feb 2019 09:11:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:11:55: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:11:55: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:11:55: #1 total tags in treatment: 123480 INFO @ Fri, 15 Feb 2019 09:11:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:11:55: #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 09:11:55: #2 number of paired peaks: 128 WARNING @ Fri, 15 Feb 2019 09:11:55: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 15 Feb 2019 09:11:55: start model_add_line... INFO @ Fri, 15 Feb 2019 09:11:55: start X-correlation... INFO @ Fri, 15 Feb 2019 09:11:55: #1 tags after filtering in treatment: 118536 INFO @ Fri, 15 Feb 2019 09:11:55: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 15 Feb 2019 09:11:55: #1 finished! INFO @ Fri, 15 Feb 2019 09:11:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:11:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:11:55: end of X-cor INFO @ Fri, 15 Feb 2019 09:11:55: #2 finished! INFO @ Fri, 15 Feb 2019 09:11:55: #2 predicted fragment length is 290 bps INFO @ Fri, 15 Feb 2019 09:11:55: #2 alternative fragment length(s) may be 36,89,161,241,269,290,315,335 bps INFO @ Fri, 15 Feb 2019 09:11:55: #2.2 Generate R script for model : ERX1420239.05_model.r INFO @ Fri, 15 Feb 2019 09:11:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:11:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:11:55: #2 number of paired peaks: 128 WARNING @ Fri, 15 Feb 2019 09:11:55: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 15 Feb 2019 09:11:55: start model_add_line... INFO @ Fri, 15 Feb 2019 09:11:55: start X-correlation... INFO @ Fri, 15 Feb 2019 09:11:55: end of X-cor INFO @ Fri, 15 Feb 2019 09:11:55: #2 finished! INFO @ Fri, 15 Feb 2019 09:11:55: #2 predicted fragment length is 290 bps INFO @ Fri, 15 Feb 2019 09:11:55: #2 alternative fragment length(s) may be 36,89,161,241,269,290,315,335 bps INFO @ Fri, 15 Feb 2019 09:11:55: #2.2 Generate R script for model : ERX1420239.20_model.r INFO @ Fri, 15 Feb 2019 09:11:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:11:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:11:55: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:11:55: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:11:55: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:11:55: #4 Write output xls file... ERX1420239.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:11:55: #4 Write peak in narrowPeak format file... ERX1420239.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:11:55: #4 Write summits bed file... ERX1420239.10_summits.bed INFO @ Fri, 15 Feb 2019 09:11:55: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 3 millis INFO @ Fri, 15 Feb 2019 09:11:55: #4 Write output xls file... ERX1420239.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:11:55: #4 Write peak in narrowPeak format file... ERX1420239.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:11:55: #4 Write output xls file... ERX1420239.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:11:55: #4 Write summits bed file... ERX1420239.05_summits.bed INFO @ Fri, 15 Feb 2019 09:11:56: #4 Write peak in narrowPeak format file... ERX1420239.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:11:56: Done! INFO @ Fri, 15 Feb 2019 09:11:56: #4 Write summits bed file... ERX1420239.20_summits.bed INFO @ Fri, 15 Feb 2019 09:11:56: Done! CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (62 records, 4 fields): 3 millis pass1 - making usageList (0 chroms): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。