Job ID = 11192737 sra ファイルのダウンロード中... Completed: 10287K bytes transferred in 2 seconds (29513K 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 330025 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924811/SRR3824842.sra Written 330025 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924811/SRR3824842.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 330025 reads; of these: 330025 (100.00%) were paired; of these: 122031 (36.98%) aligned concordantly 0 times 199435 (60.43%) aligned concordantly exactly 1 time 8559 (2.59%) aligned concordantly >1 times ---- 122031 pairs aligned concordantly 0 times; of these: 23183 (19.00%) aligned discordantly 1 time ---- 98848 pairs aligned 0 times concordantly or discordantly; of these: 197696 mates make up the pairs; of these: 106373 (53.81%) aligned 0 times 85336 (43.17%) aligned exactly 1 time 5987 (3.03%) aligned >1 times 83.88% 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] 138785 / 215787 = 0.6432 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 09:50:40: # Command line: callpeak -t SRX1924811.bam -f BAM -g 12100000 -n SRX1924811.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1924811.05 # format = BAM # ChIP-seq file = ['SRX1924811.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 09:50:40: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:50:40: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:50:40: # Command line: callpeak -t SRX1924811.bam -f BAM -g 12100000 -n SRX1924811.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1924811.20 # format = BAM # ChIP-seq file = ['SRX1924811.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 09:50:40: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:50:40: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:50:40: # Command line: callpeak -t SRX1924811.bam -f BAM -g 12100000 -n SRX1924811.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1924811.10 # format = BAM # ChIP-seq file = ['SRX1924811.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 09:50:40: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:50:40: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:50:42: #1 tag size is determined as 39 bps INFO @ Sat, 15 Sep 2018 09:50:42: #1 tag size = 39 INFO @ Sat, 15 Sep 2018 09:50:42: #1 total tags in treatment: 73328 INFO @ Sat, 15 Sep 2018 09:50:42: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:50:42: #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 09:50:42: #1 tags after filtering in treatment: 72177 INFO @ Sat, 15 Sep 2018 09:50:42: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 15 Sep 2018 09:50:42: #1 finished! INFO @ Sat, 15 Sep 2018 09:50:42: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:50:42: #2 number of paired peaks: 112 WARNING @ Sat, 15 Sep 2018 09:50:42: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 15 Sep 2018 09:50:42: start model_add_line... INFO @ Sat, 15 Sep 2018 09:50:42: start X-correlation... INFO @ Sat, 15 Sep 2018 09:50:42: end of X-cor INFO @ Sat, 15 Sep 2018 09:50:42: #2 finished! INFO @ Sat, 15 Sep 2018 09:50:42: #2 predicted fragment length is 299 bps INFO @ Sat, 15 Sep 2018 09:50:42: #2 alternative fragment length(s) may be 14,38,152,167,207,240,299,349,426,577,582 bps INFO @ Sat, 15 Sep 2018 09:50:42: #2.2 Generate R script for model : SRX1924811.05_model.r INFO @ Sat, 15 Sep 2018 09:50:42: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:50:42: #1 tag size is determined as 39 bps INFO @ Sat, 15 Sep 2018 09:50:42: #1 tag size = 39 INFO @ Sat, 15 Sep 2018 09:50:42: #1 total tags in treatment: 73328 INFO @ Sat, 15 Sep 2018 09:50:42: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:50:42: #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 09:50:42: #1 tag size is determined as 39 bps INFO @ Sat, 15 Sep 2018 09:50:42: #1 tag size = 39 INFO @ Sat, 15 Sep 2018 09:50:42: #1 total tags in treatment: 73328 INFO @ Sat, 15 Sep 2018 09:50:42: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:50:42: #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 09:50:42: #1 tags after filtering in treatment: 72177 INFO @ Sat, 15 Sep 2018 09:50:42: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 15 Sep 2018 09:50:42: #1 finished! INFO @ Sat, 15 Sep 2018 09:50:42: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:50:42: #1 tags after filtering in treatment: 72177 INFO @ Sat, 15 Sep 2018 09:50:42: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 15 Sep 2018 09:50:42: #1 finished! INFO @ Sat, 15 Sep 2018 09:50:42: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:50:42: #2 number of paired peaks: 112 WARNING @ Sat, 15 Sep 2018 09:50:42: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 15 Sep 2018 09:50:42: start model_add_line... INFO @ Sat, 15 Sep 2018 09:50:42: #2 number of paired peaks: 112 WARNING @ Sat, 15 Sep 2018 09:50:42: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 15 Sep 2018 09:50:42: start model_add_line... INFO @ Sat, 15 Sep 2018 09:50:42: start X-correlation... INFO @ Sat, 15 Sep 2018 09:50:42: start X-correlation... INFO @ Sat, 15 Sep 2018 09:50:42: end of X-cor INFO @ Sat, 15 Sep 2018 09:50:42: end of X-cor INFO @ Sat, 15 Sep 2018 09:50:42: #2 finished! INFO @ Sat, 15 Sep 2018 09:50:42: #2 finished! INFO @ Sat, 15 Sep 2018 09:50:42: #2 predicted fragment length is 299 bps INFO @ Sat, 15 Sep 2018 09:50:42: #2 predicted fragment length is 299 bps INFO @ Sat, 15 Sep 2018 09:50:42: #2 alternative fragment length(s) may be 14,38,152,167,207,240,299,349,426,577,582 bps INFO @ Sat, 15 Sep 2018 09:50:42: #2 alternative fragment length(s) may be 14,38,152,167,207,240,299,349,426,577,582 bps INFO @ Sat, 15 Sep 2018 09:50:42: #2.2 Generate R script for model : SRX1924811.20_model.r INFO @ Sat, 15 Sep 2018 09:50:42: #2.2 Generate R script for model : SRX1924811.10_model.r INFO @ Sat, 15 Sep 2018 09:50:42: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:50:42: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:50:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:50:42: #4 Write output xls file... SRX1924811.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:50:42: #4 Write peak in narrowPeak format file... SRX1924811.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:50:42: #4 Write summits bed file... SRX1924811.05_summits.bed INFO @ Sat, 15 Sep 2018 09:50:42: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:50:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:50:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:50:42: #4 Write output xls file... SRX1924811.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:50:42: #4 Write peak in narrowPeak format file... SRX1924811.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:50:42: #4 Write summits bed file... SRX1924811.20_summits.bed INFO @ Sat, 15 Sep 2018 09:50:42: Done! INFO @ Sat, 15 Sep 2018 09:50:42: #4 Write output xls file... SRX1924811.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:50:42: #4 Write peak in narrowPeak format file... SRX1924811.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:50:42: #4 Write summits bed file... SRX1924811.10_summits.bed INFO @ Sat, 15 Sep 2018 09:50:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 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。