Job ID = 11633610 sra ファイルのダウンロード中... Completed: 13169K bytes transferred in 2 seconds (36071K 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 205866 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420229/ERR1348705.sra Written 205866 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1420229/ERR1348705.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: 00:00:03 205866 reads; of these: 205866 (100.00%) were paired; of these: 194125 (94.30%) aligned concordantly 0 times 10474 (5.09%) aligned concordantly exactly 1 time 1267 (0.62%) aligned concordantly >1 times ---- 194125 pairs aligned concordantly 0 times; of these: 10562 (5.44%) aligned discordantly 1 time ---- 183563 pairs aligned 0 times concordantly or discordantly; of these: 367126 mates make up the pairs; of these: 352258 (95.95%) aligned 0 times 11590 (3.16%) aligned exactly 1 time 3278 (0.89%) aligned >1 times 14.44% overall alignment rate Time searching: 00:00:03 Overall time: 00:00:03 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] 622 / 15594 = 0.0399 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 09:10:26: # Command line: callpeak -t ERX1420229.bam -f BAM -g 12100000 -n ERX1420229.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1420229.10 # format = BAM # ChIP-seq file = ['ERX1420229.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 09:10:26: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:10:26: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:10:26: # Command line: callpeak -t ERX1420229.bam -f BAM -g 12100000 -n ERX1420229.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1420229.05 # format = BAM # ChIP-seq file = ['ERX1420229.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 09:10:26: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:10:26: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:10:26: # Command line: callpeak -t ERX1420229.bam -f BAM -g 12100000 -n ERX1420229.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1420229.20 # format = BAM # ChIP-seq file = ['ERX1420229.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 09:10:26: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:10:26: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:10:27: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:10:27: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:10:27: #1 total tags in treatment: 11282 INFO @ Fri, 15 Feb 2019 09:10:27: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:10:27: #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 09:10:27: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:10:27: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:10:27: #1 total tags in treatment: 11282 INFO @ Fri, 15 Feb 2019 09:10:27: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:10:27: #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 09:10:27: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:10:27: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:10:27: #1 total tags in treatment: 11282 INFO @ Fri, 15 Feb 2019 09:10:27: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:10:27: #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 09:10:27: #1 tags after filtering in treatment: 11251 INFO @ Fri, 15 Feb 2019 09:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:10:27: #1 finished! INFO @ Fri, 15 Feb 2019 09:10:27: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:10:27: #1 tags after filtering in treatment: 11251 INFO @ Fri, 15 Feb 2019 09:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:10:27: #1 finished! INFO @ Fri, 15 Feb 2019 09:10:27: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:10:27: #1 tags after filtering in treatment: 11251 INFO @ Fri, 15 Feb 2019 09:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 09:10:27: #1 finished! INFO @ Fri, 15 Feb 2019 09:10:27: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:10:27: #2 number of paired peaks: 590 INFO @ Fri, 15 Feb 2019 09:10:27: #2 number of paired peaks: 590 WARNING @ Fri, 15 Feb 2019 09:10:27: Fewer paired peaks (590) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 590 pairs to build model! WARNING @ Fri, 15 Feb 2019 09:10:27: Fewer paired peaks (590) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 590 pairs to build model! INFO @ Fri, 15 Feb 2019 09:10:27: start model_add_line... INFO @ Fri, 15 Feb 2019 09:10:27: start model_add_line... INFO @ Fri, 15 Feb 2019 09:10:27: start X-correlation... INFO @ Fri, 15 Feb 2019 09:10:27: start X-correlation... INFO @ Fri, 15 Feb 2019 09:10:27: #2 number of paired peaks: 590 WARNING @ Fri, 15 Feb 2019 09:10:27: Fewer paired peaks (590) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 590 pairs to build model! INFO @ Fri, 15 Feb 2019 09:10:27: start model_add_line... INFO @ Fri, 15 Feb 2019 09:10:27: start X-correlation... INFO @ Fri, 15 Feb 2019 09:10:27: end of X-cor INFO @ Fri, 15 Feb 2019 09:10:27: end of X-cor INFO @ Fri, 15 Feb 2019 09:10:27: end of X-cor INFO @ Fri, 15 Feb 2019 09:10:27: #2 finished! INFO @ Fri, 15 Feb 2019 09:10:27: #2 finished! INFO @ Fri, 15 Feb 2019 09:10:27: #2 finished! INFO @ Fri, 15 Feb 2019 09:10:27: #2 predicted fragment length is 305 bps INFO @ Fri, 15 Feb 2019 09:10:27: #2 predicted fragment length is 305 bps INFO @ Fri, 15 Feb 2019 09:10:27: #2 predicted fragment length is 305 bps INFO @ Fri, 15 Feb 2019 09:10:27: #2 alternative fragment length(s) may be 305 bps INFO @ Fri, 15 Feb 2019 09:10:27: #2 alternative fragment length(s) may be 305 bps INFO @ Fri, 15 Feb 2019 09:10:27: #2 alternative fragment length(s) may be 305 bps INFO @ Fri, 15 Feb 2019 09:10:27: #2.2 Generate R script for model : ERX1420229.10_model.r INFO @ Fri, 15 Feb 2019 09:10:27: #2.2 Generate R script for model : ERX1420229.20_model.r INFO @ Fri, 15 Feb 2019 09:10:27: #2.2 Generate R script for model : ERX1420229.05_model.r INFO @ Fri, 15 Feb 2019 09:10:27: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:10:27: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:10:27: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:10:27: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:10:27: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:10:27: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:10:27: #4 Write output xls file... ERX1420229.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:10:27: #4 Write output xls file... ERX1420229.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:10:27: #4 Write output xls file... ERX1420229.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:10:27: #4 Write peak in narrowPeak format file... ERX1420229.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:10:27: #4 Write peak in narrowPeak format file... ERX1420229.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:10:27: #4 Write peak in narrowPeak format file... ERX1420229.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:10:27: #4 Write summits bed file... ERX1420229.10_summits.bed INFO @ Fri, 15 Feb 2019 09:10:27: #4 Write summits bed file... ERX1420229.05_summits.bed INFO @ Fri, 15 Feb 2019 09:10:27: #4 Write summits bed file... ERX1420229.20_summits.bed INFO @ Fri, 15 Feb 2019 09:10:27: Done! INFO @ Fri, 15 Feb 2019 09:10:27: Done! INFO @ Fri, 15 Feb 2019 09:10:27: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 15 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。