Job ID = 11633468 sra ファイルのダウンロード中... Completed: 991K bytes transferred in 2 seconds (4015K 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 14602 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236245/ERR1162838.sra Written 14602 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236245/ERR1162838.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:00 14602 reads; of these: 14602 (100.00%) were paired; of these: 7542 (51.65%) aligned concordantly 0 times 6306 (43.19%) aligned concordantly exactly 1 time 754 (5.16%) aligned concordantly >1 times ---- 7542 pairs aligned concordantly 0 times; of these: 41 (0.54%) aligned discordantly 1 time ---- 7501 pairs aligned 0 times concordantly or discordantly; of these: 15002 mates make up the pairs; of these: 14847 (98.97%) aligned 0 times 120 (0.80%) aligned exactly 1 time 35 (0.23%) aligned >1 times 49.16% overall alignment rate Time searching: 00:00:01 Overall time: 00:00:01 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] 413 / 7086 = 0.0583 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 08:54:36: # Command line: callpeak -t ERX1236245.bam -f BAM -g 12100000 -n ERX1236245.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236245.05 # format = BAM # ChIP-seq file = ['ERX1236245.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 08:54:36: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:54:36: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:54:36: # Command line: callpeak -t ERX1236245.bam -f BAM -g 12100000 -n ERX1236245.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236245.10 # format = BAM # ChIP-seq file = ['ERX1236245.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 08:54:36: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:54:36: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:54:36: # Command line: callpeak -t ERX1236245.bam -f BAM -g 12100000 -n ERX1236245.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236245.20 # format = BAM # ChIP-seq file = ['ERX1236245.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 08:54:36: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:54:36: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:54:36: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:54:36: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:54:36: #1 total tags in treatment: 6648 INFO @ Fri, 15 Feb 2019 08:54:36: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:54:36: #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 08:54:36: #1 tags after filtering in treatment: 6645 INFO @ Fri, 15 Feb 2019 08:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:54:36: #1 finished! INFO @ Fri, 15 Feb 2019 08:54:36: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:54:36: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:54:36: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:54:36: #1 total tags in treatment: 6648 INFO @ Fri, 15 Feb 2019 08:54:36: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:54:36: #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 08:54:36: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:54:36: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:54:36: #1 total tags in treatment: 6648 INFO @ Fri, 15 Feb 2019 08:54:36: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:54:36: #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 08:54:36: #1 tags after filtering in treatment: 6645 INFO @ Fri, 15 Feb 2019 08:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:54:36: #1 finished! INFO @ Fri, 15 Feb 2019 08:54:36: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:54:36: #1 tags after filtering in treatment: 6645 INFO @ Fri, 15 Feb 2019 08:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 08:54:36: #1 finished! INFO @ Fri, 15 Feb 2019 08:54:36: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:54:36: #2 number of paired peaks: 289 WARNING @ Fri, 15 Feb 2019 08:54:36: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Fri, 15 Feb 2019 08:54:36: start model_add_line... INFO @ Fri, 15 Feb 2019 08:54:36: start X-correlation... INFO @ Fri, 15 Feb 2019 08:54:36: end of X-cor INFO @ Fri, 15 Feb 2019 08:54:36: #2 finished! INFO @ Fri, 15 Feb 2019 08:54:36: #2 predicted fragment length is 330 bps INFO @ Fri, 15 Feb 2019 08:54:36: #2 alternative fragment length(s) may be 22,54,124,153,183,253,277,304,330,403,422,454,530,552 bps INFO @ Fri, 15 Feb 2019 08:54:36: #2.2 Generate R script for model : ERX1236245.05_model.r INFO @ Fri, 15 Feb 2019 08:54:36: #2 number of paired peaks: 289 WARNING @ Fri, 15 Feb 2019 08:54:36: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Fri, 15 Feb 2019 08:54:36: start model_add_line... INFO @ Fri, 15 Feb 2019 08:54:36: start X-correlation... INFO @ Fri, 15 Feb 2019 08:54:36: #2 number of paired peaks: 289 WARNING @ Fri, 15 Feb 2019 08:54:36: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Fri, 15 Feb 2019 08:54:36: start model_add_line... INFO @ Fri, 15 Feb 2019 08:54:36: start X-correlation... INFO @ Fri, 15 Feb 2019 08:54:36: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:54:36: end of X-cor INFO @ Fri, 15 Feb 2019 08:54:36: #2 finished! INFO @ Fri, 15 Feb 2019 08:54:36: #2 predicted fragment length is 330 bps INFO @ Fri, 15 Feb 2019 08:54:36: #2 alternative fragment length(s) may be 22,54,124,153,183,253,277,304,330,403,422,454,530,552 bps INFO @ Fri, 15 Feb 2019 08:54:36: #2.2 Generate R script for model : ERX1236245.10_model.r INFO @ Fri, 15 Feb 2019 08:54:36: end of X-cor INFO @ Fri, 15 Feb 2019 08:54:36: #2 finished! INFO @ Fri, 15 Feb 2019 08:54:36: #2 predicted fragment length is 330 bps INFO @ Fri, 15 Feb 2019 08:54:36: #2 alternative fragment length(s) may be 22,54,124,153,183,253,277,304,330,403,422,454,530,552 bps INFO @ Fri, 15 Feb 2019 08:54:36: #2.2 Generate R script for model : ERX1236245.20_model.r BedGraph に変換しました。 INFO @ Fri, 15 Feb 2019 08:54:36: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:54:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換中... INFO @ Fri, 15 Feb 2019 08:54:36: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:54:36: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:54:36: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:54:36: #4 Write output xls file... ERX1236245.05_peaks.xls INFO @ Fri, 15 Feb 2019 08:54:36: #4 Write peak in narrowPeak format file... ERX1236245.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:54:36: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:54:36: #4 Write summits bed file... ERX1236245.05_summits.bed INFO @ Fri, 15 Feb 2019 08:54:36: Done! INFO @ Fri, 15 Feb 2019 08:54:36: #4 Write output xls file... ERX1236245.10_peaks.xls INFO @ Fri, 15 Feb 2019 08:54:36: #4 Write peak in narrowPeak format file... ERX1236245.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:54:36: #4 Write output xls file... ERX1236245.20_peaks.xls INFO @ Fri, 15 Feb 2019 08:54:36: #4 Write summits bed file... ERX1236245.10_summits.bed INFO @ Fri, 15 Feb 2019 08:54:36: #4 Write peak in narrowPeak format file... ERX1236245.20_peaks.narrowPeak BigWig に変換しました。 INFO @ Fri, 15 Feb 2019 08:54:36: Done! INFO @ Fri, 15 Feb 2019 08:54:36: #4 Write summits bed file... ERX1236245.20_summits.bed INFO @ Fri, 15 Feb 2019 08:54:36: Done! pass1 - making usageList (0 chroms): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 28 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling