Job ID = 11388950 sra ファイルのダウンロード中... Completed: 194587K bytes transferred in 6 seconds (248370K 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 3593752 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5041895/SRR8223347.sra Written 3593752 spots for /home/okishinya/chipatlas/results/sacCer3/SRX5041895/SRR8223347.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: 00:01:03 3593752 reads; of these: 3593752 (100.00%) were paired; of these: 3543340 (98.60%) aligned concordantly 0 times 39730 (1.11%) aligned concordantly exactly 1 time 10682 (0.30%) aligned concordantly >1 times ---- 3543340 pairs aligned concordantly 0 times; of these: 43 (0.00%) aligned discordantly 1 time ---- 3543297 pairs aligned 0 times concordantly or discordantly; of these: 7086594 mates make up the pairs; of these: 7083301 (99.95%) aligned 0 times 2541 (0.04%) aligned exactly 1 time 752 (0.01%) aligned >1 times 1.45% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 38747 / 50450 = 0.7680 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 @ Thu, 13 Dec 2018 00:21:57: # Command line: callpeak -t SRX5041895.bam -f BAM -g 12100000 -n SRX5041895.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5041895.10 # format = BAM # ChIP-seq file = ['SRX5041895.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 @ Thu, 13 Dec 2018 00:21:57: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:21:57: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:21:57: # Command line: callpeak -t SRX5041895.bam -f BAM -g 12100000 -n SRX5041895.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5041895.20 # format = BAM # ChIP-seq file = ['SRX5041895.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 @ Thu, 13 Dec 2018 00:21:57: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:21:57: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:21:57: # Command line: callpeak -t SRX5041895.bam -f BAM -g 12100000 -n SRX5041895.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5041895.05 # format = BAM # ChIP-seq file = ['SRX5041895.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 @ Thu, 13 Dec 2018 00:21:57: #1 read tag files... INFO @ Thu, 13 Dec 2018 00:21:57: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 00:21:57: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:21:57: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:21:57: #1 total tags in treatment: 11685 INFO @ Thu, 13 Dec 2018 00:21:57: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:21:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:21:57: #1 tags after filtering in treatment: 11504 INFO @ Thu, 13 Dec 2018 00:21:57: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 13 Dec 2018 00:21:57: #1 finished! INFO @ Thu, 13 Dec 2018 00:21:57: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:21:57: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:21:57: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:21:57: #1 total tags in treatment: 11685 INFO @ Thu, 13 Dec 2018 00:21:57: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:21:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:21:57: #1 tags after filtering in treatment: 11504 INFO @ Thu, 13 Dec 2018 00:21:57: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 13 Dec 2018 00:21:57: #1 finished! INFO @ Thu, 13 Dec 2018 00:21:57: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:21:57: #1 tag size is determined as 75 bps INFO @ Thu, 13 Dec 2018 00:21:57: #1 tag size = 75 INFO @ Thu, 13 Dec 2018 00:21:57: #1 total tags in treatment: 11685 INFO @ Thu, 13 Dec 2018 00:21:57: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 00:21:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 00:21:57: #1 tags after filtering in treatment: 11504 INFO @ Thu, 13 Dec 2018 00:21:57: #1 Redundant rate of treatment: 0.02 INFO @ Thu, 13 Dec 2018 00:21:57: #1 finished! INFO @ Thu, 13 Dec 2018 00:21:57: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 00:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 00:21:57: #2 number of paired peaks: 470 WARNING @ Thu, 13 Dec 2018 00:21:57: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Thu, 13 Dec 2018 00:21:57: start model_add_line... INFO @ Thu, 13 Dec 2018 00:21:57: start X-correlation... INFO @ Thu, 13 Dec 2018 00:21:57: end of X-cor INFO @ Thu, 13 Dec 2018 00:21:57: #2 finished! INFO @ Thu, 13 Dec 2018 00:21:57: #2 predicted fragment length is 292 bps INFO @ Thu, 13 Dec 2018 00:21:57: #2 alternative fragment length(s) may be 247,292,529 bps INFO @ Thu, 13 Dec 2018 00:21:57: #2.2 Generate R script for model : SRX5041895.10_model.r INFO @ Thu, 13 Dec 2018 00:21:57: #2 number of paired peaks: 470 WARNING @ Thu, 13 Dec 2018 00:21:57: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Thu, 13 Dec 2018 00:21:57: start model_add_line... INFO @ Thu, 13 Dec 2018 00:21:57: start X-correlation... INFO @ Thu, 13 Dec 2018 00:21:57: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:21:57: end of X-cor INFO @ Thu, 13 Dec 2018 00:21:57: #2 finished! INFO @ Thu, 13 Dec 2018 00:21:57: #2 predicted fragment length is 292 bps INFO @ Thu, 13 Dec 2018 00:21:57: #2 alternative fragment length(s) may be 247,292,529 bps INFO @ Thu, 13 Dec 2018 00:21:57: #2.2 Generate R script for model : SRX5041895.20_model.r INFO @ Thu, 13 Dec 2018 00:21:57: #2 number of paired peaks: 470 WARNING @ Thu, 13 Dec 2018 00:21:57: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Thu, 13 Dec 2018 00:21:57: start model_add_line... INFO @ Thu, 13 Dec 2018 00:21:57: start X-correlation... INFO @ Thu, 13 Dec 2018 00:21:57: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:21:57: end of X-cor INFO @ Thu, 13 Dec 2018 00:21:57: #2 finished! INFO @ Thu, 13 Dec 2018 00:21:57: #2 predicted fragment length is 292 bps INFO @ Thu, 13 Dec 2018 00:21:57: #2 alternative fragment length(s) may be 247,292,529 bps INFO @ Thu, 13 Dec 2018 00:21:57: #2.2 Generate R script for model : SRX5041895.05_model.r INFO @ Thu, 13 Dec 2018 00:21:57: #3 Call peaks... INFO @ Thu, 13 Dec 2018 00:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 00:21:57: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:21:57: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:21:57: #4 Write output xls file... SRX5041895.10_peaks.xls INFO @ Thu, 13 Dec 2018 00:21:57: #4 Write peak in narrowPeak format file... SRX5041895.10_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:21:57: #4 Write summits bed file... SRX5041895.10_summits.bed INFO @ Thu, 13 Dec 2018 00:21:57: #4 Write output xls file... SRX5041895.20_peaks.xls INFO @ Thu, 13 Dec 2018 00:21:57: Done! INFO @ Thu, 13 Dec 2018 00:21:57: #4 Write peak in narrowPeak format file... SRX5041895.20_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:21:57: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 00:21:57: #4 Write summits bed file... SRX5041895.20_summits.bed INFO @ Thu, 13 Dec 2018 00:21:57: Done! INFO @ Thu, 13 Dec 2018 00:21:57: #4 Write output xls file... SRX5041895.05_peaks.xls INFO @ Thu, 13 Dec 2018 00:21:57: #4 Write peak in narrowPeak format file... SRX5041895.05_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 00:21:57: #4 Write summits bed file... SRX5041895.05_summits.bed INFO @ Thu, 13 Dec 2018 00:21:57: Done! pass1 - making usageList (1 chroms): 11 millis pass2 - checking and writing primary data (1 records, 4 fields): 6 millis pass1 - making usageList (0 chroms): 14 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling pass1 - making usageList (1 chroms): 4 millis pass2 - checking and writing primary data (1 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。