Job ID = 2007873 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 193,914 reads read : 387,828 reads written : 387,828 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:06 193914 reads; of these: 193914 (100.00%) were paired; of these: 30799 (15.88%) aligned concordantly 0 times 148840 (76.76%) aligned concordantly exactly 1 time 14275 (7.36%) aligned concordantly >1 times ---- 30799 pairs aligned concordantly 0 times; of these: 4383 (14.23%) aligned discordantly 1 time ---- 26416 pairs aligned 0 times concordantly or discordantly; of these: 52832 mates make up the pairs; of these: 50243 (95.10%) aligned 0 times 1451 (2.75%) aligned exactly 1 time 1138 (2.15%) aligned >1 times 87.05% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 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] 4183 / 167228 = 0.0250 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, 05 Jul 2019 16:36:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.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, 05 Jul 2019 16:36:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:36:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.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, 05 Jul 2019 16:36:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:36:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:36:18: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:36:18: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:36:18: #1 total tags in treatment: 158998 INFO @ Fri, 05 Jul 2019 16:36:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:36:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:36:18: #1 tags after filtering in treatment: 157956 INFO @ Fri, 05 Jul 2019 16:36:18: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:36:18: #1 finished! INFO @ Fri, 05 Jul 2019 16:36:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:36:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:36:18: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 16:36:18: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 16:36:18: start model_add_line... INFO @ Fri, 05 Jul 2019 16:36:18: start X-correlation... INFO @ Fri, 05 Jul 2019 16:36:18: end of X-cor INFO @ Fri, 05 Jul 2019 16:36:18: #2 finished! INFO @ Fri, 05 Jul 2019 16:36:18: #2 predicted fragment length is 266 bps INFO @ Fri, 05 Jul 2019 16:36:18: #2 alternative fragment length(s) may be 2,27,163,215,240,266,283,314,333,354,379,421,446,531,562,574 bps INFO @ Fri, 05 Jul 2019 16:36:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.05_model.r INFO @ Fri, 05 Jul 2019 16:36:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:36:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.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, 05 Jul 2019 16:36:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:36:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:36:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:36:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:36:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.05_summits.bed INFO @ Fri, 05 Jul 2019 16:36:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:36:19: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:36:19: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:36:19: #1 total tags in treatment: 158998 INFO @ Fri, 05 Jul 2019 16:36:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:36:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:36:19: #1 tags after filtering in treatment: 157956 INFO @ Fri, 05 Jul 2019 16:36:19: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:36:19: #1 finished! INFO @ Fri, 05 Jul 2019 16:36:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:36:19: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 16:36:19: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 16:36:19: start model_add_line... INFO @ Fri, 05 Jul 2019 16:36:19: start X-correlation... INFO @ Fri, 05 Jul 2019 16:36:19: end of X-cor INFO @ Fri, 05 Jul 2019 16:36:19: #2 finished! INFO @ Fri, 05 Jul 2019 16:36:19: #2 predicted fragment length is 266 bps INFO @ Fri, 05 Jul 2019 16:36:19: #2 alternative fragment length(s) may be 2,27,163,215,240,266,283,314,333,354,379,421,446,531,562,574 bps INFO @ Fri, 05 Jul 2019 16:36:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.10_model.r INFO @ Fri, 05 Jul 2019 16:36:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:36:19: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:36:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:36:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:36:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:36:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.10_summits.bed INFO @ Fri, 05 Jul 2019 16:36:19: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 10 millis INFO @ Fri, 05 Jul 2019 16:36:20: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:36:20: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:36:20: #1 total tags in treatment: 158998 INFO @ Fri, 05 Jul 2019 16:36:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:36:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:36:20: #1 tags after filtering in treatment: 157956 INFO @ Fri, 05 Jul 2019 16:36:20: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:36:20: #1 finished! INFO @ Fri, 05 Jul 2019 16:36:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:36:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:36:20: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 16:36:20: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 16:36:20: start model_add_line... INFO @ Fri, 05 Jul 2019 16:36:20: start X-correlation... INFO @ Fri, 05 Jul 2019 16:36:20: end of X-cor INFO @ Fri, 05 Jul 2019 16:36:20: #2 finished! INFO @ Fri, 05 Jul 2019 16:36:20: #2 predicted fragment length is 266 bps INFO @ Fri, 05 Jul 2019 16:36:20: #2 alternative fragment length(s) may be 2,27,163,215,240,266,283,314,333,354,379,421,446,531,562,574 bps INFO @ Fri, 05 Jul 2019 16:36:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.20_model.r INFO @ Fri, 05 Jul 2019 16:36:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:36:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:36:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462412/ERX462412.20_summits.bed INFO @ Fri, 05 Jul 2019 16:36:20: Done! pass1 - making usageList (0 chroms): 23 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。