Job ID = 2007847 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 185,276 reads read : 370,552 reads written : 370,552 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: 00:00:05 185276 reads; of these: 185276 (100.00%) were paired; of these: 54392 (29.36%) aligned concordantly 0 times 119317 (64.40%) aligned concordantly exactly 1 time 11567 (6.24%) aligned concordantly >1 times ---- 54392 pairs aligned concordantly 0 times; of these: 3469 (6.38%) aligned discordantly 1 time ---- 50923 pairs aligned 0 times concordantly or discordantly; of these: 101846 mates make up the pairs; of these: 99692 (97.89%) aligned 0 times 1281 (1.26%) aligned exactly 1 time 873 (0.86%) aligned >1 times 73.10% overall alignment rate Time searching: 00:00:05 Overall time: 00:00:05 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] 5086 / 134090 = 0.0379 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 16:33:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.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 16:33:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:33:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:33:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.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 16:33:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:33:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:33:33: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:33:33: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:33:33: #1 total tags in treatment: 125905 INFO @ Fri, 05 Jul 2019 16:33:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:33:33: #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 16:33:33: #1 tags after filtering in treatment: 125200 INFO @ Fri, 05 Jul 2019 16:33:33: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:33:33: #1 finished! INFO @ Fri, 05 Jul 2019 16:33:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:33:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:33:33: #2 number of paired peaks: 163 WARNING @ Fri, 05 Jul 2019 16:33:33: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Fri, 05 Jul 2019 16:33:33: start model_add_line... INFO @ Fri, 05 Jul 2019 16:33:33: start X-correlation... INFO @ Fri, 05 Jul 2019 16:33:33: end of X-cor INFO @ Fri, 05 Jul 2019 16:33:33: #2 finished! INFO @ Fri, 05 Jul 2019 16:33:33: #2 predicted fragment length is 274 bps INFO @ Fri, 05 Jul 2019 16:33:33: #2 alternative fragment length(s) may be 12,51,63,100,130,134,152,180,212,241,274,299,325,349,385,419,465,498,529,541,563 bps INFO @ Fri, 05 Jul 2019 16:33:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.05_model.r INFO @ Fri, 05 Jul 2019 16:33:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:33:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:33:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.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 16:33:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:33:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:33:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:33:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:33:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:33:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.05_summits.bed INFO @ Fri, 05 Jul 2019 16:33:33: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:33:34: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:33:34: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:33:34: #1 total tags in treatment: 125905 INFO @ Fri, 05 Jul 2019 16:33:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:33:34: #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 16:33:34: #1 tags after filtering in treatment: 125200 INFO @ Fri, 05 Jul 2019 16:33:34: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:33:34: #1 finished! INFO @ Fri, 05 Jul 2019 16:33:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:33:34: #2 number of paired peaks: 163 WARNING @ Fri, 05 Jul 2019 16:33:34: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Fri, 05 Jul 2019 16:33:34: start model_add_line... INFO @ Fri, 05 Jul 2019 16:33:34: start X-correlation... INFO @ Fri, 05 Jul 2019 16:33:34: end of X-cor INFO @ Fri, 05 Jul 2019 16:33:34: #2 finished! INFO @ Fri, 05 Jul 2019 16:33:34: #2 predicted fragment length is 274 bps INFO @ Fri, 05 Jul 2019 16:33:34: #2 alternative fragment length(s) may be 12,51,63,100,130,134,152,180,212,241,274,299,325,349,385,419,465,498,529,541,563 bps INFO @ Fri, 05 Jul 2019 16:33:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.10_model.r INFO @ Fri, 05 Jul 2019 16:33:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:33:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:33:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:33:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:33:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:33:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.10_summits.bed INFO @ Fri, 05 Jul 2019 16:33:34: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:33:35: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:33:35: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:33:35: #1 total tags in treatment: 125905 INFO @ Fri, 05 Jul 2019 16:33:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:33:35: #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 16:33:35: #1 tags after filtering in treatment: 125200 INFO @ Fri, 05 Jul 2019 16:33:35: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:33:35: #1 finished! INFO @ Fri, 05 Jul 2019 16:33:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:33:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:33:35: #2 number of paired peaks: 163 WARNING @ Fri, 05 Jul 2019 16:33:35: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Fri, 05 Jul 2019 16:33:35: start model_add_line... INFO @ Fri, 05 Jul 2019 16:33:35: start X-correlation... INFO @ Fri, 05 Jul 2019 16:33:35: end of X-cor INFO @ Fri, 05 Jul 2019 16:33:35: #2 finished! INFO @ Fri, 05 Jul 2019 16:33:35: #2 predicted fragment length is 274 bps INFO @ Fri, 05 Jul 2019 16:33:35: #2 alternative fragment length(s) may be 12,51,63,100,130,134,152,180,212,241,274,299,325,349,385,419,465,498,529,541,563 bps INFO @ Fri, 05 Jul 2019 16:33:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.20_model.r INFO @ Fri, 05 Jul 2019 16:33:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:33:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:33:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:33:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:33:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:33:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462390/ERX462390.20_summits.bed INFO @ Fri, 05 Jul 2019 16:33:36: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling