Job ID = 2008305 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,814,791 reads read : 3,629,582 reads written : 3,629,582 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: 00:02:12 1814791 reads; of these: 1814791 (100.00%) were paired; of these: 91148 (5.02%) aligned concordantly 0 times 1563695 (86.16%) aligned concordantly exactly 1 time 159948 (8.81%) aligned concordantly >1 times ---- 91148 pairs aligned concordantly 0 times; of these: 12989 (14.25%) aligned discordantly 1 time ---- 78159 pairs aligned 0 times concordantly or discordantly; of these: 156318 mates make up the pairs; of these: 144639 (92.53%) aligned 0 times 6529 (4.18%) aligned exactly 1 time 5150 (3.29%) aligned >1 times 96.01% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 1644870 / 1733270 = 0.9490 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 18:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.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 18:26:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:26:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.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 18:26:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:26:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:26:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.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 18:26:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:26:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:26:56: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:26:56: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:26:56: #1 total tags in treatment: 89672 INFO @ Fri, 05 Jul 2019 18:26:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:26:56: #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 18:26:56: #1 tags after filtering in treatment: 83110 INFO @ Fri, 05 Jul 2019 18:26:56: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 18:26:56: #1 finished! INFO @ Fri, 05 Jul 2019 18:26:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:26:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:26:56: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:26:56: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:26:56: #1 total tags in treatment: 89672 INFO @ Fri, 05 Jul 2019 18:26:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:26:56: #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 18:26:56: #1 tags after filtering in treatment: 83110 INFO @ Fri, 05 Jul 2019 18:26:56: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 18:26:56: #1 finished! INFO @ Fri, 05 Jul 2019 18:26:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:26:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:26:56: #2 number of paired peaks: 308 WARNING @ Fri, 05 Jul 2019 18:26:56: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Fri, 05 Jul 2019 18:26:56: start model_add_line... INFO @ Fri, 05 Jul 2019 18:26:56: start X-correlation... INFO @ Fri, 05 Jul 2019 18:26:56: #2 number of paired peaks: 308 WARNING @ Fri, 05 Jul 2019 18:26:56: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Fri, 05 Jul 2019 18:26:56: start model_add_line... INFO @ Fri, 05 Jul 2019 18:26:56: start X-correlation... BedGraph に変換しました。 INFO @ Fri, 05 Jul 2019 18:26:56: end of X-cor INFO @ Fri, 05 Jul 2019 18:26:56: #2 finished! INFO @ Fri, 05 Jul 2019 18:26:56: #2 predicted fragment length is 177 bps INFO @ Fri, 05 Jul 2019 18:26:56: #2 alternative fragment length(s) may be 19,43,93,117,149,177,198,218,274,298,407,431,453,476,501,522,542,591 bps INFO @ Fri, 05 Jul 2019 18:26:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.05_model.r INFO @ Fri, 05 Jul 2019 18:26:56: end of X-cor INFO @ Fri, 05 Jul 2019 18:26:56: #2 finished! INFO @ Fri, 05 Jul 2019 18:26:56: #2 predicted fragment length is 177 bps INFO @ Fri, 05 Jul 2019 18:26:56: #2 alternative fragment length(s) may be 19,43,93,117,149,177,198,218,274,298,407,431,453,476,501,522,542,591 bps INFO @ Fri, 05 Jul 2019 18:26:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.10_model.r INFO @ Fri, 05 Jul 2019 18:26:57: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:26:57: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:26:57: #1 total tags in treatment: 89672 INFO @ Fri, 05 Jul 2019 18:26:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:26:57: #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 18:26:57: #1 tags after filtering in treatment: 83110 INFO @ Fri, 05 Jul 2019 18:26:57: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 18:26:57: #1 finished! INFO @ Fri, 05 Jul 2019 18:26:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:26:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:26:57: #2 number of paired peaks: 308 WARNING @ Fri, 05 Jul 2019 18:26:57: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Fri, 05 Jul 2019 18:26:57: start model_add_line... INFO @ Fri, 05 Jul 2019 18:26:57: start X-correlation... INFO @ Fri, 05 Jul 2019 18:26:57: end of X-cor INFO @ Fri, 05 Jul 2019 18:26:57: #2 finished! INFO @ Fri, 05 Jul 2019 18:26:57: #2 predicted fragment length is 177 bps INFO @ Fri, 05 Jul 2019 18:26:57: #2 alternative fragment length(s) may be 19,43,93,117,149,177,198,218,274,298,407,431,453,476,501,522,542,591 bps INFO @ Fri, 05 Jul 2019 18:26:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.20_model.r BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:27:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:27:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:27:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:27:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 18:27:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:27:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:27:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.10_summits.bed INFO @ Fri, 05 Jul 2019 18:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.20_summits.bed INFO @ Fri, 05 Jul 2019 18:27:05: Done! INFO @ Fri, 05 Jul 2019 18:27:05: Done! INFO @ Fri, 05 Jul 2019 18:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585815/ERX585815.05_summits.bed INFO @ Fri, 05 Jul 2019 18:27:05: Done! pass1 - making usageList (4 chroms)pass1 - making usageList (0 chroms): 2 millis : 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass2 - checking and writing primary data (5 records, 4 fields): 8 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling