Job ID = 2008261 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,819,582 reads read : 15,639,164 reads written : 15,639,164 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629044.sra.cache’: 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: 00:05:52 7819582 reads; of these: 7819582 (100.00%) were paired; of these: 233983 (2.99%) aligned concordantly 0 times 7065891 (90.36%) aligned concordantly exactly 1 time 519708 (6.65%) aligned concordantly >1 times ---- 233983 pairs aligned concordantly 0 times; of these: 72061 (30.80%) aligned discordantly 1 time ---- 161922 pairs aligned 0 times concordantly or discordantly; of these: 323844 mates make up the pairs; of these: 283535 (87.55%) aligned 0 times 28197 (8.71%) aligned exactly 1 time 12112 (3.74%) aligned >1 times 98.19% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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_sort_core] merging from 8 files... [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] 6946507 / 7653119 = 0.9077 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 18:19:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.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 18:19:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:19:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:19:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.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 18:19:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:19:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.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 18:19:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:19:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:19:43: 1000000 INFO @ Fri, 05 Jul 2019 18:19:45: 1000000 INFO @ Fri, 05 Jul 2019 18:19:46: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:19:46: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:19:46: #1 total tags in treatment: 655285 INFO @ Fri, 05 Jul 2019 18:19:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:19:46: #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 18:19:46: #1 tags after filtering in treatment: 536415 INFO @ Fri, 05 Jul 2019 18:19:46: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 18:19:46: #1 finished! INFO @ Fri, 05 Jul 2019 18:19:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:19:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:19:46: #2 number of paired peaks: 248 WARNING @ Fri, 05 Jul 2019 18:19:46: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Fri, 05 Jul 2019 18:19:46: start model_add_line... INFO @ Fri, 05 Jul 2019 18:19:46: start X-correlation... INFO @ Fri, 05 Jul 2019 18:19:46: end of X-cor INFO @ Fri, 05 Jul 2019 18:19:46: #2 finished! INFO @ Fri, 05 Jul 2019 18:19:46: #2 predicted fragment length is 185 bps INFO @ Fri, 05 Jul 2019 18:19:46: #2 alternative fragment length(s) may be 0,87,122,143,185,232,290,347,385,468,489,552 bps INFO @ Fri, 05 Jul 2019 18:19:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.10_model.r INFO @ Fri, 05 Jul 2019 18:19:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:19:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:19:47: 1000000 INFO @ Fri, 05 Jul 2019 18:19:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:19:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:19:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.10_summits.bed INFO @ Fri, 05 Jul 2019 18:19:48: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (31 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 18:19:49: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:19:49: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:19:49: #1 total tags in treatment: 655285 INFO @ Fri, 05 Jul 2019 18:19:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:19:49: #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 18:19:49: #1 tags after filtering in treatment: 536415 INFO @ Fri, 05 Jul 2019 18:19:49: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 18:19:49: #1 finished! INFO @ Fri, 05 Jul 2019 18:19:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:19:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:19:49: #2 number of paired peaks: 248 WARNING @ Fri, 05 Jul 2019 18:19:49: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Fri, 05 Jul 2019 18:19:49: start model_add_line... INFO @ Fri, 05 Jul 2019 18:19:49: start X-correlation... INFO @ Fri, 05 Jul 2019 18:19:49: end of X-cor INFO @ Fri, 05 Jul 2019 18:19:49: #2 finished! INFO @ Fri, 05 Jul 2019 18:19:49: #2 predicted fragment length is 185 bps INFO @ Fri, 05 Jul 2019 18:19:49: #2 alternative fragment length(s) may be 0,87,122,143,185,232,290,347,385,468,489,552 bps INFO @ Fri, 05 Jul 2019 18:19:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.05_model.r INFO @ Fri, 05 Jul 2019 18:19:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:19:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:19:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:19:51: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:19:51: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:19:51: #1 total tags in treatment: 655285 INFO @ Fri, 05 Jul 2019 18:19:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:19:51: #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 18:19:51: #1 tags after filtering in treatment: 536415 INFO @ Fri, 05 Jul 2019 18:19:51: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 18:19:51: #1 finished! INFO @ Fri, 05 Jul 2019 18:19:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:19:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:19:51: #2 number of paired peaks: 248 WARNING @ Fri, 05 Jul 2019 18:19:51: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Fri, 05 Jul 2019 18:19:51: start model_add_line... INFO @ Fri, 05 Jul 2019 18:19:51: start X-correlation... INFO @ Fri, 05 Jul 2019 18:19:51: end of X-cor INFO @ Fri, 05 Jul 2019 18:19:51: #2 finished! INFO @ Fri, 05 Jul 2019 18:19:51: #2 predicted fragment length is 185 bps INFO @ Fri, 05 Jul 2019 18:19:51: #2 alternative fragment length(s) may be 0,87,122,143,185,232,290,347,385,468,489,552 bps INFO @ Fri, 05 Jul 2019 18:19:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.20_model.r INFO @ Fri, 05 Jul 2019 18:19:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:19:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:19:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:19:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:19:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.05_summits.bed INFO @ Fri, 05 Jul 2019 18:19:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (129 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:19:53: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:19:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:19:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:19:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585783/ERX585783.20_summits.bed INFO @ Fri, 05 Jul 2019 18:19:53: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。