Job ID = 2008318 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,736,624 reads read : 25,473,248 reads written : 25,473,248 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629001.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: 00:08:56 12736624 reads; of these: 12736624 (100.00%) were paired; of these: 1565042 (12.29%) aligned concordantly 0 times 10210509 (80.17%) aligned concordantly exactly 1 time 961073 (7.55%) aligned concordantly >1 times ---- 1565042 pairs aligned concordantly 0 times; of these: 116373 (7.44%) aligned discordantly 1 time ---- 1448669 pairs aligned 0 times concordantly or discordantly; of these: 2897338 mates make up the pairs; of these: 2821768 (97.39%) aligned 0 times 41557 (1.43%) aligned exactly 1 time 34013 (1.17%) aligned >1 times 88.92% overall alignment rate Time searching: 00:08:56 Overall time: 00:08:56 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] 10606553 / 11271240 = 0.9410 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 18:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.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 18:43:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:43:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:43:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.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 18:43:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:43:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:44:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.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 18:44:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:44:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:44:35: 1000000 INFO @ Fri, 05 Jul 2019 18:44:37: 1000000 INFO @ Fri, 05 Jul 2019 18:44:38: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:44:38: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:44:38: #1 total tags in treatment: 623008 INFO @ Fri, 05 Jul 2019 18:44:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:44:38: #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 18:44:38: #1 tags after filtering in treatment: 511936 INFO @ Fri, 05 Jul 2019 18:44:38: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 18:44:38: #1 finished! INFO @ Fri, 05 Jul 2019 18:44:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:44:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:44:38: #2 number of paired peaks: 276 WARNING @ Fri, 05 Jul 2019 18:44:38: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Fri, 05 Jul 2019 18:44:38: start model_add_line... INFO @ Fri, 05 Jul 2019 18:44:38: start X-correlation... INFO @ Fri, 05 Jul 2019 18:44:38: end of X-cor INFO @ Fri, 05 Jul 2019 18:44:38: #2 finished! INFO @ Fri, 05 Jul 2019 18:44:38: #2 predicted fragment length is 183 bps INFO @ Fri, 05 Jul 2019 18:44:38: #2 alternative fragment length(s) may be 58,95,111,148,167,183,208,231,270,304,334,349,408,441,469,507,541,565,588 bps INFO @ Fri, 05 Jul 2019 18:44:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.05_model.r INFO @ Fri, 05 Jul 2019 18:44:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:44:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:44:39: 1000000 INFO @ Fri, 05 Jul 2019 18:44:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:44:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:44:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:44:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.05_summits.bed INFO @ Fri, 05 Jul 2019 18:44:41: Done! INFO @ Fri, 05 Jul 2019 18:44:41: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:44:41: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:44:41: #1 total tags in treatment: 623008 INFO @ Fri, 05 Jul 2019 18:44:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:44:41: #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 18:44:41: #1 tags after filtering in treatment: 511936 INFO @ Fri, 05 Jul 2019 18:44:41: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 18:44:41: #1 finished! INFO @ Fri, 05 Jul 2019 18:44:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:44:41: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (95 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 18:44:41: #2 number of paired peaks: 276 WARNING @ Fri, 05 Jul 2019 18:44:41: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Fri, 05 Jul 2019 18:44:41: start model_add_line... INFO @ Fri, 05 Jul 2019 18:44:41: start X-correlation... INFO @ Fri, 05 Jul 2019 18:44:41: end of X-cor INFO @ Fri, 05 Jul 2019 18:44:41: #2 finished! INFO @ Fri, 05 Jul 2019 18:44:41: #2 predicted fragment length is 183 bps INFO @ Fri, 05 Jul 2019 18:44:41: #2 alternative fragment length(s) may be 58,95,111,148,167,183,208,231,270,304,334,349,408,441,469,507,541,565,588 bps INFO @ Fri, 05 Jul 2019 18:44:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.10_model.r INFO @ Fri, 05 Jul 2019 18:44:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:44:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:44:42: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:44:42: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:44:42: #1 total tags in treatment: 623008 INFO @ Fri, 05 Jul 2019 18:44:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:44:42: #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 18:44:42: #1 tags after filtering in treatment: 511936 INFO @ Fri, 05 Jul 2019 18:44:42: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 18:44:42: #1 finished! INFO @ Fri, 05 Jul 2019 18:44:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:44:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:44:42: #2 number of paired peaks: 276 WARNING @ Fri, 05 Jul 2019 18:44:42: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Fri, 05 Jul 2019 18:44:42: start model_add_line... INFO @ Fri, 05 Jul 2019 18:44:42: start X-correlation... INFO @ Fri, 05 Jul 2019 18:44:42: end of X-cor INFO @ Fri, 05 Jul 2019 18:44:42: #2 finished! INFO @ Fri, 05 Jul 2019 18:44:42: #2 predicted fragment length is 183 bps INFO @ Fri, 05 Jul 2019 18:44:42: #2 alternative fragment length(s) may be 58,95,111,148,167,183,208,231,270,304,334,349,408,441,469,507,541,565,588 bps INFO @ Fri, 05 Jul 2019 18:44:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.20_model.r INFO @ Fri, 05 Jul 2019 18:44:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:44:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:44:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:44:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:44:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:44:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.10_summits.bed INFO @ Fri, 05 Jul 2019 18:44:43: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 18:44:44: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:44:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:44:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:44:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585827/ERX585827.20_summits.bed INFO @ Fri, 05 Jul 2019 18:44:44: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。