Job ID = 2007982 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,669,843 reads read : 3,339,686 reads written : 3,339,686 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: 00:02:20 1669843 reads; of these: 1669843 (100.00%) were paired; of these: 303332 (18.17%) aligned concordantly 0 times 1251001 (74.92%) aligned concordantly exactly 1 time 115510 (6.92%) aligned concordantly >1 times ---- 303332 pairs aligned concordantly 0 times; of these: 34073 (11.23%) aligned discordantly 1 time ---- 269259 pairs aligned 0 times concordantly or discordantly; of these: 538518 mates make up the pairs; of these: 511380 (94.96%) aligned 0 times 17230 (3.20%) aligned exactly 1 time 9908 (1.84%) aligned >1 times 84.69% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 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] 255599 / 1395899 = 0.1831 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 17:07:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.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 17:07:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:07:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.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 17:07:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:07:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:07:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.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 17:07:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:07:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:07:29: 1000000 INFO @ Fri, 05 Jul 2019 17:07:31: 1000000 INFO @ Fri, 05 Jul 2019 17:07:33: 1000000 INFO @ Fri, 05 Jul 2019 17:07:36: 2000000 INFO @ Fri, 05 Jul 2019 17:07:39: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:07:39: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:07:39: #1 total tags in treatment: 1114507 INFO @ Fri, 05 Jul 2019 17:07:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:07:39: #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 17:07:39: #1 tags after filtering in treatment: 1064131 INFO @ Fri, 05 Jul 2019 17:07:39: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:07:39: #1 finished! INFO @ Fri, 05 Jul 2019 17:07:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:07:39: #2 number of paired peaks: 163 WARNING @ Fri, 05 Jul 2019 17:07:39: 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 17:07:39: start model_add_line... INFO @ Fri, 05 Jul 2019 17:07:39: start X-correlation... INFO @ Fri, 05 Jul 2019 17:07:39: end of X-cor INFO @ Fri, 05 Jul 2019 17:07:39: #2 finished! INFO @ Fri, 05 Jul 2019 17:07:39: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 17:07:39: #2 alternative fragment length(s) may be 1,21,74,105,144,164,199,226,289,489,560,584 bps INFO @ Fri, 05 Jul 2019 17:07:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.05_model.r WARNING @ Fri, 05 Jul 2019 17:07:39: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:07:39: #2 You may need to consider one of the other alternative d(s): 1,21,74,105,144,164,199,226,289,489,560,584 WARNING @ Fri, 05 Jul 2019 17:07:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:07:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:07:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:07:39: 2000000 INFO @ Fri, 05 Jul 2019 17:07:42: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:07:42: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:07:42: #1 total tags in treatment: 1114507 INFO @ Fri, 05 Jul 2019 17:07:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:07:42: #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 17:07:42: #1 tags after filtering in treatment: 1064131 INFO @ Fri, 05 Jul 2019 17:07:42: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:07:42: #1 finished! INFO @ Fri, 05 Jul 2019 17:07:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:07:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:07:42: #2 number of paired peaks: 163 WARNING @ Fri, 05 Jul 2019 17:07:42: 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 17:07:42: start model_add_line... INFO @ Fri, 05 Jul 2019 17:07:42: start X-correlation... INFO @ Fri, 05 Jul 2019 17:07:42: end of X-cor INFO @ Fri, 05 Jul 2019 17:07:42: #2 finished! INFO @ Fri, 05 Jul 2019 17:07:42: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 17:07:42: #2 alternative fragment length(s) may be 1,21,74,105,144,164,199,226,289,489,560,584 bps INFO @ Fri, 05 Jul 2019 17:07:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.10_model.r WARNING @ Fri, 05 Jul 2019 17:07:42: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:07:42: #2 You may need to consider one of the other alternative d(s): 1,21,74,105,144,164,199,226,289,489,560,584 WARNING @ Fri, 05 Jul 2019 17:07:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:07:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:07:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:07:42: 2000000 INFO @ Fri, 05 Jul 2019 17:07:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:07:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:07:45: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:07:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:07:46: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:07:46: #1 total tags in treatment: 1114507 INFO @ Fri, 05 Jul 2019 17:07:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:07:46: #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 17:07:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:07:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.05_summits.bed INFO @ Fri, 05 Jul 2019 17:07:46: Done! INFO @ Fri, 05 Jul 2019 17:07:46: #1 tags after filtering in treatment: 1064131 INFO @ Fri, 05 Jul 2019 17:07:46: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:07:46: #1 finished! INFO @ Fri, 05 Jul 2019 17:07:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:07:46: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (90 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:07:46: #2 number of paired peaks: 163 WARNING @ Fri, 05 Jul 2019 17:07:46: 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 17:07:46: start model_add_line... INFO @ Fri, 05 Jul 2019 17:07:46: start X-correlation... INFO @ Fri, 05 Jul 2019 17:07:46: end of X-cor INFO @ Fri, 05 Jul 2019 17:07:46: #2 finished! INFO @ Fri, 05 Jul 2019 17:07:46: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 17:07:46: #2 alternative fragment length(s) may be 1,21,74,105,144,164,199,226,289,489,560,584 bps INFO @ Fri, 05 Jul 2019 17:07:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.20_model.r WARNING @ Fri, 05 Jul 2019 17:07:46: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:07:46: #2 You may need to consider one of the other alternative d(s): 1,21,74,105,144,164,199,226,289,489,560,584 WARNING @ Fri, 05 Jul 2019 17:07:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:07:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:07:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:07:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:07:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:07:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.10_summits.bed INFO @ Fri, 05 Jul 2019 17:07:47: Done! CompletedMACS2peakCalling pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 17:07:50: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:07:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:07:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:07:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471772/ERX471772.20_summits.bed INFO @ Fri, 05 Jul 2019 17:07:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。