Job ID = 2008043 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,720,454 reads read : 3,440,908 reads written : 3,440,908 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: 00:02:01 1720454 reads; of these: 1720454 (100.00%) were paired; of these: 191600 (11.14%) aligned concordantly 0 times 1414304 (82.21%) aligned concordantly exactly 1 time 114550 (6.66%) aligned concordantly >1 times ---- 191600 pairs aligned concordantly 0 times; of these: 106177 (55.42%) aligned discordantly 1 time ---- 85423 pairs aligned 0 times concordantly or discordantly; of these: 170846 mates make up the pairs; of these: 112840 (66.05%) aligned 0 times 34924 (20.44%) aligned exactly 1 time 23082 (13.51%) aligned >1 times 96.72% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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] 43890 / 1607025 = 0.0273 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 17:19:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.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 17:19:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:19:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:19:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.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 17:19:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:19:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:20:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.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 17:20:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:20:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:20:07: 1000000 INFO @ Fri, 05 Jul 2019 17:20:09: 1000000 INFO @ Fri, 05 Jul 2019 17:20:09: 1000000 INFO @ Fri, 05 Jul 2019 17:20:15: 2000000 INFO @ Fri, 05 Jul 2019 17:20:17: 2000000 INFO @ Fri, 05 Jul 2019 17:20:19: 2000000 INFO @ Fri, 05 Jul 2019 17:20:23: 3000000 INFO @ Fri, 05 Jul 2019 17:20:24: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:20:24: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:20:24: #1 total tags in treatment: 1486324 INFO @ Fri, 05 Jul 2019 17:20:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:20:24: #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 17:20:24: #1 tags after filtering in treatment: 1371081 INFO @ Fri, 05 Jul 2019 17:20:24: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 05 Jul 2019 17:20:24: #1 finished! INFO @ Fri, 05 Jul 2019 17:20:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:20:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:20:24: 3000000 INFO @ Fri, 05 Jul 2019 17:20:25: #2 number of paired peaks: 229 WARNING @ Fri, 05 Jul 2019 17:20:25: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 05 Jul 2019 17:20:25: start model_add_line... INFO @ Fri, 05 Jul 2019 17:20:25: start X-correlation... INFO @ Fri, 05 Jul 2019 17:20:25: end of X-cor INFO @ Fri, 05 Jul 2019 17:20:25: #2 finished! INFO @ Fri, 05 Jul 2019 17:20:25: #2 predicted fragment length is 189 bps INFO @ Fri, 05 Jul 2019 17:20:25: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 05 Jul 2019 17:20:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.05_model.r WARNING @ Fri, 05 Jul 2019 17:20:25: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:20:25: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Fri, 05 Jul 2019 17:20:25: #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 17:20:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:20:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:20:26: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:20:26: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:20:26: #1 total tags in treatment: 1486324 INFO @ Fri, 05 Jul 2019 17:20:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:20:26: #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 17:20:26: #1 tags after filtering in treatment: 1371081 INFO @ Fri, 05 Jul 2019 17:20:26: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 05 Jul 2019 17:20:26: #1 finished! INFO @ Fri, 05 Jul 2019 17:20:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:20:26: #2 number of paired peaks: 229 WARNING @ Fri, 05 Jul 2019 17:20:26: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 05 Jul 2019 17:20:26: start model_add_line... INFO @ Fri, 05 Jul 2019 17:20:26: start X-correlation... INFO @ Fri, 05 Jul 2019 17:20:26: end of X-cor INFO @ Fri, 05 Jul 2019 17:20:26: #2 finished! INFO @ Fri, 05 Jul 2019 17:20:26: #2 predicted fragment length is 189 bps INFO @ Fri, 05 Jul 2019 17:20:26: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 05 Jul 2019 17:20:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.20_model.r WARNING @ Fri, 05 Jul 2019 17:20:26: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:20:26: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Fri, 05 Jul 2019 17:20:26: #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 17:20:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:20:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:20:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:20:30: 3000000 INFO @ Fri, 05 Jul 2019 17:20:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:20:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:20:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:20:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.05_summits.bed INFO @ Fri, 05 Jul 2019 17:20:32: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (623 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 17:20:32: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:20:32: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:20:32: #1 total tags in treatment: 1486324 INFO @ Fri, 05 Jul 2019 17:20:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:20:32: #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 17:20:32: #1 tags after filtering in treatment: 1371081 INFO @ Fri, 05 Jul 2019 17:20:32: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 05 Jul 2019 17:20:32: #1 finished! INFO @ Fri, 05 Jul 2019 17:20:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:20:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:20:32: #2 number of paired peaks: 229 WARNING @ Fri, 05 Jul 2019 17:20:32: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 05 Jul 2019 17:20:32: start model_add_line... INFO @ Fri, 05 Jul 2019 17:20:32: start X-correlation... INFO @ Fri, 05 Jul 2019 17:20:32: end of X-cor INFO @ Fri, 05 Jul 2019 17:20:32: #2 finished! INFO @ Fri, 05 Jul 2019 17:20:32: #2 predicted fragment length is 189 bps INFO @ Fri, 05 Jul 2019 17:20:32: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 05 Jul 2019 17:20:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.10_model.r WARNING @ Fri, 05 Jul 2019 17:20:32: #2 Since the d (189) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:20:32: #2 You may need to consider one of the other alternative d(s): 189 WARNING @ Fri, 05 Jul 2019 17:20:32: #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 17:20:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:20:32: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:20:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:20:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:20:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.20_summits.bed INFO @ Fri, 05 Jul 2019 17:20:34: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:20:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:20:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:20:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:20:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471827/ERX471827.10_summits.bed INFO @ Fri, 05 Jul 2019 17:20:40: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (425 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。