Job ID = 2007916 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,842,747 reads read : 3,685,494 reads written : 3,685,494 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: 00:02:08 1842747 reads; of these: 1842747 (100.00%) were paired; of these: 180146 (9.78%) aligned concordantly 0 times 1540182 (83.58%) aligned concordantly exactly 1 time 122419 (6.64%) aligned concordantly >1 times ---- 180146 pairs aligned concordantly 0 times; of these: 108548 (60.26%) aligned discordantly 1 time ---- 71598 pairs aligned 0 times concordantly or discordantly; of these: 143196 mates make up the pairs; of these: 93338 (65.18%) aligned 0 times 28177 (19.68%) aligned exactly 1 time 21681 (15.14%) aligned >1 times 97.47% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 33519 / 1756321 = 0.0191 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 16:47:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.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 16:47:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:47:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:47:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.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 16:47:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:47:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.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 16:47:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:47:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:47:40: 1000000 INFO @ Fri, 05 Jul 2019 16:47:43: 1000000 INFO @ Fri, 05 Jul 2019 16:47:47: 1000000 INFO @ Fri, 05 Jul 2019 16:47:49: 2000000 INFO @ Fri, 05 Jul 2019 16:47:53: 2000000 INFO @ Fri, 05 Jul 2019 16:47:58: 3000000 INFO @ Fri, 05 Jul 2019 16:48:00: 2000000 INFO @ Fri, 05 Jul 2019 16:48:02: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:48:02: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:48:02: #1 total tags in treatment: 1630255 INFO @ Fri, 05 Jul 2019 16:48:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:48:02: #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 16:48:02: #1 tags after filtering in treatment: 1493219 INFO @ Fri, 05 Jul 2019 16:48:02: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 05 Jul 2019 16:48:02: #1 finished! INFO @ Fri, 05 Jul 2019 16:48:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:48:02: #2 number of paired peaks: 272 WARNING @ Fri, 05 Jul 2019 16:48:02: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Fri, 05 Jul 2019 16:48:02: start model_add_line... INFO @ Fri, 05 Jul 2019 16:48:02: start X-correlation... INFO @ Fri, 05 Jul 2019 16:48:02: end of X-cor INFO @ Fri, 05 Jul 2019 16:48:02: #2 finished! INFO @ Fri, 05 Jul 2019 16:48:02: #2 predicted fragment length is 182 bps INFO @ Fri, 05 Jul 2019 16:48:02: #2 alternative fragment length(s) may be 182,203 bps INFO @ Fri, 05 Jul 2019 16:48:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.05_model.r WARNING @ Fri, 05 Jul 2019 16:48:02: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:48:02: #2 You may need to consider one of the other alternative d(s): 182,203 WARNING @ Fri, 05 Jul 2019 16:48:02: #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 16:48:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:48:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:48:03: 3000000 INFO @ Fri, 05 Jul 2019 16:48:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:48:09: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:48:09: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:48:09: #1 total tags in treatment: 1630255 INFO @ Fri, 05 Jul 2019 16:48:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:48:09: #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 16:48:09: #1 tags after filtering in treatment: 1493219 INFO @ Fri, 05 Jul 2019 16:48:09: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 05 Jul 2019 16:48:09: #1 finished! INFO @ Fri, 05 Jul 2019 16:48:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:48:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:48:09: #2 number of paired peaks: 272 WARNING @ Fri, 05 Jul 2019 16:48:09: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Fri, 05 Jul 2019 16:48:09: start model_add_line... INFO @ Fri, 05 Jul 2019 16:48:09: start X-correlation... INFO @ Fri, 05 Jul 2019 16:48:09: end of X-cor INFO @ Fri, 05 Jul 2019 16:48:09: #2 finished! INFO @ Fri, 05 Jul 2019 16:48:09: #2 predicted fragment length is 182 bps INFO @ Fri, 05 Jul 2019 16:48:09: #2 alternative fragment length(s) may be 182,203 bps INFO @ Fri, 05 Jul 2019 16:48:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.10_model.r WARNING @ Fri, 05 Jul 2019 16:48:09: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:48:09: #2 You may need to consider one of the other alternative d(s): 182,203 WARNING @ Fri, 05 Jul 2019 16:48:09: #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 16:48:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:48:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:48:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:48:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:48:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.05_summits.bed INFO @ Fri, 05 Jul 2019 16:48:10: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (632 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 16:48:13: 3000000 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:48:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:48:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:48:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:48:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.10_summits.bed INFO @ Fri, 05 Jul 2019 16:48:16: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:48:19: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:48:19: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:48:19: #1 total tags in treatment: 1630255 INFO @ Fri, 05 Jul 2019 16:48:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:48:19: #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 16:48:19: #1 tags after filtering in treatment: 1493219 INFO @ Fri, 05 Jul 2019 16:48:19: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 05 Jul 2019 16:48:19: #1 finished! INFO @ Fri, 05 Jul 2019 16:48:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:48:19: #2 number of paired peaks: 272 WARNING @ Fri, 05 Jul 2019 16:48:19: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Fri, 05 Jul 2019 16:48:19: start model_add_line... INFO @ Fri, 05 Jul 2019 16:48:19: start X-correlation... INFO @ Fri, 05 Jul 2019 16:48:19: end of X-cor INFO @ Fri, 05 Jul 2019 16:48:19: #2 finished! INFO @ Fri, 05 Jul 2019 16:48:19: #2 predicted fragment length is 182 bps INFO @ Fri, 05 Jul 2019 16:48:19: #2 alternative fragment length(s) may be 182,203 bps INFO @ Fri, 05 Jul 2019 16:48:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.20_model.r WARNING @ Fri, 05 Jul 2019 16:48:19: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:48:19: #2 You may need to consider one of the other alternative d(s): 182,203 WARNING @ Fri, 05 Jul 2019 16:48:19: #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 16:48:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:48:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:48:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:48:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:48:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:48:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471713/ERX471713.20_summits.bed INFO @ Fri, 05 Jul 2019 16:48:27: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (267 records, 4 fields): 4 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。