Job ID = 2008067 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,638,115 reads read : 3,276,230 reads written : 3,276,230 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: 00:02:00 1638115 reads; of these: 1638115 (100.00%) were paired; of these: 162339 (9.91%) aligned concordantly 0 times 1355644 (82.76%) aligned concordantly exactly 1 time 120132 (7.33%) aligned concordantly >1 times ---- 162339 pairs aligned concordantly 0 times; of these: 74234 (45.73%) aligned discordantly 1 time ---- 88105 pairs aligned 0 times concordantly or discordantly; of these: 176210 mates make up the pairs; of these: 130571 (74.10%) aligned 0 times 28172 (15.99%) aligned exactly 1 time 17467 (9.91%) aligned >1 times 96.01% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 63887 / 1531812 = 0.0417 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 17:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.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 17:32:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:32:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:32:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.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 17:32:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:32:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:32:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.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 17:32:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:32:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:32:35: 1000000 INFO @ Fri, 05 Jul 2019 17:32:36: 1000000 INFO @ Fri, 05 Jul 2019 17:32:37: 1000000 INFO @ Fri, 05 Jul 2019 17:32:47: 2000000 INFO @ Fri, 05 Jul 2019 17:32:51: 2000000 INFO @ Fri, 05 Jul 2019 17:32:52: 2000000 INFO @ Fri, 05 Jul 2019 17:32:59: 3000000 INFO @ Fri, 05 Jul 2019 17:33:00: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:33:00: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:33:00: #1 total tags in treatment: 1413108 INFO @ Fri, 05 Jul 2019 17:33:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:33:00: #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 17:33:00: #1 tags after filtering in treatment: 1317892 INFO @ Fri, 05 Jul 2019 17:33:00: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:33:00: #1 finished! INFO @ Fri, 05 Jul 2019 17:33:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:33:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:33:00: #2 number of paired peaks: 173 WARNING @ Fri, 05 Jul 2019 17:33:00: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Fri, 05 Jul 2019 17:33:00: start model_add_line... INFO @ Fri, 05 Jul 2019 17:33:00: start X-correlation... INFO @ Fri, 05 Jul 2019 17:33:00: end of X-cor INFO @ Fri, 05 Jul 2019 17:33:00: #2 finished! INFO @ Fri, 05 Jul 2019 17:33:00: #2 predicted fragment length is 167 bps INFO @ Fri, 05 Jul 2019 17:33:00: #2 alternative fragment length(s) may be 152,167,184 bps INFO @ Fri, 05 Jul 2019 17:33:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.10_model.r WARNING @ Fri, 05 Jul 2019 17:33:00: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:33:00: #2 You may need to consider one of the other alternative d(s): 152,167,184 WARNING @ Fri, 05 Jul 2019 17:33:00: #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 17:33:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:33:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:33:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:33:05: 3000000 INFO @ Fri, 05 Jul 2019 17:33:05: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:33:05: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:33:05: #1 total tags in treatment: 1413108 INFO @ Fri, 05 Jul 2019 17:33:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:33:05: #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 17:33:05: #1 tags after filtering in treatment: 1317892 INFO @ Fri, 05 Jul 2019 17:33:05: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:33:05: #1 finished! INFO @ Fri, 05 Jul 2019 17:33:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:33:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:33:05: #2 number of paired peaks: 173 WARNING @ Fri, 05 Jul 2019 17:33:05: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Fri, 05 Jul 2019 17:33:05: start model_add_line... INFO @ Fri, 05 Jul 2019 17:33:05: start X-correlation... INFO @ Fri, 05 Jul 2019 17:33:05: end of X-cor INFO @ Fri, 05 Jul 2019 17:33:05: #2 finished! INFO @ Fri, 05 Jul 2019 17:33:05: #2 predicted fragment length is 167 bps INFO @ Fri, 05 Jul 2019 17:33:05: #2 alternative fragment length(s) may be 152,167,184 bps INFO @ Fri, 05 Jul 2019 17:33:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.05_model.r WARNING @ Fri, 05 Jul 2019 17:33:05: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:33:05: #2 You may need to consider one of the other alternative d(s): 152,167,184 WARNING @ Fri, 05 Jul 2019 17:33:05: #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 17:33:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:33:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:33:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:33:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:33:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.10_summits.bed INFO @ Fri, 05 Jul 2019 17:33:06: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (370 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:33:06: 3000000 INFO @ Fri, 05 Jul 2019 17:33:06: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:33:06: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:33:06: #1 total tags in treatment: 1413108 INFO @ Fri, 05 Jul 2019 17:33:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:33:06: #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 17:33:06: #1 tags after filtering in treatment: 1317892 INFO @ Fri, 05 Jul 2019 17:33:06: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:33:06: #1 finished! INFO @ Fri, 05 Jul 2019 17:33:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:33:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:33:06: #2 number of paired peaks: 173 WARNING @ Fri, 05 Jul 2019 17:33:06: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Fri, 05 Jul 2019 17:33:06: start model_add_line... INFO @ Fri, 05 Jul 2019 17:33:06: start X-correlation... INFO @ Fri, 05 Jul 2019 17:33:06: end of X-cor INFO @ Fri, 05 Jul 2019 17:33:06: #2 finished! INFO @ Fri, 05 Jul 2019 17:33:06: #2 predicted fragment length is 167 bps INFO @ Fri, 05 Jul 2019 17:33:06: #2 alternative fragment length(s) may be 152,167,184 bps INFO @ Fri, 05 Jul 2019 17:33:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.20_model.r WARNING @ Fri, 05 Jul 2019 17:33:06: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:33:06: #2 You may need to consider one of the other alternative d(s): 152,167,184 WARNING @ Fri, 05 Jul 2019 17:33:06: #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 17:33:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:33:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:33:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:33:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:33:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:33:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:33:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.05_summits.bed INFO @ Fri, 05 Jul 2019 17:33:12: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (591 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 17:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:33:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:33:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471850/ERX471850.20_summits.bed INFO @ Fri, 05 Jul 2019 17:33:13: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。