Job ID = 2006148 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,095,161 reads read : 4,095,161 reads written : 4,095,161 spots read : 3,943,773 reads read : 3,943,773 reads written : 3,943,773 spots read : 4,026,458 reads read : 4,026,458 reads written : 4,026,458 spots read : 3,881,456 reads read : 3,881,456 reads written : 3,881,456 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: 00:03:42 15946848 reads; of these: 15946848 (100.00%) were unpaired; of these: 797050 (5.00%) aligned 0 times 12758987 (80.01%) aligned exactly 1 time 2390811 (14.99%) aligned >1 times 95.00% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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_rmdupse_core] 14885096 / 15149798 = 0.9825 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 15:26:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.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 15:26:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:26:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:26:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.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 15:26:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:26:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:26:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.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 15:26:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:26:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:26:59: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:26:59: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:26:59: #1 total tags in treatment: 264702 INFO @ Fri, 05 Jul 2019 15:26:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:26:59: #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 15:26:59: #1 tags after filtering in treatment: 264702 INFO @ Fri, 05 Jul 2019 15:26:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:26:59: #1 finished! INFO @ Fri, 05 Jul 2019 15:26:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:26:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:27:00: #2 number of paired peaks: 514 WARNING @ Fri, 05 Jul 2019 15:27:00: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Fri, 05 Jul 2019 15:27:00: start model_add_line... INFO @ Fri, 05 Jul 2019 15:27:00: start X-correlation... INFO @ Fri, 05 Jul 2019 15:27:00: end of X-cor INFO @ Fri, 05 Jul 2019 15:27:00: #2 finished! INFO @ Fri, 05 Jul 2019 15:27:00: #2 predicted fragment length is 79 bps INFO @ Fri, 05 Jul 2019 15:27:00: #2 alternative fragment length(s) may be 32,79,86,106,142,176,237,259,412,477,495,527,548,591,595 bps INFO @ Fri, 05 Jul 2019 15:27:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.05_model.r WARNING @ Fri, 05 Jul 2019 15:27:00: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:27:00: #2 You may need to consider one of the other alternative d(s): 32,79,86,106,142,176,237,259,412,477,495,527,548,591,595 WARNING @ Fri, 05 Jul 2019 15:27:00: #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 15:27:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:27:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:27:00: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:27:00: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:27:00: #1 total tags in treatment: 264702 INFO @ Fri, 05 Jul 2019 15:27:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:27:00: #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 15:27:00: #1 tags after filtering in treatment: 264702 INFO @ Fri, 05 Jul 2019 15:27:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:27:00: #1 finished! INFO @ Fri, 05 Jul 2019 15:27:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:27:00: #2 number of paired peaks: 514 WARNING @ Fri, 05 Jul 2019 15:27:00: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Fri, 05 Jul 2019 15:27:00: start model_add_line... INFO @ Fri, 05 Jul 2019 15:27:00: start X-correlation... INFO @ Fri, 05 Jul 2019 15:27:00: end of X-cor INFO @ Fri, 05 Jul 2019 15:27:00: #2 finished! INFO @ Fri, 05 Jul 2019 15:27:00: #2 predicted fragment length is 79 bps INFO @ Fri, 05 Jul 2019 15:27:00: #2 alternative fragment length(s) may be 32,79,86,106,142,176,237,259,412,477,495,527,548,591,595 bps INFO @ Fri, 05 Jul 2019 15:27:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.10_model.r WARNING @ Fri, 05 Jul 2019 15:27:00: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:27:00: #2 You may need to consider one of the other alternative d(s): 32,79,86,106,142,176,237,259,412,477,495,527,548,591,595 WARNING @ Fri, 05 Jul 2019 15:27:00: #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 15:27:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:27:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:27:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:27:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:27:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:27:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.05_summits.bed INFO @ Fri, 05 Jul 2019 15:27:01: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (120 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 15:27:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:27:01: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:27:01: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:27:01: #1 total tags in treatment: 264702 INFO @ Fri, 05 Jul 2019 15:27:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:27:01: #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 15:27:01: #1 tags after filtering in treatment: 264702 INFO @ Fri, 05 Jul 2019 15:27:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:27:01: #1 finished! INFO @ Fri, 05 Jul 2019 15:27:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:27:01: #2 number of paired peaks: 514 WARNING @ Fri, 05 Jul 2019 15:27:01: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Fri, 05 Jul 2019 15:27:01: start model_add_line... INFO @ Fri, 05 Jul 2019 15:27:01: start X-correlation... INFO @ Fri, 05 Jul 2019 15:27:01: end of X-cor INFO @ Fri, 05 Jul 2019 15:27:01: #2 finished! INFO @ Fri, 05 Jul 2019 15:27:01: #2 predicted fragment length is 79 bps INFO @ Fri, 05 Jul 2019 15:27:01: #2 alternative fragment length(s) may be 32,79,86,106,142,176,237,259,412,477,495,527,548,591,595 bps INFO @ Fri, 05 Jul 2019 15:27:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.20_model.r WARNING @ Fri, 05 Jul 2019 15:27:01: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:27:01: #2 You may need to consider one of the other alternative d(s): 32,79,86,106,142,176,237,259,412,477,495,527,548,591,595 WARNING @ Fri, 05 Jul 2019 15:27:01: #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 15:27:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:27:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:27:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:27:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.10_summits.bed INFO @ Fri, 05 Jul 2019 15:27:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:27:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:27:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:27:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:27:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548115/ERX2548115.20_summits.bed INFO @ Fri, 05 Jul 2019 15:27:03: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling