Job ID = 2008998 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,073,115 reads read : 9,073,115 reads written : 9,073,115 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637544.sra.cache’: 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: 00:01:32 9073115 reads; of these: 9073115 (100.00%) were unpaired; of these: 2198590 (24.23%) aligned 0 times 5525421 (60.90%) aligned exactly 1 time 1349104 (14.87%) aligned >1 times 75.77% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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_rmdupse_core] 3071159 / 6874525 = 0.4467 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 19:09:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.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 19:09:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:09:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:09:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.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 19:09:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:09:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:09:40: 1000000 INFO @ Fri, 05 Jul 2019 19:09:41: 1000000 INFO @ Fri, 05 Jul 2019 19:09:48: 2000000 INFO @ Fri, 05 Jul 2019 19:09:49: 2000000 INFO @ Fri, 05 Jul 2019 19:09:55: 3000000 INFO @ Fri, 05 Jul 2019 19:09:56: 3000000 INFO @ Fri, 05 Jul 2019 19:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.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 19:09:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:09:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:10:01: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:10:01: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:10:01: #1 total tags in treatment: 3803366 INFO @ Fri, 05 Jul 2019 19:10:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:10:01: #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 19:10:02: #1 tags after filtering in treatment: 3803366 INFO @ Fri, 05 Jul 2019 19:10:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:10:02: #1 finished! INFO @ Fri, 05 Jul 2019 19:10:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:10:02: #2 number of paired peaks: 130 WARNING @ Fri, 05 Jul 2019 19:10:02: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Fri, 05 Jul 2019 19:10:02: start model_add_line... INFO @ Fri, 05 Jul 2019 19:10:02: start X-correlation... INFO @ Fri, 05 Jul 2019 19:10:02: end of X-cor INFO @ Fri, 05 Jul 2019 19:10:02: #2 finished! INFO @ Fri, 05 Jul 2019 19:10:02: #2 predicted fragment length is 57 bps INFO @ Fri, 05 Jul 2019 19:10:02: #2 alternative fragment length(s) may be 3,57 bps INFO @ Fri, 05 Jul 2019 19:10:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.05_model.r INFO @ Fri, 05 Jul 2019 19:10:02: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:10:02: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:10:02: #1 total tags in treatment: 3803366 INFO @ Fri, 05 Jul 2019 19:10:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:10:02: #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 19:10:03: #1 tags after filtering in treatment: 3803366 INFO @ Fri, 05 Jul 2019 19:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:10:03: #1 finished! INFO @ Fri, 05 Jul 2019 19:10:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:10:03: #2 number of paired peaks: 130 WARNING @ Fri, 05 Jul 2019 19:10:03: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Fri, 05 Jul 2019 19:10:03: start model_add_line... INFO @ Fri, 05 Jul 2019 19:10:03: start X-correlation... INFO @ Fri, 05 Jul 2019 19:10:03: end of X-cor INFO @ Fri, 05 Jul 2019 19:10:03: #2 finished! INFO @ Fri, 05 Jul 2019 19:10:03: #2 predicted fragment length is 57 bps INFO @ Fri, 05 Jul 2019 19:10:03: #2 alternative fragment length(s) may be 3,57 bps INFO @ Fri, 05 Jul 2019 19:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.10_model.r INFO @ Fri, 05 Jul 2019 19:10:06: 1000000 WARNING @ Fri, 05 Jul 2019 19:10:15: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:10:15: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Fri, 05 Jul 2019 19:10:15: #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 19:10:15: #3 Call peaks... WARNING @ Fri, 05 Jul 2019 19:10:15: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:10:15: #2 You may need to consider one of the other alternative d(s): 3,57 INFO @ Fri, 05 Jul 2019 19:10:15: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 05 Jul 2019 19:10:15: #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 19:10:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:10:16: 2000000 INFO @ Fri, 05 Jul 2019 19:10:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:10:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:10:25: 3000000 INFO @ Fri, 05 Jul 2019 19:10:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:10:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:10:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.05_summits.bed INFO @ Fri, 05 Jul 2019 19:10:28: Done! INFO @ Fri, 05 Jul 2019 19:10:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:10:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:10:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.10_summits.bed INFO @ Fri, 05 Jul 2019 19:10:28: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (3938 records, 4 fields): 6 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (2167 records, 4 fields): 6 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:10:32: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:10:32: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:10:32: #1 total tags in treatment: 3803366 INFO @ Fri, 05 Jul 2019 19:10:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:10:32: #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 19:10:32: #1 tags after filtering in treatment: 3803366 INFO @ Fri, 05 Jul 2019 19:10:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:10:32: #1 finished! INFO @ Fri, 05 Jul 2019 19:10:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:10:33: #2 number of paired peaks: 130 WARNING @ Fri, 05 Jul 2019 19:10:33: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Fri, 05 Jul 2019 19:10:33: start model_add_line... INFO @ Fri, 05 Jul 2019 19:10:33: start X-correlation... INFO @ Fri, 05 Jul 2019 19:10:33: end of X-cor INFO @ Fri, 05 Jul 2019 19:10:33: #2 finished! INFO @ Fri, 05 Jul 2019 19:10:33: #2 predicted fragment length is 57 bps INFO @ Fri, 05 Jul 2019 19:10:33: #2 alternative fragment length(s) may be 3,57 bps INFO @ Fri, 05 Jul 2019 19:10:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.20_model.r BedGraph に変換しました。 BigWig に変換中... WARNING @ Fri, 05 Jul 2019 19:10:51: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:10:51: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Fri, 05 Jul 2019 19:10:51: #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 19:10:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:10:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 19:11:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:11:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:11:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594018/ERX594018.20_summits.bed INFO @ Fri, 05 Jul 2019 19:11:08: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (779 records, 4 fields): 4 millis CompletedMACS2peakCalling