Job ID = 2006149 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,101,858 reads read : 2,101,858 reads written : 2,101,858 spots read : 2,015,811 reads read : 2,015,811 reads written : 2,015,811 spots read : 2,065,412 reads read : 2,065,412 reads written : 2,065,412 spots read : 1,985,946 reads read : 1,985,946 reads written : 1,985,946 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529357.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: 00:03:21 8169027 reads; of these: 8169027 (100.00%) were unpaired; of these: 782995 (9.58%) aligned 0 times 6116528 (74.87%) aligned exactly 1 time 1269504 (15.54%) aligned >1 times 90.42% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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] 7248949 / 7386032 = 0.9814 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 15:17:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.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 15:17:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:17:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:17:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.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 15:17:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:17:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:17:30: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:17:30: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:17:30: #1 total tags in treatment: 137083 INFO @ Fri, 05 Jul 2019 15:17:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:17:30: #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 15:17:30: #1 tags after filtering in treatment: 137083 INFO @ Fri, 05 Jul 2019 15:17:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:17:30: #1 finished! INFO @ Fri, 05 Jul 2019 15:17:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:17:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:17:30: #2 number of paired peaks: 417 WARNING @ Fri, 05 Jul 2019 15:17:30: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Fri, 05 Jul 2019 15:17:30: start model_add_line... INFO @ Fri, 05 Jul 2019 15:17:30: start X-correlation... INFO @ Fri, 05 Jul 2019 15:17:30: end of X-cor INFO @ Fri, 05 Jul 2019 15:17:30: #2 finished! INFO @ Fri, 05 Jul 2019 15:17:30: #2 predicted fragment length is 143 bps INFO @ Fri, 05 Jul 2019 15:17:30: #2 alternative fragment length(s) may be 52,73,134,143,164,231,256,274,343,505,523,569 bps INFO @ Fri, 05 Jul 2019 15:17:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.05_model.r WARNING @ Fri, 05 Jul 2019 15:17:30: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:17:30: #2 You may need to consider one of the other alternative d(s): 52,73,134,143,164,231,256,274,343,505,523,569 WARNING @ Fri, 05 Jul 2019 15:17:30: #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 15:17:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:17:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:17:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:17:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.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 15:17:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:17:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:17:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:17:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:17:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.05_summits.bed INFO @ Fri, 05 Jul 2019 15:17:31: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (53 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:17:31: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:17:31: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:17:31: #1 total tags in treatment: 137083 INFO @ Fri, 05 Jul 2019 15:17:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:17:31: #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 15:17:31: #1 tags after filtering in treatment: 137083 INFO @ Fri, 05 Jul 2019 15:17:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:17:31: #1 finished! INFO @ Fri, 05 Jul 2019 15:17:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:17:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:17:31: #2 number of paired peaks: 417 WARNING @ Fri, 05 Jul 2019 15:17:31: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Fri, 05 Jul 2019 15:17:31: start model_add_line... INFO @ Fri, 05 Jul 2019 15:17:31: start X-correlation... INFO @ Fri, 05 Jul 2019 15:17:31: end of X-cor INFO @ Fri, 05 Jul 2019 15:17:31: #2 finished! INFO @ Fri, 05 Jul 2019 15:17:31: #2 predicted fragment length is 143 bps INFO @ Fri, 05 Jul 2019 15:17:31: #2 alternative fragment length(s) may be 52,73,134,143,164,231,256,274,343,505,523,569 bps INFO @ Fri, 05 Jul 2019 15:17:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.10_model.r WARNING @ Fri, 05 Jul 2019 15:17:31: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:17:31: #2 You may need to consider one of the other alternative d(s): 52,73,134,143,164,231,256,274,343,505,523,569 WARNING @ Fri, 05 Jul 2019 15:17:31: #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 15:17:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:17:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:17:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:17:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:17:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:17:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.10_summits.bed INFO @ Fri, 05 Jul 2019 15:17:32: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:17:32: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:17:32: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:17:32: #1 total tags in treatment: 137083 INFO @ Fri, 05 Jul 2019 15:17:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:17:32: #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 15:17:32: #1 tags after filtering in treatment: 137083 INFO @ Fri, 05 Jul 2019 15:17:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:17:32: #1 finished! INFO @ Fri, 05 Jul 2019 15:17:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:17:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:17:32: #2 number of paired peaks: 417 WARNING @ Fri, 05 Jul 2019 15:17:32: Fewer paired peaks (417) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 417 pairs to build model! INFO @ Fri, 05 Jul 2019 15:17:32: start model_add_line... INFO @ Fri, 05 Jul 2019 15:17:32: start X-correlation... INFO @ Fri, 05 Jul 2019 15:17:32: end of X-cor INFO @ Fri, 05 Jul 2019 15:17:32: #2 finished! INFO @ Fri, 05 Jul 2019 15:17:32: #2 predicted fragment length is 143 bps INFO @ Fri, 05 Jul 2019 15:17:32: #2 alternative fragment length(s) may be 52,73,134,143,164,231,256,274,343,505,523,569 bps INFO @ Fri, 05 Jul 2019 15:17:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.20_model.r WARNING @ Fri, 05 Jul 2019 15:17:32: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:17:32: #2 You may need to consider one of the other alternative d(s): 52,73,134,143,164,231,256,274,343,505,523,569 WARNING @ Fri, 05 Jul 2019 15:17:32: #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 15:17:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:17:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:17:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:17:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:17:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:17:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548116/ERX2548116.20_summits.bed INFO @ Fri, 05 Jul 2019 15:17:33: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling