Job ID = 2006327 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,478,143 reads read : 2,478,143 reads written : 2,478,143 spots read : 2,379,807 reads read : 2,379,807 reads written : 2,379,807 spots read : 2,429,038 reads read : 2,429,038 reads written : 2,429,038 spots read : 2,341,066 reads read : 2,341,066 reads written : 2,341,066 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529498.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529499.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529500.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529501.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: 00:04:49 9628054 reads; of these: 9628054 (100.00%) were unpaired; of these: 677849 (7.04%) aligned 0 times 7510840 (78.01%) aligned exactly 1 time 1439365 (14.95%) aligned >1 times 92.96% overall alignment rate Time searching: 00:04:49 Overall time: 00:04:49 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] 8775742 / 8950205 = 0.9805 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 15:43:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.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 15:43:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:43:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:43:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.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 15:43:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:43:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:43:17: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:43:17: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:43:17: #1 total tags in treatment: 174463 INFO @ Fri, 05 Jul 2019 15:43:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:43:17: #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 15:43:17: #1 tags after filtering in treatment: 174463 INFO @ Fri, 05 Jul 2019 15:43:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:43:17: #1 finished! INFO @ Fri, 05 Jul 2019 15:43:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:43:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:43:17: #2 number of paired peaks: 470 WARNING @ Fri, 05 Jul 2019 15:43:17: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Fri, 05 Jul 2019 15:43:17: start model_add_line... INFO @ Fri, 05 Jul 2019 15:43:17: start X-correlation... INFO @ Fri, 05 Jul 2019 15:43:17: end of X-cor INFO @ Fri, 05 Jul 2019 15:43:17: #2 finished! INFO @ Fri, 05 Jul 2019 15:43:17: #2 predicted fragment length is 63 bps INFO @ Fri, 05 Jul 2019 15:43:17: #2 alternative fragment length(s) may be 4,63,156,198,257,304,382,402,433,488,528,585 bps INFO @ Fri, 05 Jul 2019 15:43:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.05_model.r WARNING @ Fri, 05 Jul 2019 15:43:17: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:43:17: #2 You may need to consider one of the other alternative d(s): 4,63,156,198,257,304,382,402,433,488,528,585 WARNING @ Fri, 05 Jul 2019 15:43:17: #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 15:43:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:43:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:43:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:43:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.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 15:43:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:43:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:43:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:43:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:43:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.05_summits.bed INFO @ Fri, 05 Jul 2019 15:43:17: Done! INFO @ Fri, 05 Jul 2019 15:43:18: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:43:18: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:43:18: #1 total tags in treatment: 174463 INFO @ Fri, 05 Jul 2019 15:43:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:43:18: #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 15:43:18: #1 tags after filtering in treatment: 174463 INFO @ Fri, 05 Jul 2019 15:43:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:43:18: #1 finished! INFO @ Fri, 05 Jul 2019 15:43:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:43:18: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:43:18: #2 number of paired peaks: 470 WARNING @ Fri, 05 Jul 2019 15:43:18: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Fri, 05 Jul 2019 15:43:18: start model_add_line... INFO @ Fri, 05 Jul 2019 15:43:18: start X-correlation... INFO @ Fri, 05 Jul 2019 15:43:18: end of X-cor INFO @ Fri, 05 Jul 2019 15:43:18: #2 finished! INFO @ Fri, 05 Jul 2019 15:43:18: #2 predicted fragment length is 63 bps INFO @ Fri, 05 Jul 2019 15:43:18: #2 alternative fragment length(s) may be 4,63,156,198,257,304,382,402,433,488,528,585 bps INFO @ Fri, 05 Jul 2019 15:43:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.10_model.r WARNING @ Fri, 05 Jul 2019 15:43:18: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:43:18: #2 You may need to consider one of the other alternative d(s): 4,63,156,198,257,304,382,402,433,488,528,585 WARNING @ Fri, 05 Jul 2019 15:43:18: #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 15:43:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:43:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:43:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:43:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:43:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:43:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.10_summits.bed INFO @ Fri, 05 Jul 2019 15:43:19: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (16 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 15:43:19: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:43:19: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:43:19: #1 total tags in treatment: 174463 INFO @ Fri, 05 Jul 2019 15:43:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:43:19: #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 15:43:19: #1 tags after filtering in treatment: 174463 INFO @ Fri, 05 Jul 2019 15:43:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:43:19: #1 finished! INFO @ Fri, 05 Jul 2019 15:43:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:43:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:43:19: #2 number of paired peaks: 470 WARNING @ Fri, 05 Jul 2019 15:43:19: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Fri, 05 Jul 2019 15:43:19: start model_add_line... INFO @ Fri, 05 Jul 2019 15:43:19: start X-correlation... INFO @ Fri, 05 Jul 2019 15:43:19: end of X-cor INFO @ Fri, 05 Jul 2019 15:43:19: #2 finished! INFO @ Fri, 05 Jul 2019 15:43:19: #2 predicted fragment length is 63 bps INFO @ Fri, 05 Jul 2019 15:43:19: #2 alternative fragment length(s) may be 4,63,156,198,257,304,382,402,433,488,528,585 bps INFO @ Fri, 05 Jul 2019 15:43:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.20_model.r WARNING @ Fri, 05 Jul 2019 15:43:19: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:43:19: #2 You may need to consider one of the other alternative d(s): 4,63,156,198,257,304,382,402,433,488,528,585 WARNING @ Fri, 05 Jul 2019 15:43:19: #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 15:43:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:43:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:43:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:43:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:43:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:43:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548158/ERX2548158.20_summits.bed INFO @ Fri, 05 Jul 2019 15:43:20: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling