Job ID = 2007592 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,834,523 reads read : 1,834,523 reads written : 1,834,523 spots read : 1,769,226 reads read : 1,769,226 reads written : 1,769,226 spots read : 1,790,914 reads read : 1,790,914 reads written : 1,790,914 spots read : 1,757,481 reads read : 1,757,481 reads written : 1,757,481 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529714.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529715.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529716.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: 00:01:47 7152144 reads; of these: 7152144 (100.00%) were unpaired; of these: 382154 (5.34%) aligned 0 times 5508156 (77.01%) aligned exactly 1 time 1261834 (17.64%) aligned >1 times 94.66% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 6402662 / 6769990 = 0.9457 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 16:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.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 16:02:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:02:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:02:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.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 16:02:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:02:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:02:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.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 16:02:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:02:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:02:03: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:02:03: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:02:03: #1 total tags in treatment: 367328 INFO @ Fri, 05 Jul 2019 16:02:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:02:03: #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 16:02:03: #1 tags after filtering in treatment: 367328 INFO @ Fri, 05 Jul 2019 16:02:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:02:03: #1 finished! INFO @ Fri, 05 Jul 2019 16:02:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:02:04: #2 number of paired peaks: 490 WARNING @ Fri, 05 Jul 2019 16:02:04: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Fri, 05 Jul 2019 16:02:04: start model_add_line... INFO @ Fri, 05 Jul 2019 16:02:04: start X-correlation... INFO @ Fri, 05 Jul 2019 16:02:04: end of X-cor INFO @ Fri, 05 Jul 2019 16:02:04: #2 finished! INFO @ Fri, 05 Jul 2019 16:02:04: #2 predicted fragment length is 80 bps INFO @ Fri, 05 Jul 2019 16:02:04: #2 alternative fragment length(s) may be 80 bps INFO @ Fri, 05 Jul 2019 16:02:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.05_model.r WARNING @ Fri, 05 Jul 2019 16:02:04: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:02:04: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Fri, 05 Jul 2019 16:02:04: #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 16:02:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:02:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:02:04: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:02:04: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:02:04: #1 total tags in treatment: 367328 INFO @ Fri, 05 Jul 2019 16:02:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:02:04: #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 16:02:04: #1 tags after filtering in treatment: 367328 INFO @ Fri, 05 Jul 2019 16:02:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:02:04: #1 finished! INFO @ Fri, 05 Jul 2019 16:02:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:02:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:02:04: #2 number of paired peaks: 490 WARNING @ Fri, 05 Jul 2019 16:02:04: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Fri, 05 Jul 2019 16:02:04: start model_add_line... INFO @ Fri, 05 Jul 2019 16:02:04: start X-correlation... INFO @ Fri, 05 Jul 2019 16:02:04: end of X-cor INFO @ Fri, 05 Jul 2019 16:02:04: #2 finished! INFO @ Fri, 05 Jul 2019 16:02:04: #2 predicted fragment length is 80 bps INFO @ Fri, 05 Jul 2019 16:02:04: #2 alternative fragment length(s) may be 80 bps INFO @ Fri, 05 Jul 2019 16:02:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.10_model.r WARNING @ Fri, 05 Jul 2019 16:02:04: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:02:04: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Fri, 05 Jul 2019 16:02:04: #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 16:02:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:02:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:02:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:02:05: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:02:05: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:02:05: #1 total tags in treatment: 367328 INFO @ Fri, 05 Jul 2019 16:02:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:02:05: #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 16:02:05: #1 tags after filtering in treatment: 367328 INFO @ Fri, 05 Jul 2019 16:02:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:02:05: #1 finished! INFO @ Fri, 05 Jul 2019 16:02:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:02:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:02:05: #2 number of paired peaks: 490 WARNING @ Fri, 05 Jul 2019 16:02:05: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Fri, 05 Jul 2019 16:02:05: start model_add_line... INFO @ Fri, 05 Jul 2019 16:02:05: start X-correlation... INFO @ Fri, 05 Jul 2019 16:02:05: end of X-cor INFO @ Fri, 05 Jul 2019 16:02:05: #2 finished! INFO @ Fri, 05 Jul 2019 16:02:05: #2 predicted fragment length is 80 bps INFO @ Fri, 05 Jul 2019 16:02:05: #2 alternative fragment length(s) may be 80 bps INFO @ Fri, 05 Jul 2019 16:02:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.20_model.r WARNING @ Fri, 05 Jul 2019 16:02:05: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:02:05: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Fri, 05 Jul 2019 16:02:05: #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 16:02:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:02:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:02:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:02:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:02:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:02:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.05_summits.bed INFO @ Fri, 05 Jul 2019 16:02:06: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (232 records, 4 fields): 7 millis INFO @ Fri, 05 Jul 2019 16:02:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:02:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:02:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.10_summits.bed INFO @ Fri, 05 Jul 2019 16:02:06: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (173 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:02:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:02:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:02:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:02:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548218/ERX2548218.20_summits.bed INFO @ Fri, 05 Jul 2019 16:02:07: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling