Job ID = 2007224 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,364,653 reads read : 1,364,653 reads written : 1,364,653 spots read : 1,347,890 reads read : 1,347,890 reads written : 1,347,890 spots read : 1,333,000 reads read : 1,333,000 reads written : 1,333,000 spots read : 1,286,292 reads read : 1,286,292 reads written : 1,286,292 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529618.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529619.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529620.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529621.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: 00:04:34 5331835 reads; of these: 5331835 (100.00%) were unpaired; of these: 240082 (4.50%) aligned 0 times 4312132 (80.88%) aligned exactly 1 time 779621 (14.62%) aligned >1 times 95.50% overall alignment rate Time searching: 00:04:34 Overall time: 00:04:34 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] 4991556 / 5091753 = 0.9803 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 15:56:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.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 15:56:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:56:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:56:49: #1 tag size is determined as 147 bps INFO @ Fri, 05 Jul 2019 15:56:49: #1 tag size = 147 INFO @ Fri, 05 Jul 2019 15:56:49: #1 total tags in treatment: 100197 INFO @ Fri, 05 Jul 2019 15:56:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:56:49: #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 15:56:49: #1 tags after filtering in treatment: 100197 INFO @ Fri, 05 Jul 2019 15:56:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:56:49: #1 finished! INFO @ Fri, 05 Jul 2019 15:56:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:56:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:56:49: #2 number of paired peaks: 275 WARNING @ Fri, 05 Jul 2019 15:56:49: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Fri, 05 Jul 2019 15:56:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.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 15:56:49: start model_add_line... INFO @ Fri, 05 Jul 2019 15:56:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:56:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:56:49: start X-correlation... INFO @ Fri, 05 Jul 2019 15:56:49: end of X-cor INFO @ Fri, 05 Jul 2019 15:56:49: #2 finished! INFO @ Fri, 05 Jul 2019 15:56:49: #2 predicted fragment length is 227 bps INFO @ Fri, 05 Jul 2019 15:56:49: #2 alternative fragment length(s) may be 4,146,185,227,269,292,333,371,409,506,546,564,585 bps INFO @ Fri, 05 Jul 2019 15:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.05_model.r WARNING @ Fri, 05 Jul 2019 15:56:49: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:56:49: #2 You may need to consider one of the other alternative d(s): 4,146,185,227,269,292,333,371,409,506,546,564,585 WARNING @ Fri, 05 Jul 2019 15:56:49: #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 15:56:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:56:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:56:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:56:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:56:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.05_summits.bed INFO @ Fri, 05 Jul 2019 15:56:50: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (28 records, 4 fields): 14 millis INFO @ Fri, 05 Jul 2019 15:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.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 15:56:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:56:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:56:50: #1 tag size is determined as 147 bps INFO @ Fri, 05 Jul 2019 15:56:50: #1 tag size = 147 INFO @ Fri, 05 Jul 2019 15:56:50: #1 total tags in treatment: 100197 INFO @ Fri, 05 Jul 2019 15:56:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:56:50: #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 15:56:50: #1 tags after filtering in treatment: 100197 INFO @ Fri, 05 Jul 2019 15:56:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:56:50: #1 finished! INFO @ Fri, 05 Jul 2019 15:56:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:56:50: #2 number of paired peaks: 275 WARNING @ Fri, 05 Jul 2019 15:56:50: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Fri, 05 Jul 2019 15:56:50: start model_add_line... INFO @ Fri, 05 Jul 2019 15:56:50: start X-correlation... INFO @ Fri, 05 Jul 2019 15:56:50: end of X-cor INFO @ Fri, 05 Jul 2019 15:56:50: #2 finished! INFO @ Fri, 05 Jul 2019 15:56:50: #2 predicted fragment length is 227 bps INFO @ Fri, 05 Jul 2019 15:56:50: #2 alternative fragment length(s) may be 4,146,185,227,269,292,333,371,409,506,546,564,585 bps INFO @ Fri, 05 Jul 2019 15:56:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.10_model.r WARNING @ Fri, 05 Jul 2019 15:56:50: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:56:50: #2 You may need to consider one of the other alternative d(s): 4,146,185,227,269,292,333,371,409,506,546,564,585 WARNING @ Fri, 05 Jul 2019 15:56:50: #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 15:56:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:56:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:56:51: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:56:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:56:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:56:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.10_summits.bed INFO @ Fri, 05 Jul 2019 15:56:51: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 8 millis INFO @ Fri, 05 Jul 2019 15:56:51: #1 tag size is determined as 147 bps INFO @ Fri, 05 Jul 2019 15:56:51: #1 tag size = 147 INFO @ Fri, 05 Jul 2019 15:56:51: #1 total tags in treatment: 100197 INFO @ Fri, 05 Jul 2019 15:56:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:56:51: #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 15:56:51: #1 tags after filtering in treatment: 100197 INFO @ Fri, 05 Jul 2019 15:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:56:51: #1 finished! INFO @ Fri, 05 Jul 2019 15:56:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:56:51: #2 number of paired peaks: 275 WARNING @ Fri, 05 Jul 2019 15:56:51: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Fri, 05 Jul 2019 15:56:51: start model_add_line... INFO @ Fri, 05 Jul 2019 15:56:51: start X-correlation... INFO @ Fri, 05 Jul 2019 15:56:51: end of X-cor INFO @ Fri, 05 Jul 2019 15:56:51: #2 finished! INFO @ Fri, 05 Jul 2019 15:56:51: #2 predicted fragment length is 227 bps INFO @ Fri, 05 Jul 2019 15:56:51: #2 alternative fragment length(s) may be 4,146,185,227,269,292,333,371,409,506,546,564,585 bps INFO @ Fri, 05 Jul 2019 15:56:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.20_model.r WARNING @ Fri, 05 Jul 2019 15:56:51: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:56:51: #2 You may need to consider one of the other alternative d(s): 4,146,185,227,269,292,333,371,409,506,546,564,585 WARNING @ Fri, 05 Jul 2019 15:56:51: #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 15:56:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:56:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:56:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:56:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:56:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548194/ERX2548194.20_summits.bed INFO @ Fri, 05 Jul 2019 15:56:53: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling