Job ID = 2006324 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,089,340 reads read : 2,089,340 reads written : 2,089,340 spots read : 2,002,488 reads read : 2,002,488 reads written : 2,002,488 spots read : 2,028,512 reads read : 2,028,512 reads written : 2,028,512 spots read : 1,960,056 reads read : 1,960,056 reads written : 1,960,056 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529494.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529495.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529496.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: 00:00:02 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:33 8080396 reads; of these: 8080396 (100.00%) were unpaired; of these: 549888 (6.81%) aligned 0 times 6310801 (78.10%) aligned exactly 1 time 1219707 (15.09%) aligned >1 times 93.19% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:36 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] 7380107 / 7530508 = 0.9800 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.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 15:41:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:41:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.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 15:41:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:41:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.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 15:41:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:41:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:41:18: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:41:18: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:41:18: #1 total tags in treatment: 150401 INFO @ Fri, 05 Jul 2019 15:41:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:41:18: #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 15:41:18: #1 tags after filtering in treatment: 150401 INFO @ Fri, 05 Jul 2019 15:41:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:41:18: #1 finished! INFO @ Fri, 05 Jul 2019 15:41:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:41:18: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:41:18: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:41:18: #1 total tags in treatment: 150401 INFO @ Fri, 05 Jul 2019 15:41:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:41:18: #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 15:41:18: #1 tags after filtering in treatment: 150401 INFO @ Fri, 05 Jul 2019 15:41:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:41:18: #1 finished! INFO @ Fri, 05 Jul 2019 15:41:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:41:18: #2 number of paired peaks: 451 WARNING @ Fri, 05 Jul 2019 15:41:18: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Fri, 05 Jul 2019 15:41:18: start model_add_line... INFO @ Fri, 05 Jul 2019 15:41:18: start X-correlation... INFO @ Fri, 05 Jul 2019 15:41:18: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 15:41:18: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 15:41:18: #1 total tags in treatment: 150401 INFO @ Fri, 05 Jul 2019 15:41:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:41:18: #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 15:41:18: #1 tags after filtering in treatment: 150401 INFO @ Fri, 05 Jul 2019 15:41:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:41:18: #1 finished! INFO @ Fri, 05 Jul 2019 15:41:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:41:18: #2 number of paired peaks: 451 WARNING @ Fri, 05 Jul 2019 15:41:18: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Fri, 05 Jul 2019 15:41:18: start model_add_line... INFO @ Fri, 05 Jul 2019 15:41:18: start X-correlation... INFO @ Fri, 05 Jul 2019 15:41:18: end of X-cor INFO @ Fri, 05 Jul 2019 15:41:18: #2 finished! INFO @ Fri, 05 Jul 2019 15:41:18: #2 predicted fragment length is 57 bps INFO @ Fri, 05 Jul 2019 15:41:18: #2 alternative fragment length(s) may be 36,57,73,98,124,171,198,224,250,269,294,335,385,430,454,486,553,583 bps INFO @ Fri, 05 Jul 2019 15:41:18: end of X-cor INFO @ Fri, 05 Jul 2019 15:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.10_model.r INFO @ Fri, 05 Jul 2019 15:41:18: #2 finished! INFO @ Fri, 05 Jul 2019 15:41:18: #2 predicted fragment length is 57 bps INFO @ Fri, 05 Jul 2019 15:41:18: #2 alternative fragment length(s) may be 36,57,73,98,124,171,198,224,250,269,294,335,385,430,454,486,553,583 bps INFO @ Fri, 05 Jul 2019 15:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.20_model.r INFO @ Fri, 05 Jul 2019 15:41:18: #2 number of paired peaks: 451 WARNING @ Fri, 05 Jul 2019 15:41:18: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Fri, 05 Jul 2019 15:41:18: start model_add_line... INFO @ Fri, 05 Jul 2019 15:41:18: start X-correlation... WARNING @ Fri, 05 Jul 2019 15:41:18: #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 15:41:18: #2 You may need to consider one of the other alternative d(s): 36,57,73,98,124,171,198,224,250,269,294,335,385,430,454,486,553,583 WARNING @ Fri, 05 Jul 2019 15:41:18: #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 15:41:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:41:18: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 05 Jul 2019 15:41:18: #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 15:41:18: #2 You may need to consider one of the other alternative d(s): 36,57,73,98,124,171,198,224,250,269,294,335,385,430,454,486,553,583 WARNING @ Fri, 05 Jul 2019 15:41:18: #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 15:41:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:41:18: end of X-cor INFO @ Fri, 05 Jul 2019 15:41:18: #2 finished! INFO @ Fri, 05 Jul 2019 15:41:18: #2 predicted fragment length is 57 bps INFO @ Fri, 05 Jul 2019 15:41:18: #2 alternative fragment length(s) may be 36,57,73,98,124,171,198,224,250,269,294,335,385,430,454,486,553,583 bps INFO @ Fri, 05 Jul 2019 15:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.05_model.r WARNING @ Fri, 05 Jul 2019 15:41:18: #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 15:41:18: #2 You may need to consider one of the other alternative d(s): 36,57,73,98,124,171,198,224,250,269,294,335,385,430,454,486,553,583 WARNING @ Fri, 05 Jul 2019 15:41:18: #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 15:41:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:41:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:41:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:41:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:41:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:41:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:41:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.10_summits.bed INFO @ Fri, 05 Jul 2019 15:41:19: Done! INFO @ Fri, 05 Jul 2019 15:41:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:41:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:41:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.20_summits.bed INFO @ Fri, 05 Jul 2019 15:41:19: Done! INFO @ Fri, 05 Jul 2019 15:41:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:41:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:41:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548157/ERX2548157.05_summits.bed INFO @ Fri, 05 Jul 2019 15:41:19: Done! pass1 - making usageList (1 chroms)pass1 - making usageList (8 chroms)pass1 - making usageList (16 chroms): 1827 millis : 1826 millis : 1826 millis pass2 - checking and writing primary data (1 records, 4 fields): 8738 millis pass2 - checking and writing primary data (14 records, 4 fields): 8739 millis pass2 - checking and writing primary data (56 records, 4 fields): 8739 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling