Job ID = 2007593 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,614,372 reads read : 2,614,372 reads written : 2,614,372 spots read : 2,515,697 reads read : 2,515,697 reads written : 2,515,697 spots read : 2,578,084 reads read : 2,578,084 reads written : 2,578,084 spots read : 2,617,403 reads read : 2,617,403 reads written : 2,617,403 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529718.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529719.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529720.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529721.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: 00:04:54 10325556 reads; of these: 10325556 (100.00%) were unpaired; of these: 363468 (3.52%) aligned 0 times 8203595 (79.45%) aligned exactly 1 time 1758493 (17.03%) aligned >1 times 96.48% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9839917 / 9962088 = 0.9877 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 16:23:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.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 16:23:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:23:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:23:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.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 16:23:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:23:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:23:34: #1 tag size is determined as 142 bps INFO @ Fri, 05 Jul 2019 16:23:34: #1 tag size = 142 INFO @ Fri, 05 Jul 2019 16:23:34: #1 total tags in treatment: 122171 INFO @ Fri, 05 Jul 2019 16:23:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:23:34: #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 16:23:34: #1 tags after filtering in treatment: 122171 INFO @ Fri, 05 Jul 2019 16:23:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:23:34: #1 finished! INFO @ Fri, 05 Jul 2019 16:23:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:23:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:23:34: #2 number of paired peaks: 302 WARNING @ Fri, 05 Jul 2019 16:23:34: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Fri, 05 Jul 2019 16:23:34: start model_add_line... INFO @ Fri, 05 Jul 2019 16:23:34: start X-correlation... INFO @ Fri, 05 Jul 2019 16:23:34: end of X-cor INFO @ Fri, 05 Jul 2019 16:23:34: #2 finished! INFO @ Fri, 05 Jul 2019 16:23:34: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 16:23:34: #2 alternative fragment length(s) may be 100,128,530 bps INFO @ Fri, 05 Jul 2019 16:23:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.05_model.r WARNING @ Fri, 05 Jul 2019 16:23:34: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:23:34: #2 You may need to consider one of the other alternative d(s): 100,128,530 WARNING @ Fri, 05 Jul 2019 16:23:34: #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 16:23:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:23:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:23:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.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 16:23:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:23:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:23:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:23:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:23:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:23:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.05_summits.bed INFO @ Fri, 05 Jul 2019 16:23:35: Done! INFO @ Fri, 05 Jul 2019 16:23:35: #1 tag size is determined as 142 bps INFO @ Fri, 05 Jul 2019 16:23:35: #1 tag size = 142 INFO @ Fri, 05 Jul 2019 16:23:35: #1 total tags in treatment: 122171 INFO @ Fri, 05 Jul 2019 16:23:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:23:35: #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 16:23:35: #1 tags after filtering in treatment: 122171 INFO @ Fri, 05 Jul 2019 16:23:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:23:35: #1 finished! INFO @ Fri, 05 Jul 2019 16:23:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:23:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:23:35: #2 number of paired peaks: 302 WARNING @ Fri, 05 Jul 2019 16:23:35: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Fri, 05 Jul 2019 16:23:35: start model_add_line... INFO @ Fri, 05 Jul 2019 16:23:35: start X-correlation... INFO @ Fri, 05 Jul 2019 16:23:35: end of X-cor INFO @ Fri, 05 Jul 2019 16:23:35: #2 finished! INFO @ Fri, 05 Jul 2019 16:23:35: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 16:23:35: #2 alternative fragment length(s) may be 100,128,530 bps INFO @ Fri, 05 Jul 2019 16:23:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.10_model.r WARNING @ Fri, 05 Jul 2019 16:23:35: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:23:35: #2 You may need to consider one of the other alternative d(s): 100,128,530 WARNING @ Fri, 05 Jul 2019 16:23:35: #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 16:23:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:23:35: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:23:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:23:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:23:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:23:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.10_summits.bed INFO @ Fri, 05 Jul 2019 16:23:36: Done! BigWig に変換しました。 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (42 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:23:36: #1 tag size is determined as 142 bps INFO @ Fri, 05 Jul 2019 16:23:36: #1 tag size = 142 INFO @ Fri, 05 Jul 2019 16:23:36: #1 total tags in treatment: 122171 INFO @ Fri, 05 Jul 2019 16:23:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:23:36: #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 16:23:36: #1 tags after filtering in treatment: 122171 INFO @ Fri, 05 Jul 2019 16:23:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:23:36: #1 finished! INFO @ Fri, 05 Jul 2019 16:23:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:23:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:23:36: #2 number of paired peaks: 302 WARNING @ Fri, 05 Jul 2019 16:23:36: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Fri, 05 Jul 2019 16:23:36: start model_add_line... INFO @ Fri, 05 Jul 2019 16:23:36: start X-correlation... INFO @ Fri, 05 Jul 2019 16:23:36: end of X-cor INFO @ Fri, 05 Jul 2019 16:23:36: #2 finished! INFO @ Fri, 05 Jul 2019 16:23:36: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 16:23:36: #2 alternative fragment length(s) may be 100,128,530 bps INFO @ Fri, 05 Jul 2019 16:23:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.20_model.r WARNING @ Fri, 05 Jul 2019 16:23:36: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:23:36: #2 You may need to consider one of the other alternative d(s): 100,128,530 WARNING @ Fri, 05 Jul 2019 16:23:36: #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 16:23:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:23:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:23:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:23:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:23:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:23:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548219/ERX2548219.20_summits.bed INFO @ Fri, 05 Jul 2019 16:23:37: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (37 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling