Job ID = 2007232 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,216,542 reads read : 1,216,542 reads written : 1,216,542 spots read : 1,170,376 reads read : 1,170,376 reads written : 1,170,376 spots read : 1,199,791 reads read : 1,199,791 reads written : 1,199,791 spots read : 1,216,636 reads read : 1,216,636 reads written : 1,216,636 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529651.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529653.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: 00:02:17 4803345 reads; of these: 4803345 (100.00%) were unpaired; of these: 232258 (4.84%) aligned 0 times 3861870 (80.40%) aligned exactly 1 time 709217 (14.77%) aligned >1 times 95.16% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 4525274 / 4571087 = 0.9900 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 15:57:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.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 15:57:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:57:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:57:46: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 15:57:46: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 15:57:46: #1 total tags in treatment: 45813 INFO @ Fri, 05 Jul 2019 15:57:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:57:46: #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 15:57:46: #1 tags after filtering in treatment: 45813 INFO @ Fri, 05 Jul 2019 15:57:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:57:46: #1 finished! INFO @ Fri, 05 Jul 2019 15:57:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:57:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:57:46: #2 number of paired peaks: 219 WARNING @ Fri, 05 Jul 2019 15:57:46: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Fri, 05 Jul 2019 15:57:46: start model_add_line... INFO @ Fri, 05 Jul 2019 15:57:46: start X-correlation... INFO @ Fri, 05 Jul 2019 15:57:46: end of X-cor INFO @ Fri, 05 Jul 2019 15:57:46: #2 finished! INFO @ Fri, 05 Jul 2019 15:57:46: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 15:57:46: #2 alternative fragment length(s) may be 9,42,64,97,135,173,202,219,249,269,290,332,360,382,409,455,477,501,532,573 bps INFO @ Fri, 05 Jul 2019 15:57:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.05_model.r WARNING @ Fri, 05 Jul 2019 15:57:46: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:57:46: #2 You may need to consider one of the other alternative d(s): 9,42,64,97,135,173,202,219,249,269,290,332,360,382,409,455,477,501,532,573 WARNING @ Fri, 05 Jul 2019 15:57:46: #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 15:57:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:57:46: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:57:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:57:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.05_summits.bed INFO @ Fri, 05 Jul 2019 15:57:46: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 15:57:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.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 15:57:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:57:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:57:47: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 15:57:47: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 15:57:47: #1 total tags in treatment: 45813 INFO @ Fri, 05 Jul 2019 15:57:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:57:47: #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 15:57:47: #1 tags after filtering in treatment: 45813 INFO @ Fri, 05 Jul 2019 15:57:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:57:47: #1 finished! INFO @ Fri, 05 Jul 2019 15:57:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:57:47: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:57:47: #2 number of paired peaks: 219 WARNING @ Fri, 05 Jul 2019 15:57:47: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Fri, 05 Jul 2019 15:57:47: start model_add_line... INFO @ Fri, 05 Jul 2019 15:57:47: start X-correlation... INFO @ Fri, 05 Jul 2019 15:57:47: end of X-cor INFO @ Fri, 05 Jul 2019 15:57:47: #2 finished! INFO @ Fri, 05 Jul 2019 15:57:47: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 15:57:47: #2 alternative fragment length(s) may be 9,42,64,97,135,173,202,219,249,269,290,332,360,382,409,455,477,501,532,573 bps INFO @ Fri, 05 Jul 2019 15:57:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.10_model.r WARNING @ Fri, 05 Jul 2019 15:57:47: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:57:47: #2 You may need to consider one of the other alternative d(s): 9,42,64,97,135,173,202,219,249,269,290,332,360,382,409,455,477,501,532,573 WARNING @ Fri, 05 Jul 2019 15:57:47: #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 15:57:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:57:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:57:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:57:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:57:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:57:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.10_summits.bed INFO @ Fri, 05 Jul 2019 15:57:47: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 15:57:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.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 15:57:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:57:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:57:48: #1 tag size is determined as 150 bps INFO @ Fri, 05 Jul 2019 15:57:48: #1 tag size = 150 INFO @ Fri, 05 Jul 2019 15:57:48: #1 total tags in treatment: 45813 INFO @ Fri, 05 Jul 2019 15:57:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:57:48: #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 15:57:48: #1 tags after filtering in treatment: 45813 INFO @ Fri, 05 Jul 2019 15:57:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:57:48: #1 finished! INFO @ Fri, 05 Jul 2019 15:57:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:57:48: #2 number of paired peaks: 219 WARNING @ Fri, 05 Jul 2019 15:57:48: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Fri, 05 Jul 2019 15:57:48: start model_add_line... INFO @ Fri, 05 Jul 2019 15:57:48: start X-correlation... INFO @ Fri, 05 Jul 2019 15:57:48: end of X-cor INFO @ Fri, 05 Jul 2019 15:57:48: #2 finished! INFO @ Fri, 05 Jul 2019 15:57:48: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 15:57:48: #2 alternative fragment length(s) may be 9,42,64,97,135,173,202,219,249,269,290,332,360,382,409,455,477,501,532,573 bps INFO @ Fri, 05 Jul 2019 15:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.20_model.r WARNING @ Fri, 05 Jul 2019 15:57:48: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:57:48: #2 You may need to consider one of the other alternative d(s): 9,42,64,97,135,173,202,219,249,269,290,332,360,382,409,455,477,501,532,573 WARNING @ Fri, 05 Jul 2019 15:57:48: #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 15:57:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:57:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:57:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:57:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:57:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548202/ERX2548202.20_summits.bed INFO @ Fri, 05 Jul 2019 15:57:48: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling