Job ID = 2010883 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,863,623 reads read : 9,727,246 reads written : 4,863,623 reads 0-length : 4,863,623 rm: cannot remove ‘[DSE]RR*’: 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: 00:01:46 4863623 reads; of these: 4863623 (100.00%) were unpaired; of these: 379334 (7.80%) aligned 0 times 3986929 (81.97%) aligned exactly 1 time 497360 (10.23%) aligned >1 times 92.20% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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] 1037102 / 4484289 = 0.2313 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 @ Sat, 06 Jul 2019 01:15:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.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 @ Sat, 06 Jul 2019 01:15:47: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:15:47: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:15:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.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 @ Sat, 06 Jul 2019 01:15:48: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:15:48: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.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 @ Sat, 06 Jul 2019 01:15:50: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:15:50: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:15:57: 1000000 INFO @ Sat, 06 Jul 2019 01:16:01: 1000000 INFO @ Sat, 06 Jul 2019 01:16:03: 1000000 INFO @ Sat, 06 Jul 2019 01:16:07: 2000000 INFO @ Sat, 06 Jul 2019 01:16:13: 2000000 INFO @ Sat, 06 Jul 2019 01:16:17: 3000000 INFO @ Sat, 06 Jul 2019 01:16:17: 2000000 INFO @ Sat, 06 Jul 2019 01:16:21: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:16:21: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:16:21: #1 total tags in treatment: 3447187 INFO @ Sat, 06 Jul 2019 01:16:21: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:16:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:16:21: #1 tags after filtering in treatment: 3447187 INFO @ Sat, 06 Jul 2019 01:16:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:16:21: #1 finished! INFO @ Sat, 06 Jul 2019 01:16:21: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:16:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:16:21: #2 number of paired peaks: 121 WARNING @ Sat, 06 Jul 2019 01:16:21: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Sat, 06 Jul 2019 01:16:21: start model_add_line... INFO @ Sat, 06 Jul 2019 01:16:21: start X-correlation... INFO @ Sat, 06 Jul 2019 01:16:21: end of X-cor INFO @ Sat, 06 Jul 2019 01:16:21: #2 finished! INFO @ Sat, 06 Jul 2019 01:16:21: #2 predicted fragment length is 130 bps INFO @ Sat, 06 Jul 2019 01:16:21: #2 alternative fragment length(s) may be 1,85,100,130,146,178 bps INFO @ Sat, 06 Jul 2019 01:16:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.05_model.r WARNING @ Sat, 06 Jul 2019 01:16:21: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 01:16:21: #2 You may need to consider one of the other alternative d(s): 1,85,100,130,146,178 WARNING @ Sat, 06 Jul 2019 01:16:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 01:16:21: #3 Call peaks... INFO @ Sat, 06 Jul 2019 01:16:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 01:16:25: 3000000 INFO @ Sat, 06 Jul 2019 01:16:29: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 01:16:30: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:16:30: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:16:30: #1 total tags in treatment: 3447187 INFO @ Sat, 06 Jul 2019 01:16:30: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:16:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:16:30: #1 tags after filtering in treatment: 3447187 INFO @ Sat, 06 Jul 2019 01:16:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:16:30: #1 finished! INFO @ Sat, 06 Jul 2019 01:16:30: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:16:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:16:30: 3000000 INFO @ Sat, 06 Jul 2019 01:16:30: #2 number of paired peaks: 121 WARNING @ Sat, 06 Jul 2019 01:16:30: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Sat, 06 Jul 2019 01:16:30: start model_add_line... INFO @ Sat, 06 Jul 2019 01:16:30: start X-correlation... INFO @ Sat, 06 Jul 2019 01:16:30: end of X-cor INFO @ Sat, 06 Jul 2019 01:16:30: #2 finished! INFO @ Sat, 06 Jul 2019 01:16:30: #2 predicted fragment length is 130 bps INFO @ Sat, 06 Jul 2019 01:16:30: #2 alternative fragment length(s) may be 1,85,100,130,146,178 bps INFO @ Sat, 06 Jul 2019 01:16:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.10_model.r WARNING @ Sat, 06 Jul 2019 01:16:30: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 01:16:30: #2 You may need to consider one of the other alternative d(s): 1,85,100,130,146,178 WARNING @ Sat, 06 Jul 2019 01:16:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 01:16:30: #3 Call peaks... INFO @ Sat, 06 Jul 2019 01:16:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 01:16:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.05_peaks.xls INFO @ Sat, 06 Jul 2019 01:16:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 01:16:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.05_summits.bed INFO @ Sat, 06 Jul 2019 01:16:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (101 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:16:36: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:16:36: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:16:36: #1 total tags in treatment: 3447187 INFO @ Sat, 06 Jul 2019 01:16:36: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:16:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 01:16:36: #1 tags after filtering in treatment: 3447187 INFO @ Sat, 06 Jul 2019 01:16:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 01:16:36: #1 finished! INFO @ Sat, 06 Jul 2019 01:16:36: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:16:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:16:36: #2 number of paired peaks: 121 WARNING @ Sat, 06 Jul 2019 01:16:36: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Sat, 06 Jul 2019 01:16:36: start model_add_line... INFO @ Sat, 06 Jul 2019 01:16:36: start X-correlation... INFO @ Sat, 06 Jul 2019 01:16:36: end of X-cor INFO @ Sat, 06 Jul 2019 01:16:36: #2 finished! INFO @ Sat, 06 Jul 2019 01:16:36: #2 predicted fragment length is 130 bps INFO @ Sat, 06 Jul 2019 01:16:36: #2 alternative fragment length(s) may be 1,85,100,130,146,178 bps INFO @ Sat, 06 Jul 2019 01:16:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.20_model.r WARNING @ Sat, 06 Jul 2019 01:16:36: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 01:16:36: #2 You may need to consider one of the other alternative d(s): 1,85,100,130,146,178 WARNING @ Sat, 06 Jul 2019 01:16:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 01:16:36: #3 Call peaks... INFO @ Sat, 06 Jul 2019 01:16:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 01:16:38: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 01:16:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.10_peaks.xls INFO @ Sat, 06 Jul 2019 01:16:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 01:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.10_summits.bed INFO @ Sat, 06 Jul 2019 01:16:41: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (35 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 01:16:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 01:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.20_peaks.xls INFO @ Sat, 06 Jul 2019 01:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 01:16:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4140980/SRX4140980.20_summits.bed INFO @ Sat, 06 Jul 2019 01:16:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。