Job ID = 1292354 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,041,594 reads read : 17,041,594 reads written : 17,041,594 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:04:24 17041594 reads; of these: 17041594 (100.00%) were unpaired; of these: 1267825 (7.44%) aligned 0 times 12909216 (75.75%) aligned exactly 1 time 2864553 (16.81%) aligned >1 times 92.56% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4739302 / 15773769 = 0.3005 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 @ Sun, 02 Jun 2019 18:11:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 18:11:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:11:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:11:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 18:11:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:11:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:11:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 18:11:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:11:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:11:24: 1000000 INFO @ Sun, 02 Jun 2019 18:11:27: 1000000 INFO @ Sun, 02 Jun 2019 18:11:27: 1000000 INFO @ Sun, 02 Jun 2019 18:11:32: 2000000 INFO @ Sun, 02 Jun 2019 18:11:38: 2000000 INFO @ Sun, 02 Jun 2019 18:11:38: 2000000 INFO @ Sun, 02 Jun 2019 18:11:40: 3000000 INFO @ Sun, 02 Jun 2019 18:11:49: 4000000 INFO @ Sun, 02 Jun 2019 18:11:49: 3000000 INFO @ Sun, 02 Jun 2019 18:11:49: 3000000 INFO @ Sun, 02 Jun 2019 18:11:57: 5000000 INFO @ Sun, 02 Jun 2019 18:12:00: 4000000 INFO @ Sun, 02 Jun 2019 18:12:00: 4000000 INFO @ Sun, 02 Jun 2019 18:12:05: 6000000 INFO @ Sun, 02 Jun 2019 18:12:11: 5000000 INFO @ Sun, 02 Jun 2019 18:12:11: 5000000 INFO @ Sun, 02 Jun 2019 18:12:13: 7000000 INFO @ Sun, 02 Jun 2019 18:12:21: 8000000 INFO @ Sun, 02 Jun 2019 18:12:22: 6000000 INFO @ Sun, 02 Jun 2019 18:12:22: 6000000 INFO @ Sun, 02 Jun 2019 18:12:30: 9000000 INFO @ Sun, 02 Jun 2019 18:12:34: 7000000 INFO @ Sun, 02 Jun 2019 18:12:34: 7000000 INFO @ Sun, 02 Jun 2019 18:12:38: 10000000 INFO @ Sun, 02 Jun 2019 18:12:45: 8000000 INFO @ Sun, 02 Jun 2019 18:12:45: 8000000 INFO @ Sun, 02 Jun 2019 18:12:47: 11000000 INFO @ Sun, 02 Jun 2019 18:12:47: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:12:47: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:12:47: #1 total tags in treatment: 11034467 INFO @ Sun, 02 Jun 2019 18:12:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:12:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:12:47: #1 tags after filtering in treatment: 11034467 INFO @ Sun, 02 Jun 2019 18:12:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:12:47: #1 finished! INFO @ Sun, 02 Jun 2019 18:12:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:12:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:12:48: #2 number of paired peaks: 339 WARNING @ Sun, 02 Jun 2019 18:12:48: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 02 Jun 2019 18:12:48: start model_add_line... INFO @ Sun, 02 Jun 2019 18:12:48: start X-correlation... INFO @ Sun, 02 Jun 2019 18:12:48: end of X-cor INFO @ Sun, 02 Jun 2019 18:12:48: #2 finished! INFO @ Sun, 02 Jun 2019 18:12:48: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 18:12:48: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sun, 02 Jun 2019 18:12:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.05_model.r WARNING @ Sun, 02 Jun 2019 18:12:48: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:12:48: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sun, 02 Jun 2019 18:12:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:12:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:12:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:12:56: 9000000 INFO @ Sun, 02 Jun 2019 18:12:56: 9000000 INFO @ Sun, 02 Jun 2019 18:13:07: 10000000 INFO @ Sun, 02 Jun 2019 18:13:07: 10000000 INFO @ Sun, 02 Jun 2019 18:13:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:13:18: 11000000 INFO @ Sun, 02 Jun 2019 18:13:18: 11000000 INFO @ Sun, 02 Jun 2019 18:13:19: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:13:19: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:13:19: #1 total tags in treatment: 11034467 INFO @ Sun, 02 Jun 2019 18:13:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:13:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:13:19: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:13:19: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:13:19: #1 total tags in treatment: 11034467 INFO @ Sun, 02 Jun 2019 18:13:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:13:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:13:19: #1 tags after filtering in treatment: 11034467 INFO @ Sun, 02 Jun 2019 18:13:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:13:19: #1 finished! INFO @ Sun, 02 Jun 2019 18:13:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:13:19: #1 tags after filtering in treatment: 11034467 INFO @ Sun, 02 Jun 2019 18:13:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:13:19: #1 finished! INFO @ Sun, 02 Jun 2019 18:13:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:13:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:13:20: #2 number of paired peaks: 339 WARNING @ Sun, 02 Jun 2019 18:13:20: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 02 Jun 2019 18:13:20: start model_add_line... INFO @ Sun, 02 Jun 2019 18:13:20: start X-correlation... INFO @ Sun, 02 Jun 2019 18:13:20: end of X-cor INFO @ Sun, 02 Jun 2019 18:13:20: #2 finished! INFO @ Sun, 02 Jun 2019 18:13:20: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 18:13:20: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sun, 02 Jun 2019 18:13:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.20_model.r WARNING @ Sun, 02 Jun 2019 18:13:20: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:13:20: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sun, 02 Jun 2019 18:13:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:13:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:13:20: #2 number of paired peaks: 339 WARNING @ Sun, 02 Jun 2019 18:13:20: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 02 Jun 2019 18:13:20: start model_add_line... INFO @ Sun, 02 Jun 2019 18:13:20: start X-correlation... INFO @ Sun, 02 Jun 2019 18:13:20: end of X-cor INFO @ Sun, 02 Jun 2019 18:13:20: #2 finished! INFO @ Sun, 02 Jun 2019 18:13:20: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 18:13:20: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sun, 02 Jun 2019 18:13:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.10_model.r WARNING @ Sun, 02 Jun 2019 18:13:20: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:13:20: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sun, 02 Jun 2019 18:13:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:13:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.05_summits.bed INFO @ Sun, 02 Jun 2019 18:13:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (670 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:13:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:13:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:14:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:14:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:14:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.20_summits.bed INFO @ Sun, 02 Jun 2019 18:14:03: Done! INFO @ Sun, 02 Jun 2019 18:14:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:14:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:14:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373267/SRX373267.10_summits.bed INFO @ Sun, 02 Jun 2019 18:14:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (181 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。