Job ID = 2590153 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,075,319 reads read : 10,075,319 reads written : 10,075,319 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: 00:02:10 10075319 reads; of these: 10075319 (100.00%) were unpaired; of these: 1468386 (14.57%) aligned 0 times 6958979 (69.07%) aligned exactly 1 time 1647954 (16.36%) aligned >1 times 85.43% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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_rmdupse_core] 1384668 / 8606933 = 0.1609 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 @ Mon, 12 Aug 2019 19:48:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.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 @ Mon, 12 Aug 2019 19:48:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:48:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:48:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.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 @ Mon, 12 Aug 2019 19:48:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:48:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.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 @ Mon, 12 Aug 2019 19:48:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:48:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:48:41: 1000000 INFO @ Mon, 12 Aug 2019 19:48:45: 1000000 INFO @ Mon, 12 Aug 2019 19:48:46: 1000000 INFO @ Mon, 12 Aug 2019 19:48:49: 2000000 INFO @ Mon, 12 Aug 2019 19:48:57: 2000000 INFO @ Mon, 12 Aug 2019 19:48:57: 2000000 INFO @ Mon, 12 Aug 2019 19:48:57: 3000000 INFO @ Mon, 12 Aug 2019 19:49:06: 4000000 INFO @ Mon, 12 Aug 2019 19:49:07: 3000000 INFO @ Mon, 12 Aug 2019 19:49:08: 3000000 INFO @ Mon, 12 Aug 2019 19:49:14: 5000000 INFO @ Mon, 12 Aug 2019 19:49:17: 4000000 INFO @ Mon, 12 Aug 2019 19:49:19: 4000000 INFO @ Mon, 12 Aug 2019 19:49:22: 6000000 INFO @ Mon, 12 Aug 2019 19:49:28: 5000000 INFO @ Mon, 12 Aug 2019 19:49:30: 5000000 INFO @ Mon, 12 Aug 2019 19:49:31: 7000000 INFO @ Mon, 12 Aug 2019 19:49:32: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:49:32: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:49:32: #1 total tags in treatment: 7222265 INFO @ Mon, 12 Aug 2019 19:49:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:49:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:49:32: #1 tags after filtering in treatment: 7222265 INFO @ Mon, 12 Aug 2019 19:49:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:49:32: #1 finished! INFO @ Mon, 12 Aug 2019 19:49:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:49:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:49:33: #2 number of paired peaks: 553 WARNING @ Mon, 12 Aug 2019 19:49:33: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Mon, 12 Aug 2019 19:49:33: start model_add_line... INFO @ Mon, 12 Aug 2019 19:49:33: start X-correlation... INFO @ Mon, 12 Aug 2019 19:49:33: end of X-cor INFO @ Mon, 12 Aug 2019 19:49:33: #2 finished! INFO @ Mon, 12 Aug 2019 19:49:33: #2 predicted fragment length is 71 bps INFO @ Mon, 12 Aug 2019 19:49:33: #2 alternative fragment length(s) may be 4,54,71,103 bps INFO @ Mon, 12 Aug 2019 19:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.05_model.r WARNING @ Mon, 12 Aug 2019 19:49:33: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:49:33: #2 You may need to consider one of the other alternative d(s): 4,54,71,103 WARNING @ Mon, 12 Aug 2019 19:49:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:49:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:49:39: 6000000 INFO @ Mon, 12 Aug 2019 19:49:41: 6000000 INFO @ Mon, 12 Aug 2019 19:49:49: 7000000 INFO @ Mon, 12 Aug 2019 19:49:51: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:49:51: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:49:51: #1 total tags in treatment: 7222265 INFO @ Mon, 12 Aug 2019 19:49:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:49:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:49:52: #1 tags after filtering in treatment: 7222265 INFO @ Mon, 12 Aug 2019 19:49:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:49:52: #1 finished! INFO @ Mon, 12 Aug 2019 19:49:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:49:52: 7000000 INFO @ Mon, 12 Aug 2019 19:49:52: #2 number of paired peaks: 553 WARNING @ Mon, 12 Aug 2019 19:49:52: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Mon, 12 Aug 2019 19:49:52: start model_add_line... INFO @ Mon, 12 Aug 2019 19:49:52: start X-correlation... INFO @ Mon, 12 Aug 2019 19:49:52: end of X-cor INFO @ Mon, 12 Aug 2019 19:49:52: #2 finished! INFO @ Mon, 12 Aug 2019 19:49:52: #2 predicted fragment length is 71 bps INFO @ Mon, 12 Aug 2019 19:49:52: #2 alternative fragment length(s) may be 4,54,71,103 bps INFO @ Mon, 12 Aug 2019 19:49:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.20_model.r WARNING @ Mon, 12 Aug 2019 19:49:52: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:49:52: #2 You may need to consider one of the other alternative d(s): 4,54,71,103 WARNING @ Mon, 12 Aug 2019 19:49:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:49:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:49:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:49:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:49:54: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:49:54: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:49:54: #1 total tags in treatment: 7222265 INFO @ Mon, 12 Aug 2019 19:49:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:49:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:49:54: #1 tags after filtering in treatment: 7222265 INFO @ Mon, 12 Aug 2019 19:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:49:54: #1 finished! INFO @ Mon, 12 Aug 2019 19:49:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:49:55: #2 number of paired peaks: 553 WARNING @ Mon, 12 Aug 2019 19:49:55: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Mon, 12 Aug 2019 19:49:55: start model_add_line... INFO @ Mon, 12 Aug 2019 19:49:55: start X-correlation... INFO @ Mon, 12 Aug 2019 19:49:55: end of X-cor INFO @ Mon, 12 Aug 2019 19:49:55: #2 finished! INFO @ Mon, 12 Aug 2019 19:49:55: #2 predicted fragment length is 71 bps INFO @ Mon, 12 Aug 2019 19:49:55: #2 alternative fragment length(s) may be 4,54,71,103 bps INFO @ Mon, 12 Aug 2019 19:49:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.10_model.r WARNING @ Mon, 12 Aug 2019 19:49:55: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:49:55: #2 You may need to consider one of the other alternative d(s): 4,54,71,103 WARNING @ Mon, 12 Aug 2019 19:49:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:49:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:50:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:50:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:50:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.05_summits.bed INFO @ Mon, 12 Aug 2019 19:50:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2107 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:50:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:50:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:50:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:50:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:50:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.20_summits.bed INFO @ Mon, 12 Aug 2019 19:50:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (233 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:50:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:50:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:50:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495001/SRX495001.10_summits.bed INFO @ Mon, 12 Aug 2019 19:50:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (647 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。