Job ID = 1290674 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,322,250 reads read : 15,322,250 reads written : 15,322,250 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: 00:02:23 15322250 reads; of these: 15322250 (100.00%) were unpaired; of these: 4439756 (28.98%) aligned 0 times 9304491 (60.73%) aligned exactly 1 time 1578003 (10.30%) aligned >1 times 71.02% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 995234 / 10882494 = 0.0915 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, 01 Jun 2019 22:01:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.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 @ Sat, 01 Jun 2019 22:01:23: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:01:23: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:01:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.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 @ Sat, 01 Jun 2019 22:01:23: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:01:23: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:01:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.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 @ Sat, 01 Jun 2019 22:01:23: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:01:23: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:01:31: 1000000 INFO @ Sat, 01 Jun 2019 22:01:32: 1000000 INFO @ Sat, 01 Jun 2019 22:01:32: 1000000 INFO @ Sat, 01 Jun 2019 22:01:39: 2000000 INFO @ Sat, 01 Jun 2019 22:01:41: 2000000 INFO @ Sat, 01 Jun 2019 22:01:41: 2000000 INFO @ Sat, 01 Jun 2019 22:01:47: 3000000 INFO @ Sat, 01 Jun 2019 22:01:50: 3000000 INFO @ Sat, 01 Jun 2019 22:01:50: 3000000 INFO @ Sat, 01 Jun 2019 22:01:56: 4000000 INFO @ Sat, 01 Jun 2019 22:01:59: 4000000 INFO @ Sat, 01 Jun 2019 22:01:59: 4000000 INFO @ Sat, 01 Jun 2019 22:02:04: 5000000 INFO @ Sat, 01 Jun 2019 22:02:07: 5000000 INFO @ Sat, 01 Jun 2019 22:02:08: 5000000 INFO @ Sat, 01 Jun 2019 22:02:12: 6000000 INFO @ Sat, 01 Jun 2019 22:02:16: 6000000 INFO @ Sat, 01 Jun 2019 22:02:17: 6000000 INFO @ Sat, 01 Jun 2019 22:02:19: 7000000 INFO @ Sat, 01 Jun 2019 22:02:25: 7000000 INFO @ Sat, 01 Jun 2019 22:02:26: 7000000 INFO @ Sat, 01 Jun 2019 22:02:26: 8000000 INFO @ Sat, 01 Jun 2019 22:02:33: 8000000 INFO @ Sat, 01 Jun 2019 22:02:34: 9000000 INFO @ Sat, 01 Jun 2019 22:02:35: 8000000 INFO @ Sat, 01 Jun 2019 22:02:41: #1 tag size is determined as 36 bps INFO @ Sat, 01 Jun 2019 22:02:41: #1 tag size = 36 INFO @ Sat, 01 Jun 2019 22:02:41: #1 total tags in treatment: 9887260 INFO @ Sat, 01 Jun 2019 22:02:41: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:02:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:02:41: #1 tags after filtering in treatment: 9887260 INFO @ Sat, 01 Jun 2019 22:02:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:02:41: #1 finished! INFO @ Sat, 01 Jun 2019 22:02:41: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:02:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:02:42: #2 number of paired peaks: 256 WARNING @ Sat, 01 Jun 2019 22:02:42: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Sat, 01 Jun 2019 22:02:42: start model_add_line... INFO @ Sat, 01 Jun 2019 22:02:42: 9000000 INFO @ Sat, 01 Jun 2019 22:02:42: start X-correlation... INFO @ Sat, 01 Jun 2019 22:02:42: end of X-cor INFO @ Sat, 01 Jun 2019 22:02:42: #2 finished! INFO @ Sat, 01 Jun 2019 22:02:42: #2 predicted fragment length is 45 bps INFO @ Sat, 01 Jun 2019 22:02:42: #2 alternative fragment length(s) may be 4,45,69,532,583 bps INFO @ Sat, 01 Jun 2019 22:02:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.05_model.r WARNING @ Sat, 01 Jun 2019 22:02:42: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 22:02:42: #2 You may need to consider one of the other alternative d(s): 4,45,69,532,583 WARNING @ Sat, 01 Jun 2019 22:02:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 22:02:42: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:02:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:43: 9000000 INFO @ Sat, 01 Jun 2019 22:02:50: #1 tag size is determined as 36 bps INFO @ Sat, 01 Jun 2019 22:02:50: #1 tag size = 36 INFO @ Sat, 01 Jun 2019 22:02:50: #1 total tags in treatment: 9887260 INFO @ Sat, 01 Jun 2019 22:02:50: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:02:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:02:50: #1 tags after filtering in treatment: 9887260 INFO @ Sat, 01 Jun 2019 22:02:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:02:50: #1 finished! INFO @ Sat, 01 Jun 2019 22:02:50: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:02:51: #2 number of paired peaks: 256 WARNING @ Sat, 01 Jun 2019 22:02:51: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Sat, 01 Jun 2019 22:02:51: start model_add_line... INFO @ Sat, 01 Jun 2019 22:02:51: start X-correlation... INFO @ Sat, 01 Jun 2019 22:02:51: end of X-cor INFO @ Sat, 01 Jun 2019 22:02:51: #2 finished! INFO @ Sat, 01 Jun 2019 22:02:51: #2 predicted fragment length is 45 bps INFO @ Sat, 01 Jun 2019 22:02:51: #2 alternative fragment length(s) may be 4,45,69,532,583 bps INFO @ Sat, 01 Jun 2019 22:02:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.10_model.r WARNING @ Sat, 01 Jun 2019 22:02:51: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 22:02:51: #2 You may need to consider one of the other alternative d(s): 4,45,69,532,583 WARNING @ Sat, 01 Jun 2019 22:02:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 22:02:51: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:02:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:51: #1 tag size is determined as 36 bps INFO @ Sat, 01 Jun 2019 22:02:51: #1 tag size = 36 INFO @ Sat, 01 Jun 2019 22:02:51: #1 total tags in treatment: 9887260 INFO @ Sat, 01 Jun 2019 22:02:51: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:02:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:02:51: #1 tags after filtering in treatment: 9887260 INFO @ Sat, 01 Jun 2019 22:02:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:02:51: #1 finished! INFO @ Sat, 01 Jun 2019 22:02:51: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:02:52: #2 number of paired peaks: 256 WARNING @ Sat, 01 Jun 2019 22:02:52: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Sat, 01 Jun 2019 22:02:52: start model_add_line... INFO @ Sat, 01 Jun 2019 22:02:52: start X-correlation... INFO @ Sat, 01 Jun 2019 22:02:52: end of X-cor INFO @ Sat, 01 Jun 2019 22:02:52: #2 finished! INFO @ Sat, 01 Jun 2019 22:02:52: #2 predicted fragment length is 45 bps INFO @ Sat, 01 Jun 2019 22:02:52: #2 alternative fragment length(s) may be 4,45,69,532,583 bps INFO @ Sat, 01 Jun 2019 22:02:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.20_model.r WARNING @ Sat, 01 Jun 2019 22:02:52: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 22:02:52: #2 You may need to consider one of the other alternative d(s): 4,45,69,532,583 WARNING @ Sat, 01 Jun 2019 22:02:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 22:02:52: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:03:08: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:03:17: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:03:18: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:03:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.05_peaks.xls INFO @ Sat, 01 Jun 2019 22:03:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:03:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.05_summits.bed INFO @ Sat, 01 Jun 2019 22:03:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2544 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:03:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.10_peaks.xls INFO @ Sat, 01 Jun 2019 22:03:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:03:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.10_summits.bed INFO @ Sat, 01 Jun 2019 22:03:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (503 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:03:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.20_peaks.xls INFO @ Sat, 01 Jun 2019 22:03:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:03:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX059237/SRX059237.20_summits.bed INFO @ Sat, 01 Jun 2019 22:03:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。