Job ID = 2589111 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,638,871 reads read : 9,638,871 reads written : 9,638,871 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: 00:03:02 9638871 reads; of these: 9638871 (100.00%) were unpaired; of these: 72790 (0.76%) aligned 0 times 7201837 (74.72%) aligned exactly 1 time 2364244 (24.53%) aligned >1 times 99.24% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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] 2881682 / 9566081 = 0.3012 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 17:03:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.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 17:03:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:03:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:03:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.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 17:03:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:03:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:03:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.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 17:03:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:03:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:03:41: 1000000 INFO @ Mon, 12 Aug 2019 17:03:42: 1000000 INFO @ Mon, 12 Aug 2019 17:03:42: 1000000 INFO @ Mon, 12 Aug 2019 17:03:50: 2000000 INFO @ Mon, 12 Aug 2019 17:03:50: 2000000 INFO @ Mon, 12 Aug 2019 17:03:51: 2000000 INFO @ Mon, 12 Aug 2019 17:03:58: 3000000 INFO @ Mon, 12 Aug 2019 17:03:58: 3000000 INFO @ Mon, 12 Aug 2019 17:03:59: 3000000 INFO @ Mon, 12 Aug 2019 17:04:05: 4000000 INFO @ Mon, 12 Aug 2019 17:04:07: 4000000 INFO @ Mon, 12 Aug 2019 17:04:08: 4000000 INFO @ Mon, 12 Aug 2019 17:04:13: 5000000 INFO @ Mon, 12 Aug 2019 17:04:15: 5000000 INFO @ Mon, 12 Aug 2019 17:04:16: 5000000 INFO @ Mon, 12 Aug 2019 17:04:20: 6000000 INFO @ Mon, 12 Aug 2019 17:04:24: 6000000 INFO @ Mon, 12 Aug 2019 17:04:25: 6000000 INFO @ Mon, 12 Aug 2019 17:04:26: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 17:04:26: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 17:04:26: #1 total tags in treatment: 6684399 INFO @ Mon, 12 Aug 2019 17:04:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:04:26: #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 17:04:26: #1 tags after filtering in treatment: 6684399 INFO @ Mon, 12 Aug 2019 17:04:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:04:26: #1 finished! INFO @ Mon, 12 Aug 2019 17:04:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:04:27: #2 number of paired peaks: 365 WARNING @ Mon, 12 Aug 2019 17:04:27: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Mon, 12 Aug 2019 17:04:27: start model_add_line... INFO @ Mon, 12 Aug 2019 17:04:27: start X-correlation... INFO @ Mon, 12 Aug 2019 17:04:27: end of X-cor INFO @ Mon, 12 Aug 2019 17:04:27: #2 finished! INFO @ Mon, 12 Aug 2019 17:04:27: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 17:04:27: #2 alternative fragment length(s) may be 3,43,62,597 bps INFO @ Mon, 12 Aug 2019 17:04:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.20_model.r WARNING @ Mon, 12 Aug 2019 17:04:27: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:04:27: #2 You may need to consider one of the other alternative d(s): 3,43,62,597 WARNING @ Mon, 12 Aug 2019 17:04:27: #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 17:04:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:04:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:04:29: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 17:04:29: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 17:04:29: #1 total tags in treatment: 6684399 INFO @ Mon, 12 Aug 2019 17:04:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:04:29: #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 17:04:29: #1 tags after filtering in treatment: 6684399 INFO @ Mon, 12 Aug 2019 17:04:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:04:29: #1 finished! INFO @ Mon, 12 Aug 2019 17:04:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:04:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:04:30: #2 number of paired peaks: 365 WARNING @ Mon, 12 Aug 2019 17:04:30: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Mon, 12 Aug 2019 17:04:30: start model_add_line... INFO @ Mon, 12 Aug 2019 17:04:30: start X-correlation... INFO @ Mon, 12 Aug 2019 17:04:30: end of X-cor INFO @ Mon, 12 Aug 2019 17:04:30: #2 finished! INFO @ Mon, 12 Aug 2019 17:04:30: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 17:04:30: #2 alternative fragment length(s) may be 3,43,62,597 bps INFO @ Mon, 12 Aug 2019 17:04:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.05_model.r WARNING @ Mon, 12 Aug 2019 17:04:30: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:04:30: #2 You may need to consider one of the other alternative d(s): 3,43,62,597 WARNING @ Mon, 12 Aug 2019 17:04:30: #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 17:04:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:04:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:04:30: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 17:04:30: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 17:04:30: #1 total tags in treatment: 6684399 INFO @ Mon, 12 Aug 2019 17:04:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:04:30: #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 17:04:30: #1 tags after filtering in treatment: 6684399 INFO @ Mon, 12 Aug 2019 17:04:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:04:30: #1 finished! INFO @ Mon, 12 Aug 2019 17:04:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:04:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:04:31: #2 number of paired peaks: 365 WARNING @ Mon, 12 Aug 2019 17:04:31: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Mon, 12 Aug 2019 17:04:31: start model_add_line... INFO @ Mon, 12 Aug 2019 17:04:31: start X-correlation... INFO @ Mon, 12 Aug 2019 17:04:31: end of X-cor INFO @ Mon, 12 Aug 2019 17:04:31: #2 finished! INFO @ Mon, 12 Aug 2019 17:04:31: #2 predicted fragment length is 43 bps INFO @ Mon, 12 Aug 2019 17:04:31: #2 alternative fragment length(s) may be 3,43,62,597 bps INFO @ Mon, 12 Aug 2019 17:04:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.10_model.r WARNING @ Mon, 12 Aug 2019 17:04:31: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:04:31: #2 You may need to consider one of the other alternative d(s): 3,43,62,597 WARNING @ Mon, 12 Aug 2019 17:04:31: #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 17:04:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:04:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:04:46: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:04:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:04:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:04:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:04:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:04:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.20_summits.bed INFO @ Mon, 12 Aug 2019 17:04:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (50 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.10_summits.bed INFO @ Mon, 12 Aug 2019 17:04:59: Done! INFO @ Mon, 12 Aug 2019 17:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999213/ERX1999213.05_summits.bed INFO @ Mon, 12 Aug 2019 17:04:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (669 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。