Job ID = 1292025 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,916,550 reads read : 7,916,550 reads written : 7,916,550 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: 00:01:52 7916550 reads; of these: 7916550 (100.00%) were unpaired; of these: 1543182 (19.49%) aligned 0 times 5226174 (66.02%) aligned exactly 1 time 1147194 (14.49%) aligned >1 times 80.51% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 1124579 / 6373368 = 0.1764 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 17:16:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.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 17:16:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:16:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:16:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.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 17:16:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:16:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:16:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.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 17:16:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:16:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:16:47: 1000000 INFO @ Sun, 02 Jun 2019 17:16:48: 1000000 INFO @ Sun, 02 Jun 2019 17:16:50: 1000000 INFO @ Sun, 02 Jun 2019 17:16:55: 2000000 INFO @ Sun, 02 Jun 2019 17:16:56: 2000000 INFO @ Sun, 02 Jun 2019 17:16:59: 2000000 INFO @ Sun, 02 Jun 2019 17:17:03: 3000000 INFO @ Sun, 02 Jun 2019 17:17:04: 3000000 INFO @ Sun, 02 Jun 2019 17:17:09: 3000000 INFO @ Sun, 02 Jun 2019 17:17:10: 4000000 INFO @ Sun, 02 Jun 2019 17:17:12: 4000000 INFO @ Sun, 02 Jun 2019 17:17:18: 5000000 INFO @ Sun, 02 Jun 2019 17:17:19: 4000000 INFO @ Sun, 02 Jun 2019 17:17:20: 5000000 INFO @ Sun, 02 Jun 2019 17:17:20: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:17:20: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:17:20: #1 total tags in treatment: 5248789 INFO @ Sun, 02 Jun 2019 17:17:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:17:20: #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 17:17:20: #1 tags after filtering in treatment: 5248789 INFO @ Sun, 02 Jun 2019 17:17:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:17:20: #1 finished! INFO @ Sun, 02 Jun 2019 17:17:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:17:20: #2 number of paired peaks: 435 WARNING @ Sun, 02 Jun 2019 17:17:20: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Sun, 02 Jun 2019 17:17:20: start model_add_line... INFO @ Sun, 02 Jun 2019 17:17:20: start X-correlation... INFO @ Sun, 02 Jun 2019 17:17:20: end of X-cor INFO @ Sun, 02 Jun 2019 17:17:20: #2 finished! INFO @ Sun, 02 Jun 2019 17:17:20: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 17:17:20: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 02 Jun 2019 17:17:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.05_model.r WARNING @ Sun, 02 Jun 2019 17:17:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:17:20: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 02 Jun 2019 17:17:20: #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 17:17:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:17:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:17:21: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:17:21: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:17:21: #1 total tags in treatment: 5248789 INFO @ Sun, 02 Jun 2019 17:17:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:17:21: #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 17:17:22: #1 tags after filtering in treatment: 5248789 INFO @ Sun, 02 Jun 2019 17:17:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:17:22: #1 finished! INFO @ Sun, 02 Jun 2019 17:17:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:17:22: #2 number of paired peaks: 435 WARNING @ Sun, 02 Jun 2019 17:17:22: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Sun, 02 Jun 2019 17:17:22: start model_add_line... INFO @ Sun, 02 Jun 2019 17:17:22: start X-correlation... INFO @ Sun, 02 Jun 2019 17:17:22: end of X-cor INFO @ Sun, 02 Jun 2019 17:17:22: #2 finished! INFO @ Sun, 02 Jun 2019 17:17:22: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 17:17:22: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 02 Jun 2019 17:17:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.20_model.r WARNING @ Sun, 02 Jun 2019 17:17:22: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:17:22: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 02 Jun 2019 17:17:22: #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 17:17:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:17:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:17:29: 5000000 INFO @ Sun, 02 Jun 2019 17:17:31: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:17:31: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:17:31: #1 total tags in treatment: 5248789 INFO @ Sun, 02 Jun 2019 17:17:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:17:31: #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 17:17:31: #1 tags after filtering in treatment: 5248789 INFO @ Sun, 02 Jun 2019 17:17:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:17:31: #1 finished! INFO @ Sun, 02 Jun 2019 17:17:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:17:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:17:32: #2 number of paired peaks: 435 WARNING @ Sun, 02 Jun 2019 17:17:32: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Sun, 02 Jun 2019 17:17:32: start model_add_line... INFO @ Sun, 02 Jun 2019 17:17:32: start X-correlation... INFO @ Sun, 02 Jun 2019 17:17:32: end of X-cor INFO @ Sun, 02 Jun 2019 17:17:32: #2 finished! INFO @ Sun, 02 Jun 2019 17:17:32: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 17:17:32: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 02 Jun 2019 17:17:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.10_model.r WARNING @ Sun, 02 Jun 2019 17:17:32: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:17:32: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 02 Jun 2019 17:17:32: #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 17:17:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:17:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:17:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:17:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:17:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:17:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:17:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.05_summits.bed INFO @ Sun, 02 Jun 2019 17:17:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (586 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.20_summits.bed INFO @ Sun, 02 Jun 2019 17:17:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:17:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:17:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:17:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:17:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX312081/SRX312081.10_summits.bed INFO @ Sun, 02 Jun 2019 17:17:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (377 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。