Job ID = 2590002 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,161,388 reads read : 7,161,388 reads written : 7,161,388 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: 00:01:14 7161388 reads; of these: 7161388 (100.00%) were unpaired; of these: 669090 (9.34%) aligned 0 times 5398305 (75.38%) aligned exactly 1 time 1093993 (15.28%) aligned >1 times 90.66% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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] 380275 / 6492298 = 0.0586 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 19:01:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.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 19:01:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:01:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:01:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.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 19:01:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:01:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.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 19:01:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:01:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:02:00: 1000000 INFO @ Mon, 12 Aug 2019 19:02:01: 1000000 INFO @ Mon, 12 Aug 2019 19:02:03: 1000000 INFO @ Mon, 12 Aug 2019 19:02:07: 2000000 INFO @ Mon, 12 Aug 2019 19:02:08: 2000000 INFO @ Mon, 12 Aug 2019 19:02:11: 2000000 INFO @ Mon, 12 Aug 2019 19:02:14: 3000000 INFO @ Mon, 12 Aug 2019 19:02:15: 3000000 INFO @ Mon, 12 Aug 2019 19:02:19: 3000000 INFO @ Mon, 12 Aug 2019 19:02:22: 4000000 INFO @ Mon, 12 Aug 2019 19:02:23: 4000000 INFO @ Mon, 12 Aug 2019 19:02:26: 4000000 INFO @ Mon, 12 Aug 2019 19:02:29: 5000000 INFO @ Mon, 12 Aug 2019 19:02:30: 5000000 INFO @ Mon, 12 Aug 2019 19:02:34: 5000000 INFO @ Mon, 12 Aug 2019 19:02:36: 6000000 INFO @ Mon, 12 Aug 2019 19:02:37: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 19:02:37: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 19:02:37: #1 total tags in treatment: 6112023 INFO @ Mon, 12 Aug 2019 19:02:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:02:37: #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 19:02:37: 6000000 INFO @ Mon, 12 Aug 2019 19:02:37: #1 tags after filtering in treatment: 6112023 INFO @ Mon, 12 Aug 2019 19:02:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:02:37: #1 finished! INFO @ Mon, 12 Aug 2019 19:02:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:02:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:02:38: #2 number of paired peaks: 327 WARNING @ Mon, 12 Aug 2019 19:02:38: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Mon, 12 Aug 2019 19:02:38: start model_add_line... INFO @ Mon, 12 Aug 2019 19:02:38: start X-correlation... INFO @ Mon, 12 Aug 2019 19:02:38: end of X-cor INFO @ Mon, 12 Aug 2019 19:02:38: #2 finished! INFO @ Mon, 12 Aug 2019 19:02:38: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 19:02:38: #2 alternative fragment length(s) may be 3,31,541 bps INFO @ Mon, 12 Aug 2019 19:02:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.05_model.r WARNING @ Mon, 12 Aug 2019 19:02:38: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:02:38: #2 You may need to consider one of the other alternative d(s): 3,31,541 WARNING @ Mon, 12 Aug 2019 19:02:38: #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 19:02:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:02:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:02:38: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 19:02:38: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 19:02:38: #1 total tags in treatment: 6112023 INFO @ Mon, 12 Aug 2019 19:02:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:02:38: #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 19:02:38: #1 tags after filtering in treatment: 6112023 INFO @ Mon, 12 Aug 2019 19:02:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:02:38: #1 finished! INFO @ Mon, 12 Aug 2019 19:02:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:02:39: #2 number of paired peaks: 327 WARNING @ Mon, 12 Aug 2019 19:02:39: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Mon, 12 Aug 2019 19:02:39: start model_add_line... INFO @ Mon, 12 Aug 2019 19:02:39: start X-correlation... INFO @ Mon, 12 Aug 2019 19:02:39: end of X-cor INFO @ Mon, 12 Aug 2019 19:02:39: #2 finished! INFO @ Mon, 12 Aug 2019 19:02:39: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 19:02:39: #2 alternative fragment length(s) may be 3,31,541 bps INFO @ Mon, 12 Aug 2019 19:02:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.10_model.r WARNING @ Mon, 12 Aug 2019 19:02:39: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:02:39: #2 You may need to consider one of the other alternative d(s): 3,31,541 WARNING @ Mon, 12 Aug 2019 19:02:39: #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 19:02:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:02:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:02:43: 6000000 INFO @ Mon, 12 Aug 2019 19:02:43: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 19:02:43: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 19:02:43: #1 total tags in treatment: 6112023 INFO @ Mon, 12 Aug 2019 19:02:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:02:43: #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 19:02:43: #1 tags after filtering in treatment: 6112023 INFO @ Mon, 12 Aug 2019 19:02:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:02:43: #1 finished! INFO @ Mon, 12 Aug 2019 19:02:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:02:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:02:44: #2 number of paired peaks: 327 WARNING @ Mon, 12 Aug 2019 19:02:44: Fewer paired peaks (327) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 327 pairs to build model! INFO @ Mon, 12 Aug 2019 19:02:44: start model_add_line... INFO @ Mon, 12 Aug 2019 19:02:44: start X-correlation... INFO @ Mon, 12 Aug 2019 19:02:44: end of X-cor INFO @ Mon, 12 Aug 2019 19:02:44: #2 finished! INFO @ Mon, 12 Aug 2019 19:02:44: #2 predicted fragment length is 31 bps INFO @ Mon, 12 Aug 2019 19:02:44: #2 alternative fragment length(s) may be 3,31,541 bps INFO @ Mon, 12 Aug 2019 19:02:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.20_model.r WARNING @ Mon, 12 Aug 2019 19:02:44: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:02:44: #2 You may need to consider one of the other alternative d(s): 3,31,541 WARNING @ Mon, 12 Aug 2019 19:02:44: #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 19:02:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:02:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:02:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:02:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:03:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:03:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:03:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:03:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.05_summits.bed INFO @ Mon, 12 Aug 2019 19:03:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (479 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:03:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:03:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:03:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.10_summits.bed INFO @ Mon, 12 Aug 2019 19:03:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:03:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:03:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:03:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467180/SRX467180.20_summits.bed INFO @ Mon, 12 Aug 2019 19:03:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (83 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。