Job ID = 1291990 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,769,198 reads read : 19,769,198 reads written : 19,769,198 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:39 19769198 reads; of these: 19769198 (100.00%) were unpaired; of these: 10279679 (52.00%) aligned 0 times 7849770 (39.71%) aligned exactly 1 time 1639749 (8.29%) aligned >1 times 48.00% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 861312 / 9489519 = 0.0908 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 17:33:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.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 17:33:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:33:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:33:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.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 17:33:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:33:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:33:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.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 17:33:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:33:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:33:56: 1000000 INFO @ Sun, 02 Jun 2019 17:34:00: 1000000 INFO @ Sun, 02 Jun 2019 17:34:02: 1000000 INFO @ Sun, 02 Jun 2019 17:34:05: 2000000 INFO @ Sun, 02 Jun 2019 17:34:13: 2000000 INFO @ Sun, 02 Jun 2019 17:34:14: 3000000 INFO @ Sun, 02 Jun 2019 17:34:16: 2000000 INFO @ Sun, 02 Jun 2019 17:34:22: 4000000 INFO @ Sun, 02 Jun 2019 17:34:26: 3000000 INFO @ Sun, 02 Jun 2019 17:34:29: 3000000 INFO @ Sun, 02 Jun 2019 17:34:31: 5000000 INFO @ Sun, 02 Jun 2019 17:34:38: 4000000 INFO @ Sun, 02 Jun 2019 17:34:40: 6000000 INFO @ Sun, 02 Jun 2019 17:34:43: 4000000 INFO @ Sun, 02 Jun 2019 17:34:48: 7000000 INFO @ Sun, 02 Jun 2019 17:34:50: 5000000 INFO @ Sun, 02 Jun 2019 17:34:56: 5000000 INFO @ Sun, 02 Jun 2019 17:34:57: 8000000 INFO @ Sun, 02 Jun 2019 17:35:02: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 17:35:02: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 17:35:02: #1 total tags in treatment: 8628207 INFO @ Sun, 02 Jun 2019 17:35:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:35:02: #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 17:35:03: #1 tags after filtering in treatment: 8628207 INFO @ Sun, 02 Jun 2019 17:35:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:35:03: #1 finished! INFO @ Sun, 02 Jun 2019 17:35:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:35:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:35:03: 6000000 INFO @ Sun, 02 Jun 2019 17:35:03: #2 number of paired peaks: 397 WARNING @ Sun, 02 Jun 2019 17:35:03: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Sun, 02 Jun 2019 17:35:03: start model_add_line... INFO @ Sun, 02 Jun 2019 17:35:03: start X-correlation... INFO @ Sun, 02 Jun 2019 17:35:03: end of X-cor INFO @ Sun, 02 Jun 2019 17:35:03: #2 finished! INFO @ Sun, 02 Jun 2019 17:35:03: #2 predicted fragment length is 69 bps INFO @ Sun, 02 Jun 2019 17:35:03: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 02 Jun 2019 17:35:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.10_model.r WARNING @ Sun, 02 Jun 2019 17:35:03: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:35:03: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 02 Jun 2019 17:35:03: #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 17:35:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:35:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:35:09: 6000000 INFO @ Sun, 02 Jun 2019 17:35:15: 7000000 INFO @ Sun, 02 Jun 2019 17:35:23: 7000000 INFO @ Sun, 02 Jun 2019 17:35:27: 8000000 INFO @ Sun, 02 Jun 2019 17:35:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:35:35: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 17:35:35: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 17:35:35: #1 total tags in treatment: 8628207 INFO @ Sun, 02 Jun 2019 17:35:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:35:35: #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 17:35:35: 8000000 INFO @ Sun, 02 Jun 2019 17:35:35: #1 tags after filtering in treatment: 8628207 INFO @ Sun, 02 Jun 2019 17:35:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:35:35: #1 finished! INFO @ Sun, 02 Jun 2019 17:35:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:35:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:35:36: #2 number of paired peaks: 397 WARNING @ Sun, 02 Jun 2019 17:35:36: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Sun, 02 Jun 2019 17:35:36: start model_add_line... INFO @ Sun, 02 Jun 2019 17:35:36: start X-correlation... INFO @ Sun, 02 Jun 2019 17:35:36: end of X-cor INFO @ Sun, 02 Jun 2019 17:35:36: #2 finished! INFO @ Sun, 02 Jun 2019 17:35:36: #2 predicted fragment length is 69 bps INFO @ Sun, 02 Jun 2019 17:35:36: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 02 Jun 2019 17:35:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.20_model.r WARNING @ Sun, 02 Jun 2019 17:35:36: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:35:36: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 02 Jun 2019 17:35:36: #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 17:35:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:35:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:35:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:35:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:35:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.10_summits.bed INFO @ Sun, 02 Jun 2019 17:35:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:35:42: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 17:35:42: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 17:35:42: #1 total tags in treatment: 8628207 INFO @ Sun, 02 Jun 2019 17:35:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:35:42: #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 17:35:42: #1 tags after filtering in treatment: 8628207 INFO @ Sun, 02 Jun 2019 17:35:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:35:42: #1 finished! INFO @ Sun, 02 Jun 2019 17:35:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:35:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:35:43: #2 number of paired peaks: 397 WARNING @ Sun, 02 Jun 2019 17:35:43: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Sun, 02 Jun 2019 17:35:43: start model_add_line... INFO @ Sun, 02 Jun 2019 17:35:43: start X-correlation... INFO @ Sun, 02 Jun 2019 17:35:43: end of X-cor INFO @ Sun, 02 Jun 2019 17:35:43: #2 finished! INFO @ Sun, 02 Jun 2019 17:35:43: #2 predicted fragment length is 69 bps INFO @ Sun, 02 Jun 2019 17:35:43: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 02 Jun 2019 17:35:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.05_model.r WARNING @ Sun, 02 Jun 2019 17:35:43: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:35:43: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 02 Jun 2019 17:35:43: #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 17:35:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:35:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:36:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:36:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:36:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:36:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:36:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.20_summits.bed INFO @ Sun, 02 Jun 2019 17:36:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:36:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:36:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:36:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX278066/SRX278066.05_summits.bed INFO @ Sun, 02 Jun 2019 17:36:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (616 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。