Job ID = 2590015 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,661,015 reads read : 17,661,015 reads written : 17,661,015 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: 00:04:41 17661015 reads; of these: 17661015 (100.00%) were unpaired; of these: 793503 (4.49%) aligned 0 times 14185354 (80.32%) aligned exactly 1 time 2682158 (15.19%) aligned >1 times 95.51% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4629367 / 16867512 = 0.2745 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 19:20:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.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 19:20:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:20:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:20:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.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 19:20:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:20:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:20:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.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 19:20:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:20:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:20:29: 1000000 INFO @ Mon, 12 Aug 2019 19:20:30: 1000000 INFO @ Mon, 12 Aug 2019 19:20:31: 1000000 INFO @ Mon, 12 Aug 2019 19:20:38: 2000000 INFO @ Mon, 12 Aug 2019 19:20:38: 2000000 INFO @ Mon, 12 Aug 2019 19:20:40: 2000000 INFO @ Mon, 12 Aug 2019 19:20:46: 3000000 INFO @ Mon, 12 Aug 2019 19:20:47: 3000000 INFO @ Mon, 12 Aug 2019 19:20:48: 3000000 INFO @ Mon, 12 Aug 2019 19:20:54: 4000000 INFO @ Mon, 12 Aug 2019 19:20:55: 4000000 INFO @ Mon, 12 Aug 2019 19:20:56: 4000000 INFO @ Mon, 12 Aug 2019 19:21:02: 5000000 INFO @ Mon, 12 Aug 2019 19:21:03: 5000000 INFO @ Mon, 12 Aug 2019 19:21:04: 5000000 INFO @ Mon, 12 Aug 2019 19:21:11: 6000000 INFO @ Mon, 12 Aug 2019 19:21:11: 6000000 INFO @ Mon, 12 Aug 2019 19:21:12: 6000000 INFO @ Mon, 12 Aug 2019 19:21:19: 7000000 INFO @ Mon, 12 Aug 2019 19:21:19: 7000000 INFO @ Mon, 12 Aug 2019 19:21:20: 7000000 INFO @ Mon, 12 Aug 2019 19:21:27: 8000000 INFO @ Mon, 12 Aug 2019 19:21:28: 8000000 INFO @ Mon, 12 Aug 2019 19:21:29: 8000000 INFO @ Mon, 12 Aug 2019 19:21:35: 9000000 INFO @ Mon, 12 Aug 2019 19:21:36: 9000000 INFO @ Mon, 12 Aug 2019 19:21:37: 9000000 INFO @ Mon, 12 Aug 2019 19:21:43: 10000000 INFO @ Mon, 12 Aug 2019 19:21:44: 10000000 INFO @ Mon, 12 Aug 2019 19:21:45: 10000000 INFO @ Mon, 12 Aug 2019 19:21:52: 11000000 INFO @ Mon, 12 Aug 2019 19:21:52: 11000000 INFO @ Mon, 12 Aug 2019 19:21:53: 11000000 INFO @ Mon, 12 Aug 2019 19:22:00: 12000000 INFO @ Mon, 12 Aug 2019 19:22:00: 12000000 INFO @ Mon, 12 Aug 2019 19:22:01: 12000000 INFO @ Mon, 12 Aug 2019 19:22:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:22:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:22:02: #1 total tags in treatment: 12238145 INFO @ Mon, 12 Aug 2019 19:22:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:22:02: #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 19:22:02: #1 tags after filtering in treatment: 12238145 INFO @ Mon, 12 Aug 2019 19:22:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:22:02: #1 finished! INFO @ Mon, 12 Aug 2019 19:22:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:22:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:22:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:22:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:22:02: #1 total tags in treatment: 12238145 INFO @ Mon, 12 Aug 2019 19:22:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:22:02: #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 19:22:03: #1 tags after filtering in treatment: 12238145 INFO @ Mon, 12 Aug 2019 19:22:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:22:03: #1 finished! INFO @ Mon, 12 Aug 2019 19:22:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:22:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:22:03: #2 number of paired peaks: 277 WARNING @ Mon, 12 Aug 2019 19:22:03: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Mon, 12 Aug 2019 19:22:03: start model_add_line... INFO @ Mon, 12 Aug 2019 19:22:03: start X-correlation... INFO @ Mon, 12 Aug 2019 19:22:03: end of X-cor INFO @ Mon, 12 Aug 2019 19:22:03: #2 finished! INFO @ Mon, 12 Aug 2019 19:22:03: #2 predicted fragment length is 46 bps INFO @ Mon, 12 Aug 2019 19:22:03: #2 alternative fragment length(s) may be 2,46 bps INFO @ Mon, 12 Aug 2019 19:22:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.05_model.r WARNING @ Mon, 12 Aug 2019 19:22:03: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:22:03: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Mon, 12 Aug 2019 19:22:03: #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 19:22:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:22:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:22:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:22:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:22:03: #1 total tags in treatment: 12238145 INFO @ Mon, 12 Aug 2019 19:22:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:22:03: #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 19:22:04: #1 tags after filtering in treatment: 12238145 INFO @ Mon, 12 Aug 2019 19:22:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:22:04: #1 finished! INFO @ Mon, 12 Aug 2019 19:22:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:22:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:22:04: #2 number of paired peaks: 277 WARNING @ Mon, 12 Aug 2019 19:22:04: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Mon, 12 Aug 2019 19:22:04: start model_add_line... INFO @ Mon, 12 Aug 2019 19:22:04: start X-correlation... INFO @ Mon, 12 Aug 2019 19:22:04: end of X-cor INFO @ Mon, 12 Aug 2019 19:22:04: #2 finished! INFO @ Mon, 12 Aug 2019 19:22:04: #2 predicted fragment length is 46 bps INFO @ Mon, 12 Aug 2019 19:22:04: #2 alternative fragment length(s) may be 2,46 bps INFO @ Mon, 12 Aug 2019 19:22:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.10_model.r WARNING @ Mon, 12 Aug 2019 19:22:04: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:22:04: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Mon, 12 Aug 2019 19:22:04: #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 19:22:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:22:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:22:05: #2 number of paired peaks: 277 WARNING @ Mon, 12 Aug 2019 19:22:05: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Mon, 12 Aug 2019 19:22:05: start model_add_line... INFO @ Mon, 12 Aug 2019 19:22:05: start X-correlation... INFO @ Mon, 12 Aug 2019 19:22:05: end of X-cor INFO @ Mon, 12 Aug 2019 19:22:05: #2 finished! INFO @ Mon, 12 Aug 2019 19:22:05: #2 predicted fragment length is 46 bps INFO @ Mon, 12 Aug 2019 19:22:05: #2 alternative fragment length(s) may be 2,46 bps INFO @ Mon, 12 Aug 2019 19:22:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.20_model.r WARNING @ Mon, 12 Aug 2019 19:22:05: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:22:05: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Mon, 12 Aug 2019 19:22:05: #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 19:22:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:22:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:22:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:22:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:22:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:22:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:22:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.05_summits.bed INFO @ Mon, 12 Aug 2019 19:22:50: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (637 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:22:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:22:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:22:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.10_summits.bed INFO @ Mon, 12 Aug 2019 19:22:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (403 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:22:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:22:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:22:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494859/SRX494859.20_summits.bed INFO @ Mon, 12 Aug 2019 19:22:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 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。