Job ID = 2590016 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,388,946 reads read : 18,388,946 reads written : 18,388,946 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198392.sra.cache’: 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: 00:04:29 18388946 reads; of these: 18388946 (100.00%) were unpaired; of these: 4337542 (23.59%) aligned 0 times 11667806 (63.45%) aligned exactly 1 time 2383598 (12.96%) aligned >1 times 76.41% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:29 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] 1117549 / 14051404 = 0.0795 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 19:13:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.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 19:13:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:13:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.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 19:13:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:13:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:13:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.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 19:13:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:13:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:13:56: 1000000 INFO @ Mon, 12 Aug 2019 19:13:56: 1000000 INFO @ Mon, 12 Aug 2019 19:13:58: 1000000 INFO @ Mon, 12 Aug 2019 19:14:03: 2000000 INFO @ Mon, 12 Aug 2019 19:14:03: 2000000 INFO @ Mon, 12 Aug 2019 19:14:05: 2000000 INFO @ Mon, 12 Aug 2019 19:14:10: 3000000 INFO @ Mon, 12 Aug 2019 19:14:11: 3000000 INFO @ Mon, 12 Aug 2019 19:14:12: 3000000 INFO @ Mon, 12 Aug 2019 19:14:16: 4000000 INFO @ Mon, 12 Aug 2019 19:14:18: 4000000 INFO @ Mon, 12 Aug 2019 19:14:19: 4000000 INFO @ Mon, 12 Aug 2019 19:14:23: 5000000 INFO @ Mon, 12 Aug 2019 19:14:25: 5000000 INFO @ Mon, 12 Aug 2019 19:14:27: 5000000 INFO @ Mon, 12 Aug 2019 19:14:30: 6000000 INFO @ Mon, 12 Aug 2019 19:14:32: 6000000 INFO @ Mon, 12 Aug 2019 19:14:34: 6000000 INFO @ Mon, 12 Aug 2019 19:14:36: 7000000 INFO @ Mon, 12 Aug 2019 19:14:39: 7000000 INFO @ Mon, 12 Aug 2019 19:14:41: 7000000 INFO @ Mon, 12 Aug 2019 19:14:43: 8000000 INFO @ Mon, 12 Aug 2019 19:14:47: 8000000 INFO @ Mon, 12 Aug 2019 19:14:48: 8000000 INFO @ Mon, 12 Aug 2019 19:14:50: 9000000 INFO @ Mon, 12 Aug 2019 19:14:54: 9000000 INFO @ Mon, 12 Aug 2019 19:14:56: 9000000 INFO @ Mon, 12 Aug 2019 19:14:56: 10000000 INFO @ Mon, 12 Aug 2019 19:15:01: 10000000 INFO @ Mon, 12 Aug 2019 19:15:03: 10000000 INFO @ Mon, 12 Aug 2019 19:15:03: 11000000 INFO @ Mon, 12 Aug 2019 19:15:08: 11000000 INFO @ Mon, 12 Aug 2019 19:15:10: 12000000 INFO @ Mon, 12 Aug 2019 19:15:10: 11000000 INFO @ Mon, 12 Aug 2019 19:15:16: 12000000 INFO @ Mon, 12 Aug 2019 19:15:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:15:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:15:16: #1 total tags in treatment: 12933855 INFO @ Mon, 12 Aug 2019 19:15:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:15:16: #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 19:15:16: #1 tags after filtering in treatment: 12933855 INFO @ Mon, 12 Aug 2019 19:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:15:16: #1 finished! INFO @ Mon, 12 Aug 2019 19:15:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:15:17: 12000000 INFO @ Mon, 12 Aug 2019 19:15:17: #2 number of paired peaks: 332 WARNING @ Mon, 12 Aug 2019 19:15:17: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Mon, 12 Aug 2019 19:15:17: start model_add_line... INFO @ Mon, 12 Aug 2019 19:15:17: start X-correlation... INFO @ Mon, 12 Aug 2019 19:15:17: end of X-cor INFO @ Mon, 12 Aug 2019 19:15:17: #2 finished! INFO @ Mon, 12 Aug 2019 19:15:17: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 19:15:17: #2 alternative fragment length(s) may be 2,41,555,587 bps INFO @ Mon, 12 Aug 2019 19:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.10_model.r WARNING @ Mon, 12 Aug 2019 19:15:18: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:15:18: #2 You may need to consider one of the other alternative d(s): 2,41,555,587 WARNING @ Mon, 12 Aug 2019 19:15:18: #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 19:15:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:15:22: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:15:22: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:15:22: #1 total tags in treatment: 12933855 INFO @ Mon, 12 Aug 2019 19:15:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:15:22: #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 19:15:23: #1 tags after filtering in treatment: 12933855 INFO @ Mon, 12 Aug 2019 19:15:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:15:23: #1 finished! INFO @ Mon, 12 Aug 2019 19:15:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:15:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:15:24: #2 number of paired peaks: 332 WARNING @ Mon, 12 Aug 2019 19:15:24: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Mon, 12 Aug 2019 19:15:24: start model_add_line... INFO @ Mon, 12 Aug 2019 19:15:24: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:15:24: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:15:24: #1 total tags in treatment: 12933855 INFO @ Mon, 12 Aug 2019 19:15:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:15:24: #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 19:15:24: start X-correlation... INFO @ Mon, 12 Aug 2019 19:15:24: end of X-cor INFO @ Mon, 12 Aug 2019 19:15:24: #2 finished! INFO @ Mon, 12 Aug 2019 19:15:24: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 19:15:24: #2 alternative fragment length(s) may be 2,41,555,587 bps INFO @ Mon, 12 Aug 2019 19:15:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.05_model.r WARNING @ Mon, 12 Aug 2019 19:15:24: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:15:24: #2 You may need to consider one of the other alternative d(s): 2,41,555,587 WARNING @ Mon, 12 Aug 2019 19:15:24: #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 19:15:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:15:24: #1 tags after filtering in treatment: 12933855 INFO @ Mon, 12 Aug 2019 19:15:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:15:24: #1 finished! INFO @ Mon, 12 Aug 2019 19:15:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:15:25: #2 number of paired peaks: 332 WARNING @ Mon, 12 Aug 2019 19:15:25: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Mon, 12 Aug 2019 19:15:25: start model_add_line... INFO @ Mon, 12 Aug 2019 19:15:25: start X-correlation... INFO @ Mon, 12 Aug 2019 19:15:25: end of X-cor INFO @ Mon, 12 Aug 2019 19:15:25: #2 finished! INFO @ Mon, 12 Aug 2019 19:15:25: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 19:15:25: #2 alternative fragment length(s) may be 2,41,555,587 bps INFO @ Mon, 12 Aug 2019 19:15:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.20_model.r WARNING @ Mon, 12 Aug 2019 19:15:25: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:15:25: #2 You may need to consider one of the other alternative d(s): 2,41,555,587 WARNING @ Mon, 12 Aug 2019 19:15:25: #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 19:15:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:15:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:15:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:15:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:15:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:16:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:16:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:16:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.10_summits.bed INFO @ Mon, 12 Aug 2019 19:16:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:16:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:16:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:16:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.05_summits.bed INFO @ Mon, 12 Aug 2019 19:16:13: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (686 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:16:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494860/SRX494860.20_summits.bed INFO @ Mon, 12 Aug 2019 19:16:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。