Job ID = 2590050 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,695,316 reads read : 15,695,316 reads written : 15,695,316 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: 00:03:43 15695316 reads; of these: 15695316 (100.00%) were unpaired; of these: 1827119 (11.64%) aligned 0 times 11334844 (72.22%) aligned exactly 1 time 2533353 (16.14%) aligned >1 times 88.36% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 1282279 / 13868197 = 0.0925 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 19:28:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.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 19:28:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:28:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:28:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.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 19:28:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:28:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:28:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.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 19:28:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:28:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:28:38: 1000000 INFO @ Mon, 12 Aug 2019 19:28:39: 1000000 INFO @ Mon, 12 Aug 2019 19:28:40: 1000000 INFO @ Mon, 12 Aug 2019 19:28:46: 2000000 INFO @ Mon, 12 Aug 2019 19:28:48: 2000000 INFO @ Mon, 12 Aug 2019 19:28:49: 2000000 INFO @ Mon, 12 Aug 2019 19:28:53: 3000000 INFO @ Mon, 12 Aug 2019 19:28:58: 3000000 INFO @ Mon, 12 Aug 2019 19:28:59: 3000000 INFO @ Mon, 12 Aug 2019 19:29:01: 4000000 INFO @ Mon, 12 Aug 2019 19:29:08: 4000000 INFO @ Mon, 12 Aug 2019 19:29:08: 4000000 INFO @ Mon, 12 Aug 2019 19:29:09: 5000000 INFO @ Mon, 12 Aug 2019 19:29:17: 6000000 INFO @ Mon, 12 Aug 2019 19:29:17: 5000000 INFO @ Mon, 12 Aug 2019 19:29:17: 5000000 INFO @ Mon, 12 Aug 2019 19:29:26: 7000000 INFO @ Mon, 12 Aug 2019 19:29:26: 6000000 INFO @ Mon, 12 Aug 2019 19:29:26: 6000000 INFO @ Mon, 12 Aug 2019 19:29:35: 7000000 INFO @ Mon, 12 Aug 2019 19:29:35: 7000000 INFO @ Mon, 12 Aug 2019 19:29:38: 8000000 INFO @ Mon, 12 Aug 2019 19:29:44: 8000000 INFO @ Mon, 12 Aug 2019 19:29:44: 8000000 INFO @ Mon, 12 Aug 2019 19:29:49: 9000000 INFO @ Mon, 12 Aug 2019 19:29:53: 9000000 INFO @ Mon, 12 Aug 2019 19:29:53: 9000000 INFO @ Mon, 12 Aug 2019 19:30:00: 10000000 INFO @ Mon, 12 Aug 2019 19:30:02: 10000000 INFO @ Mon, 12 Aug 2019 19:30:03: 10000000 INFO @ Mon, 12 Aug 2019 19:30:11: 11000000 INFO @ Mon, 12 Aug 2019 19:30:12: 11000000 INFO @ Mon, 12 Aug 2019 19:30:12: 11000000 INFO @ Mon, 12 Aug 2019 19:30:22: 12000000 INFO @ Mon, 12 Aug 2019 19:30:22: 12000000 INFO @ Mon, 12 Aug 2019 19:30:22: 12000000 INFO @ Mon, 12 Aug 2019 19:30:27: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:30:27: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:30:27: #1 total tags in treatment: 12585918 INFO @ Mon, 12 Aug 2019 19:30:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:30:27: #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 19:30:28: #1 tags after filtering in treatment: 12585918 INFO @ Mon, 12 Aug 2019 19:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:30:28: #1 finished! INFO @ Mon, 12 Aug 2019 19:30:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:30:28: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:30:28: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:30:28: #1 total tags in treatment: 12585918 INFO @ Mon, 12 Aug 2019 19:30:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:30:28: #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 19:30:28: #1 tags after filtering in treatment: 12585918 INFO @ Mon, 12 Aug 2019 19:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:30:28: #1 finished! INFO @ Mon, 12 Aug 2019 19:30:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:30:28: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:30:28: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:30:28: #1 total tags in treatment: 12585918 INFO @ Mon, 12 Aug 2019 19:30:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:30:28: #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 19:30:29: #1 tags after filtering in treatment: 12585918 INFO @ Mon, 12 Aug 2019 19:30:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:30:29: #1 finished! INFO @ Mon, 12 Aug 2019 19:30:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:30:29: #2 number of paired peaks: 349 WARNING @ Mon, 12 Aug 2019 19:30:29: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Mon, 12 Aug 2019 19:30:29: start model_add_line... INFO @ Mon, 12 Aug 2019 19:30:29: start X-correlation... INFO @ Mon, 12 Aug 2019 19:30:29: end of X-cor INFO @ Mon, 12 Aug 2019 19:30:29: #2 finished! INFO @ Mon, 12 Aug 2019 19:30:29: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 19:30:29: #2 alternative fragment length(s) may be 2,48,563,571,577 bps INFO @ Mon, 12 Aug 2019 19:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.20_model.r WARNING @ Mon, 12 Aug 2019 19:30:29: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:30:29: #2 You may need to consider one of the other alternative d(s): 2,48,563,571,577 WARNING @ Mon, 12 Aug 2019 19:30:29: #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 19:30:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:30:29: #2 number of paired peaks: 349 WARNING @ Mon, 12 Aug 2019 19:30:29: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Mon, 12 Aug 2019 19:30:29: start model_add_line... INFO @ Mon, 12 Aug 2019 19:30:29: start X-correlation... INFO @ Mon, 12 Aug 2019 19:30:29: end of X-cor INFO @ Mon, 12 Aug 2019 19:30:29: #2 finished! INFO @ Mon, 12 Aug 2019 19:30:29: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 19:30:29: #2 alternative fragment length(s) may be 2,48,563,571,577 bps INFO @ Mon, 12 Aug 2019 19:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.05_model.r WARNING @ Mon, 12 Aug 2019 19:30:29: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:30:29: #2 You may need to consider one of the other alternative d(s): 2,48,563,571,577 WARNING @ Mon, 12 Aug 2019 19:30:29: #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 19:30:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:30:30: #2 number of paired peaks: 349 WARNING @ Mon, 12 Aug 2019 19:30:30: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Mon, 12 Aug 2019 19:30:30: start model_add_line... INFO @ Mon, 12 Aug 2019 19:30:30: start X-correlation... INFO @ Mon, 12 Aug 2019 19:30:30: end of X-cor INFO @ Mon, 12 Aug 2019 19:30:30: #2 finished! INFO @ Mon, 12 Aug 2019 19:30:30: #2 predicted fragment length is 48 bps INFO @ Mon, 12 Aug 2019 19:30:30: #2 alternative fragment length(s) may be 2,48,563,571,577 bps INFO @ Mon, 12 Aug 2019 19:30:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.10_model.r WARNING @ Mon, 12 Aug 2019 19:30:30: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:30:30: #2 You may need to consider one of the other alternative d(s): 2,48,563,571,577 WARNING @ Mon, 12 Aug 2019 19:30:30: #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 19:30:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:30:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:31:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:31:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:31:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:31:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:31:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:31:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.20_summits.bed INFO @ Mon, 12 Aug 2019 19:31:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:31:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:31:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:31:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.10_summits.bed INFO @ Mon, 12 Aug 2019 19:31:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (502 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:31:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:31:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:31:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494894/SRX494894.05_summits.bed INFO @ Mon, 12 Aug 2019 19:31:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (651 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。