Job ID = 1293210 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,434,432 reads read : 26,434,432 reads written : 26,434,432 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:50 26434432 reads; of these: 26434432 (100.00%) were unpaired; of these: 1352398 (5.12%) aligned 0 times 20745500 (78.48%) aligned exactly 1 time 4336534 (16.40%) aligned >1 times 94.88% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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 12 files... [bam_rmdupse_core] 6143241 / 25082034 = 0.2449 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 22:40:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.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 22:40:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:40:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:40:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.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 22:40:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:40:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:40:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.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 22:40:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:40:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:40:10: 1000000 INFO @ Sun, 02 Jun 2019 22:40:11: 1000000 INFO @ Sun, 02 Jun 2019 22:40:11: 1000000 INFO @ Sun, 02 Jun 2019 22:40:17: 2000000 INFO @ Sun, 02 Jun 2019 22:40:19: 2000000 INFO @ Sun, 02 Jun 2019 22:40:19: 2000000 INFO @ Sun, 02 Jun 2019 22:40:24: 3000000 INFO @ Sun, 02 Jun 2019 22:40:26: 3000000 INFO @ Sun, 02 Jun 2019 22:40:26: 3000000 INFO @ Sun, 02 Jun 2019 22:40:30: 4000000 INFO @ Sun, 02 Jun 2019 22:40:34: 4000000 INFO @ Sun, 02 Jun 2019 22:40:34: 4000000 INFO @ Sun, 02 Jun 2019 22:40:37: 5000000 INFO @ Sun, 02 Jun 2019 22:40:41: 5000000 INFO @ Sun, 02 Jun 2019 22:40:41: 5000000 INFO @ Sun, 02 Jun 2019 22:40:44: 6000000 INFO @ Sun, 02 Jun 2019 22:40:49: 6000000 INFO @ Sun, 02 Jun 2019 22:40:50: 6000000 INFO @ Sun, 02 Jun 2019 22:40:50: 7000000 INFO @ Sun, 02 Jun 2019 22:40:57: 8000000 INFO @ Sun, 02 Jun 2019 22:40:57: 7000000 INFO @ Sun, 02 Jun 2019 22:40:58: 7000000 INFO @ Sun, 02 Jun 2019 22:41:03: 9000000 INFO @ Sun, 02 Jun 2019 22:41:05: 8000000 INFO @ Sun, 02 Jun 2019 22:41:05: 8000000 INFO @ Sun, 02 Jun 2019 22:41:10: 10000000 INFO @ Sun, 02 Jun 2019 22:41:12: 9000000 INFO @ Sun, 02 Jun 2019 22:41:12: 9000000 INFO @ Sun, 02 Jun 2019 22:41:17: 11000000 INFO @ Sun, 02 Jun 2019 22:41:20: 10000000 INFO @ Sun, 02 Jun 2019 22:41:20: 10000000 INFO @ Sun, 02 Jun 2019 22:41:23: 12000000 INFO @ Sun, 02 Jun 2019 22:41:27: 11000000 INFO @ Sun, 02 Jun 2019 22:41:27: 11000000 INFO @ Sun, 02 Jun 2019 22:41:30: 13000000 INFO @ Sun, 02 Jun 2019 22:41:34: 12000000 INFO @ Sun, 02 Jun 2019 22:41:34: 12000000 INFO @ Sun, 02 Jun 2019 22:41:36: 14000000 INFO @ Sun, 02 Jun 2019 22:41:42: 13000000 INFO @ Sun, 02 Jun 2019 22:41:42: 13000000 INFO @ Sun, 02 Jun 2019 22:41:43: 15000000 INFO @ Sun, 02 Jun 2019 22:41:49: 14000000 INFO @ Sun, 02 Jun 2019 22:41:50: 14000000 INFO @ Sun, 02 Jun 2019 22:41:50: 16000000 INFO @ Sun, 02 Jun 2019 22:41:57: 17000000 INFO @ Sun, 02 Jun 2019 22:41:58: 15000000 INFO @ Sun, 02 Jun 2019 22:41:58: 15000000 INFO @ Sun, 02 Jun 2019 22:42:03: 18000000 INFO @ Sun, 02 Jun 2019 22:42:05: 16000000 INFO @ Sun, 02 Jun 2019 22:42:05: 16000000 INFO @ Sun, 02 Jun 2019 22:42:10: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:42:10: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:42:10: #1 total tags in treatment: 18938793 INFO @ Sun, 02 Jun 2019 22:42:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:42:10: #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 22:42:10: #1 tags after filtering in treatment: 18938793 INFO @ Sun, 02 Jun 2019 22:42:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:42:10: #1 finished! INFO @ Sun, 02 Jun 2019 22:42:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:42:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:42:12: #2 number of paired peaks: 296 WARNING @ Sun, 02 Jun 2019 22:42:12: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sun, 02 Jun 2019 22:42:12: start model_add_line... INFO @ Sun, 02 Jun 2019 22:42:12: start X-correlation... INFO @ Sun, 02 Jun 2019 22:42:12: end of X-cor INFO @ Sun, 02 Jun 2019 22:42:12: #2 finished! INFO @ Sun, 02 Jun 2019 22:42:12: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:42:12: #2 alternative fragment length(s) may be 1,37,552 bps INFO @ Sun, 02 Jun 2019 22:42:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.05_model.r WARNING @ Sun, 02 Jun 2019 22:42:12: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:42:12: #2 You may need to consider one of the other alternative d(s): 1,37,552 WARNING @ Sun, 02 Jun 2019 22:42:12: #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 22:42:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:42:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:42:13: 17000000 INFO @ Sun, 02 Jun 2019 22:42:13: 17000000 INFO @ Sun, 02 Jun 2019 22:42:20: 18000000 INFO @ Sun, 02 Jun 2019 22:42:20: 18000000 INFO @ Sun, 02 Jun 2019 22:42:27: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:42:27: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:42:27: #1 total tags in treatment: 18938793 INFO @ Sun, 02 Jun 2019 22:42:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:42:27: #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 22:42:27: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:42:27: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:42:27: #1 total tags in treatment: 18938793 INFO @ Sun, 02 Jun 2019 22:42:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:42:27: #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 22:42:27: #1 tags after filtering in treatment: 18938793 INFO @ Sun, 02 Jun 2019 22:42:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:42:27: #1 finished! INFO @ Sun, 02 Jun 2019 22:42:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:42:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:42:28: #1 tags after filtering in treatment: 18938793 INFO @ Sun, 02 Jun 2019 22:42:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:42:28: #1 finished! INFO @ Sun, 02 Jun 2019 22:42:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:42:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:42:29: #2 number of paired peaks: 296 WARNING @ Sun, 02 Jun 2019 22:42:29: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sun, 02 Jun 2019 22:42:29: start model_add_line... INFO @ Sun, 02 Jun 2019 22:42:29: #2 number of paired peaks: 296 WARNING @ Sun, 02 Jun 2019 22:42:29: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Sun, 02 Jun 2019 22:42:29: start model_add_line... INFO @ Sun, 02 Jun 2019 22:42:29: start X-correlation... INFO @ Sun, 02 Jun 2019 22:42:29: end of X-cor INFO @ Sun, 02 Jun 2019 22:42:29: #2 finished! INFO @ Sun, 02 Jun 2019 22:42:29: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:42:29: #2 alternative fragment length(s) may be 1,37,552 bps INFO @ Sun, 02 Jun 2019 22:42:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.20_model.r WARNING @ Sun, 02 Jun 2019 22:42:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:42:29: #2 You may need to consider one of the other alternative d(s): 1,37,552 WARNING @ Sun, 02 Jun 2019 22:42:29: #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 22:42:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:42:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:42:29: start X-correlation... INFO @ Sun, 02 Jun 2019 22:42:29: end of X-cor INFO @ Sun, 02 Jun 2019 22:42:29: #2 finished! INFO @ Sun, 02 Jun 2019 22:42:29: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:42:29: #2 alternative fragment length(s) may be 1,37,552 bps INFO @ Sun, 02 Jun 2019 22:42:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.10_model.r WARNING @ Sun, 02 Jun 2019 22:42:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:42:29: #2 You may need to consider one of the other alternative d(s): 1,37,552 WARNING @ Sun, 02 Jun 2019 22:42:29: #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 22:42:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:42:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:42:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:43:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:43:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:43:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:43:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:43:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.05_summits.bed INFO @ Sun, 02 Jun 2019 22:43:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:43:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:43:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:43:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.20_summits.bed INFO @ Sun, 02 Jun 2019 22:43:30: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:43:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:43:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:43:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402760/SRX5402760.10_summits.bed INFO @ Sun, 02 Jun 2019 22:43:31: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。