Job ID = 1292506 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,609,564 reads read : 19,609,564 reads written : 19,609,564 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: 00:05:01 19609564 reads; of these: 19609564 (100.00%) were unpaired; of these: 899478 (4.59%) aligned 0 times 14523144 (74.06%) aligned exactly 1 time 4186942 (21.35%) aligned >1 times 95.41% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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] 5402013 / 18710086 = 0.2887 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 19:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.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 19:20:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:20:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.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 19:20:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:20:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.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 19:20:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:20:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:20:36: 1000000 INFO @ Sun, 02 Jun 2019 19:20:36: 1000000 INFO @ Sun, 02 Jun 2019 19:20:36: 1000000 INFO @ Sun, 02 Jun 2019 19:20:45: 2000000 INFO @ Sun, 02 Jun 2019 19:20:45: 2000000 INFO @ Sun, 02 Jun 2019 19:20:45: 2000000 INFO @ Sun, 02 Jun 2019 19:20:53: 3000000 INFO @ Sun, 02 Jun 2019 19:20:54: 3000000 INFO @ Sun, 02 Jun 2019 19:20:54: 3000000 INFO @ Sun, 02 Jun 2019 19:21:02: 4000000 INFO @ Sun, 02 Jun 2019 19:21:03: 4000000 INFO @ Sun, 02 Jun 2019 19:21:03: 4000000 INFO @ Sun, 02 Jun 2019 19:21:11: 5000000 INFO @ Sun, 02 Jun 2019 19:21:12: 5000000 INFO @ Sun, 02 Jun 2019 19:21:12: 5000000 INFO @ Sun, 02 Jun 2019 19:21:20: 6000000 INFO @ Sun, 02 Jun 2019 19:21:21: 6000000 INFO @ Sun, 02 Jun 2019 19:21:21: 6000000 INFO @ Sun, 02 Jun 2019 19:21:28: 7000000 INFO @ Sun, 02 Jun 2019 19:21:30: 7000000 INFO @ Sun, 02 Jun 2019 19:21:30: 7000000 INFO @ Sun, 02 Jun 2019 19:21:37: 8000000 INFO @ Sun, 02 Jun 2019 19:21:39: 8000000 INFO @ Sun, 02 Jun 2019 19:21:39: 8000000 INFO @ Sun, 02 Jun 2019 19:21:46: 9000000 INFO @ Sun, 02 Jun 2019 19:21:48: 9000000 INFO @ Sun, 02 Jun 2019 19:21:48: 9000000 INFO @ Sun, 02 Jun 2019 19:21:54: 10000000 INFO @ Sun, 02 Jun 2019 19:21:57: 10000000 INFO @ Sun, 02 Jun 2019 19:21:58: 10000000 INFO @ Sun, 02 Jun 2019 19:22:03: 11000000 INFO @ Sun, 02 Jun 2019 19:22:06: 11000000 INFO @ Sun, 02 Jun 2019 19:22:07: 11000000 INFO @ Sun, 02 Jun 2019 19:22:12: 12000000 INFO @ Sun, 02 Jun 2019 19:22:15: 12000000 INFO @ Sun, 02 Jun 2019 19:22:16: 12000000 INFO @ Sun, 02 Jun 2019 19:22:21: 13000000 INFO @ Sun, 02 Jun 2019 19:22:24: 13000000 INFO @ Sun, 02 Jun 2019 19:22:24: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:22:24: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:22:24: #1 total tags in treatment: 13308073 INFO @ Sun, 02 Jun 2019 19:22:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:22:24: #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 19:22:24: #1 tags after filtering in treatment: 13308073 INFO @ Sun, 02 Jun 2019 19:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:22:24: #1 finished! INFO @ Sun, 02 Jun 2019 19:22:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:22:25: #2 number of paired peaks: 476 WARNING @ Sun, 02 Jun 2019 19:22:25: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Sun, 02 Jun 2019 19:22:25: start model_add_line... INFO @ Sun, 02 Jun 2019 19:22:25: 13000000 INFO @ Sun, 02 Jun 2019 19:22:25: start X-correlation... INFO @ Sun, 02 Jun 2019 19:22:25: end of X-cor INFO @ Sun, 02 Jun 2019 19:22:25: #2 finished! INFO @ Sun, 02 Jun 2019 19:22:25: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 19:22:25: #2 alternative fragment length(s) may be 2,45 bps INFO @ Sun, 02 Jun 2019 19:22:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.10_model.r WARNING @ Sun, 02 Jun 2019 19:22:25: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:22:25: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Sun, 02 Jun 2019 19:22:25: #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 19:22:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:22:26: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:22:26: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:22:26: #1 total tags in treatment: 13308073 INFO @ Sun, 02 Jun 2019 19:22:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:22:26: #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 19:22:27: #1 tags after filtering in treatment: 13308073 INFO @ Sun, 02 Jun 2019 19:22:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:22:27: #1 finished! INFO @ Sun, 02 Jun 2019 19:22:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:22:28: #2 number of paired peaks: 476 WARNING @ Sun, 02 Jun 2019 19:22:28: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Sun, 02 Jun 2019 19:22:28: start model_add_line... INFO @ Sun, 02 Jun 2019 19:22:28: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:22:28: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:22:28: #1 total tags in treatment: 13308073 INFO @ Sun, 02 Jun 2019 19:22:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:22:28: #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 19:22:28: start X-correlation... INFO @ Sun, 02 Jun 2019 19:22:28: end of X-cor INFO @ Sun, 02 Jun 2019 19:22:28: #2 finished! INFO @ Sun, 02 Jun 2019 19:22:28: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 19:22:28: #2 alternative fragment length(s) may be 2,45 bps INFO @ Sun, 02 Jun 2019 19:22:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.20_model.r WARNING @ Sun, 02 Jun 2019 19:22:28: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:22:28: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Sun, 02 Jun 2019 19:22:28: #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 19:22:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:22:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:22:28: #1 tags after filtering in treatment: 13308073 INFO @ Sun, 02 Jun 2019 19:22:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:22:28: #1 finished! INFO @ Sun, 02 Jun 2019 19:22:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:22:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:22:29: #2 number of paired peaks: 476 WARNING @ Sun, 02 Jun 2019 19:22:29: Fewer paired peaks (476) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 476 pairs to build model! INFO @ Sun, 02 Jun 2019 19:22:29: start model_add_line... INFO @ Sun, 02 Jun 2019 19:22:30: start X-correlation... INFO @ Sun, 02 Jun 2019 19:22:30: end of X-cor INFO @ Sun, 02 Jun 2019 19:22:30: #2 finished! INFO @ Sun, 02 Jun 2019 19:22:30: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 19:22:30: #2 alternative fragment length(s) may be 2,45 bps INFO @ Sun, 02 Jun 2019 19:22:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.05_model.r WARNING @ Sun, 02 Jun 2019 19:22:30: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:22:30: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Sun, 02 Jun 2019 19:22:30: #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 19:22:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:22:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:22:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:23:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:23:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:23:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:23:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:23:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.10_summits.bed INFO @ Sun, 02 Jun 2019 19:23:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (519 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:23:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:23:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:23:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.20_summits.bed INFO @ Sun, 02 Jun 2019 19:23:18: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (201 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:23:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:23:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:23:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466481/SRX466481.05_summits.bed INFO @ Sun, 02 Jun 2019 19:23:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (832 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。