Job ID = 1292472 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,725,094 reads read : 24,725,094 reads written : 24,725,094 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: 00:06:30 24725094 reads; of these: 24725094 (100.00%) were unpaired; of these: 977233 (3.95%) aligned 0 times 17576196 (71.09%) aligned exactly 1 time 6171665 (24.96%) aligned >1 times 96.05% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 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] 7584045 / 23747861 = 0.3194 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 19:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.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 19:17:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:17:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.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 19:17:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:17:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.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 19:17:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:17:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:17:48: 1000000 INFO @ Sun, 02 Jun 2019 19:17:48: 1000000 INFO @ Sun, 02 Jun 2019 19:17:49: 1000000 INFO @ Sun, 02 Jun 2019 19:17:56: 2000000 INFO @ Sun, 02 Jun 2019 19:17:57: 2000000 INFO @ Sun, 02 Jun 2019 19:17:59: 2000000 INFO @ Sun, 02 Jun 2019 19:18:05: 3000000 INFO @ Sun, 02 Jun 2019 19:18:06: 3000000 INFO @ Sun, 02 Jun 2019 19:18:08: 3000000 INFO @ Sun, 02 Jun 2019 19:18:13: 4000000 INFO @ Sun, 02 Jun 2019 19:18:15: 4000000 INFO @ Sun, 02 Jun 2019 19:18:17: 4000000 INFO @ Sun, 02 Jun 2019 19:18:21: 5000000 INFO @ Sun, 02 Jun 2019 19:18:25: 5000000 INFO @ Sun, 02 Jun 2019 19:18:27: 5000000 INFO @ Sun, 02 Jun 2019 19:18:30: 6000000 INFO @ Sun, 02 Jun 2019 19:18:34: 6000000 INFO @ Sun, 02 Jun 2019 19:18:36: 6000000 INFO @ Sun, 02 Jun 2019 19:18:38: 7000000 INFO @ Sun, 02 Jun 2019 19:18:43: 7000000 INFO @ Sun, 02 Jun 2019 19:18:46: 7000000 INFO @ Sun, 02 Jun 2019 19:18:47: 8000000 INFO @ Sun, 02 Jun 2019 19:18:53: 8000000 INFO @ Sun, 02 Jun 2019 19:18:55: 9000000 INFO @ Sun, 02 Jun 2019 19:18:56: 8000000 INFO @ Sun, 02 Jun 2019 19:19:02: 9000000 INFO @ Sun, 02 Jun 2019 19:19:03: 10000000 INFO @ Sun, 02 Jun 2019 19:19:05: 9000000 INFO @ Sun, 02 Jun 2019 19:19:11: 10000000 INFO @ Sun, 02 Jun 2019 19:19:12: 11000000 INFO @ Sun, 02 Jun 2019 19:19:15: 10000000 INFO @ Sun, 02 Jun 2019 19:19:20: 12000000 INFO @ Sun, 02 Jun 2019 19:19:21: 11000000 INFO @ Sun, 02 Jun 2019 19:19:25: 11000000 INFO @ Sun, 02 Jun 2019 19:19:28: 13000000 INFO @ Sun, 02 Jun 2019 19:19:30: 12000000 INFO @ Sun, 02 Jun 2019 19:19:34: 12000000 INFO @ Sun, 02 Jun 2019 19:19:37: 14000000 INFO @ Sun, 02 Jun 2019 19:19:40: 13000000 INFO @ Sun, 02 Jun 2019 19:19:44: 13000000 INFO @ Sun, 02 Jun 2019 19:19:45: 15000000 INFO @ Sun, 02 Jun 2019 19:19:50: 14000000 INFO @ Sun, 02 Jun 2019 19:19:54: 16000000 INFO @ Sun, 02 Jun 2019 19:19:54: 14000000 INFO @ Sun, 02 Jun 2019 19:19:55: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:19:55: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:19:55: #1 total tags in treatment: 16163816 INFO @ Sun, 02 Jun 2019 19:19:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:19:55: #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 19:19:56: #1 tags after filtering in treatment: 16163816 INFO @ Sun, 02 Jun 2019 19:19:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:19:56: #1 finished! INFO @ Sun, 02 Jun 2019 19:19:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:19:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:19:57: #2 number of paired peaks: 695 WARNING @ Sun, 02 Jun 2019 19:19:57: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Sun, 02 Jun 2019 19:19:57: start model_add_line... INFO @ Sun, 02 Jun 2019 19:19:57: start X-correlation... INFO @ Sun, 02 Jun 2019 19:19:57: end of X-cor INFO @ Sun, 02 Jun 2019 19:19:57: #2 finished! INFO @ Sun, 02 Jun 2019 19:19:57: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 19:19:57: #2 alternative fragment length(s) may be 2,49,598 bps INFO @ Sun, 02 Jun 2019 19:19:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.20_model.r WARNING @ Sun, 02 Jun 2019 19:19:57: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:19:57: #2 You may need to consider one of the other alternative d(s): 2,49,598 WARNING @ Sun, 02 Jun 2019 19:19:57: #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 19:19:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:19:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:20:00: 15000000 INFO @ Sun, 02 Jun 2019 19:20:04: 15000000 INFO @ Sun, 02 Jun 2019 19:20:09: 16000000 INFO @ Sun, 02 Jun 2019 19:20:11: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:20:11: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:20:11: #1 total tags in treatment: 16163816 INFO @ Sun, 02 Jun 2019 19:20:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:20:11: #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 19:20:11: #1 tags after filtering in treatment: 16163816 INFO @ Sun, 02 Jun 2019 19:20:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:20:11: #1 finished! INFO @ Sun, 02 Jun 2019 19:20:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:20:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:20:12: #2 number of paired peaks: 695 WARNING @ Sun, 02 Jun 2019 19:20:12: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Sun, 02 Jun 2019 19:20:12: start model_add_line... INFO @ Sun, 02 Jun 2019 19:20:13: start X-correlation... INFO @ Sun, 02 Jun 2019 19:20:13: end of X-cor INFO @ Sun, 02 Jun 2019 19:20:13: #2 finished! INFO @ Sun, 02 Jun 2019 19:20:13: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 19:20:13: #2 alternative fragment length(s) may be 2,49,598 bps INFO @ Sun, 02 Jun 2019 19:20:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.05_model.r WARNING @ Sun, 02 Jun 2019 19:20:13: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:20:13: #2 You may need to consider one of the other alternative d(s): 2,49,598 WARNING @ Sun, 02 Jun 2019 19:20:13: #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 19:20:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:20:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:20:13: 16000000 INFO @ Sun, 02 Jun 2019 19:20:15: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:20:15: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:20:15: #1 total tags in treatment: 16163816 INFO @ Sun, 02 Jun 2019 19:20:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:20:15: #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 19:20:15: #1 tags after filtering in treatment: 16163816 INFO @ Sun, 02 Jun 2019 19:20:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:20:15: #1 finished! INFO @ Sun, 02 Jun 2019 19:20:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:20:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:20:16: #2 number of paired peaks: 695 WARNING @ Sun, 02 Jun 2019 19:20:16: Fewer paired peaks (695) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 695 pairs to build model! INFO @ Sun, 02 Jun 2019 19:20:16: start model_add_line... INFO @ Sun, 02 Jun 2019 19:20:17: start X-correlation... INFO @ Sun, 02 Jun 2019 19:20:17: end of X-cor INFO @ Sun, 02 Jun 2019 19:20:17: #2 finished! INFO @ Sun, 02 Jun 2019 19:20:17: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 19:20:17: #2 alternative fragment length(s) may be 2,49,598 bps INFO @ Sun, 02 Jun 2019 19:20:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.10_model.r WARNING @ Sun, 02 Jun 2019 19:20:17: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:20:17: #2 You may need to consider one of the other alternative d(s): 2,49,598 WARNING @ Sun, 02 Jun 2019 19:20:17: #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 19:20:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:20:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:20:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:20:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:20:57: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:20:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:20:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:20:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.20_summits.bed INFO @ Sun, 02 Jun 2019 19:20:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (212 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:21:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:21:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:21:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.05_summits.bed INFO @ Sun, 02 Jun 2019 19:21:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1110 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:21:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:21:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:21:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466461/SRX466461.10_summits.bed INFO @ Sun, 02 Jun 2019 19:21:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (532 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。