Job ID = 1292932 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,125,724 reads read : 20,125,724 reads written : 20,125,724 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: 00:05:13 20125724 reads; of these: 20125724 (100.00%) were unpaired; of these: 418331 (2.08%) aligned 0 times 16122573 (80.11%) aligned exactly 1 time 3584820 (17.81%) aligned >1 times 97.92% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 2496292 / 19707393 = 0.1267 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 21:18:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.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 21:18:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.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 21:18:08: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:18:08: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:18:08: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:18:08: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:18:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.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 21:18:08: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:18:08: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:18:16: 1000000 INFO @ Sun, 02 Jun 2019 21:18:16: 1000000 INFO @ Sun, 02 Jun 2019 21:18:17: 1000000 INFO @ Sun, 02 Jun 2019 21:18:24: 2000000 INFO @ Sun, 02 Jun 2019 21:18:24: 2000000 INFO @ Sun, 02 Jun 2019 21:18:25: 2000000 INFO @ Sun, 02 Jun 2019 21:18:31: 3000000 INFO @ Sun, 02 Jun 2019 21:18:33: 3000000 INFO @ Sun, 02 Jun 2019 21:18:33: 3000000 INFO @ Sun, 02 Jun 2019 21:18:38: 4000000 INFO @ Sun, 02 Jun 2019 21:18:40: 4000000 INFO @ Sun, 02 Jun 2019 21:18:41: 4000000 INFO @ Sun, 02 Jun 2019 21:18:45: 5000000 INFO @ Sun, 02 Jun 2019 21:18:48: 5000000 INFO @ Sun, 02 Jun 2019 21:18:49: 5000000 INFO @ Sun, 02 Jun 2019 21:18:52: 6000000 INFO @ Sun, 02 Jun 2019 21:18:56: 6000000 INFO @ Sun, 02 Jun 2019 21:18:56: 6000000 INFO @ Sun, 02 Jun 2019 21:18:59: 7000000 INFO @ Sun, 02 Jun 2019 21:19:03: 7000000 INFO @ Sun, 02 Jun 2019 21:19:04: 7000000 INFO @ Sun, 02 Jun 2019 21:19:06: 8000000 INFO @ Sun, 02 Jun 2019 21:19:11: 8000000 INFO @ Sun, 02 Jun 2019 21:19:12: 8000000 INFO @ Sun, 02 Jun 2019 21:19:13: 9000000 INFO @ Sun, 02 Jun 2019 21:19:19: 9000000 INFO @ Sun, 02 Jun 2019 21:19:20: 9000000 INFO @ Sun, 02 Jun 2019 21:19:20: 10000000 INFO @ Sun, 02 Jun 2019 21:19:26: 10000000 INFO @ Sun, 02 Jun 2019 21:19:27: 11000000 INFO @ Sun, 02 Jun 2019 21:19:28: 10000000 INFO @ Sun, 02 Jun 2019 21:19:34: 11000000 INFO @ Sun, 02 Jun 2019 21:19:34: 12000000 INFO @ Sun, 02 Jun 2019 21:19:35: 11000000 INFO @ Sun, 02 Jun 2019 21:19:41: 13000000 INFO @ Sun, 02 Jun 2019 21:19:41: 12000000 INFO @ Sun, 02 Jun 2019 21:19:43: 12000000 INFO @ Sun, 02 Jun 2019 21:19:48: 14000000 INFO @ Sun, 02 Jun 2019 21:19:49: 13000000 INFO @ Sun, 02 Jun 2019 21:19:51: 13000000 INFO @ Sun, 02 Jun 2019 21:19:55: 15000000 INFO @ Sun, 02 Jun 2019 21:19:57: 14000000 INFO @ Sun, 02 Jun 2019 21:19:59: 14000000 INFO @ Sun, 02 Jun 2019 21:20:02: 16000000 INFO @ Sun, 02 Jun 2019 21:20:04: 15000000 INFO @ Sun, 02 Jun 2019 21:20:06: 15000000 INFO @ Sun, 02 Jun 2019 21:20:09: 17000000 INFO @ Sun, 02 Jun 2019 21:20:11: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:20:11: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:20:11: #1 total tags in treatment: 17211101 INFO @ Sun, 02 Jun 2019 21:20:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:20:11: #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 21:20:11: #1 tags after filtering in treatment: 17211101 INFO @ Sun, 02 Jun 2019 21:20:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:20:11: #1 finished! INFO @ Sun, 02 Jun 2019 21:20:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:20:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:20:12: 16000000 INFO @ Sun, 02 Jun 2019 21:20:12: #2 number of paired peaks: 260 WARNING @ Sun, 02 Jun 2019 21:20:12: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Sun, 02 Jun 2019 21:20:12: start model_add_line... INFO @ Sun, 02 Jun 2019 21:20:13: start X-correlation... INFO @ Sun, 02 Jun 2019 21:20:13: end of X-cor INFO @ Sun, 02 Jun 2019 21:20:13: #2 finished! INFO @ Sun, 02 Jun 2019 21:20:13: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 21:20:13: #2 alternative fragment length(s) may be 1,48 bps INFO @ Sun, 02 Jun 2019 21:20:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.20_model.r WARNING @ Sun, 02 Jun 2019 21:20:13: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:20:13: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Sun, 02 Jun 2019 21:20:13: #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 21:20:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:20:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:20:14: 16000000 INFO @ Sun, 02 Jun 2019 21:20:19: 17000000 INFO @ Sun, 02 Jun 2019 21:20:21: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:20:21: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:20:21: #1 total tags in treatment: 17211101 INFO @ Sun, 02 Jun 2019 21:20:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:20:21: #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 21:20:21: #1 tags after filtering in treatment: 17211101 INFO @ Sun, 02 Jun 2019 21:20:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:20:21: #1 finished! INFO @ Sun, 02 Jun 2019 21:20:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:20:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:20:21: 17000000 INFO @ Sun, 02 Jun 2019 21:20:23: #2 number of paired peaks: 260 WARNING @ Sun, 02 Jun 2019 21:20:23: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Sun, 02 Jun 2019 21:20:23: start model_add_line... INFO @ Sun, 02 Jun 2019 21:20:23: start X-correlation... INFO @ Sun, 02 Jun 2019 21:20:23: end of X-cor INFO @ Sun, 02 Jun 2019 21:20:23: #2 finished! INFO @ Sun, 02 Jun 2019 21:20:23: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 21:20:23: #2 alternative fragment length(s) may be 1,48 bps INFO @ Sun, 02 Jun 2019 21:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.10_model.r WARNING @ Sun, 02 Jun 2019 21:20:23: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:20:23: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Sun, 02 Jun 2019 21:20:23: #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 21:20:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:20:23: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:20:23: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:20:23: #1 total tags in treatment: 17211101 INFO @ Sun, 02 Jun 2019 21:20:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:20:23: #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 21:20:23: #1 tags after filtering in treatment: 17211101 INFO @ Sun, 02 Jun 2019 21:20:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:20:23: #1 finished! INFO @ Sun, 02 Jun 2019 21:20:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:20:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:20:25: #2 number of paired peaks: 260 WARNING @ Sun, 02 Jun 2019 21:20:25: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Sun, 02 Jun 2019 21:20:25: start model_add_line... INFO @ Sun, 02 Jun 2019 21:20:25: start X-correlation... INFO @ Sun, 02 Jun 2019 21:20:25: end of X-cor INFO @ Sun, 02 Jun 2019 21:20:25: #2 finished! INFO @ Sun, 02 Jun 2019 21:20:25: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 21:20:25: #2 alternative fragment length(s) may be 1,48 bps INFO @ Sun, 02 Jun 2019 21:20:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.05_model.r WARNING @ Sun, 02 Jun 2019 21:20:25: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:20:25: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Sun, 02 Jun 2019 21:20:25: #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 21:20:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:20:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:20:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:21:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:21:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:21:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:21:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:21:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.20_summits.bed INFO @ Sun, 02 Jun 2019 21:21:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (176 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:21:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:21:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:21:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.10_summits.bed INFO @ Sun, 02 Jun 2019 21:21:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (463 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:21:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:21:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:21:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020723/SRX5020723.05_summits.bed INFO @ Sun, 02 Jun 2019 21:21:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (875 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。