Job ID = 1293013 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,728,448 reads read : 31,456,896 reads written : 15,728,448 reads 0-length : 15,728,448 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: 00:06:02 15728448 reads; of these: 15728448 (100.00%) were unpaired; of these: 3977265 (25.29%) aligned 0 times 9720758 (61.80%) aligned exactly 1 time 2030425 (12.91%) aligned >1 times 74.71% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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] 1840345 / 11751183 = 0.1566 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 21:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.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 21:42:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.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 21:42:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.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 21:42:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:27: 1000000 INFO @ Sun, 02 Jun 2019 21:42:27: 1000000 INFO @ Sun, 02 Jun 2019 21:42:29: 1000000 INFO @ Sun, 02 Jun 2019 21:42:36: 2000000 INFO @ Sun, 02 Jun 2019 21:42:37: 2000000 INFO @ Sun, 02 Jun 2019 21:42:40: 2000000 INFO @ Sun, 02 Jun 2019 21:42:46: 3000000 INFO @ Sun, 02 Jun 2019 21:42:46: 3000000 INFO @ Sun, 02 Jun 2019 21:42:54: 3000000 INFO @ Sun, 02 Jun 2019 21:42:55: 4000000 INFO @ Sun, 02 Jun 2019 21:42:56: 4000000 INFO @ Sun, 02 Jun 2019 21:43:04: 5000000 INFO @ Sun, 02 Jun 2019 21:43:05: 5000000 INFO @ Sun, 02 Jun 2019 21:43:07: 4000000 INFO @ Sun, 02 Jun 2019 21:43:14: 6000000 INFO @ Sun, 02 Jun 2019 21:43:15: 6000000 INFO @ Sun, 02 Jun 2019 21:43:20: 5000000 INFO @ Sun, 02 Jun 2019 21:43:23: 7000000 INFO @ Sun, 02 Jun 2019 21:43:25: 7000000 INFO @ Sun, 02 Jun 2019 21:43:32: 8000000 INFO @ Sun, 02 Jun 2019 21:43:34: 6000000 INFO @ Sun, 02 Jun 2019 21:43:35: 8000000 INFO @ Sun, 02 Jun 2019 21:43:42: 9000000 INFO @ Sun, 02 Jun 2019 21:43:45: 9000000 INFO @ Sun, 02 Jun 2019 21:43:47: 7000000 INFO @ Sun, 02 Jun 2019 21:43:50: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:43:50: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:43:50: #1 total tags in treatment: 9910838 INFO @ Sun, 02 Jun 2019 21:43:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:43:50: #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 21:43:51: #1 tags after filtering in treatment: 9910838 INFO @ Sun, 02 Jun 2019 21:43:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:43:51: #1 finished! INFO @ Sun, 02 Jun 2019 21:43:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:43:52: #2 number of paired peaks: 392 WARNING @ Sun, 02 Jun 2019 21:43:52: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Sun, 02 Jun 2019 21:43:52: start model_add_line... INFO @ Sun, 02 Jun 2019 21:43:52: start X-correlation... INFO @ Sun, 02 Jun 2019 21:43:52: end of X-cor INFO @ Sun, 02 Jun 2019 21:43:52: #2 finished! INFO @ Sun, 02 Jun 2019 21:43:52: #2 predicted fragment length is 68 bps INFO @ Sun, 02 Jun 2019 21:43:52: #2 alternative fragment length(s) may be 4,68 bps INFO @ Sun, 02 Jun 2019 21:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.10_model.r WARNING @ Sun, 02 Jun 2019 21:43:52: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:43:52: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Sun, 02 Jun 2019 21:43:52: #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 21:43:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:43:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:43:53: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:43:53: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:43:53: #1 total tags in treatment: 9910838 INFO @ Sun, 02 Jun 2019 21:43:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:43:53: #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 21:43:54: #1 tags after filtering in treatment: 9910838 INFO @ Sun, 02 Jun 2019 21:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:43:54: #1 finished! INFO @ Sun, 02 Jun 2019 21:43:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:43:55: #2 number of paired peaks: 392 WARNING @ Sun, 02 Jun 2019 21:43:55: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Sun, 02 Jun 2019 21:43:55: start model_add_line... INFO @ Sun, 02 Jun 2019 21:43:55: start X-correlation... INFO @ Sun, 02 Jun 2019 21:43:55: end of X-cor INFO @ Sun, 02 Jun 2019 21:43:55: #2 finished! INFO @ Sun, 02 Jun 2019 21:43:55: #2 predicted fragment length is 68 bps INFO @ Sun, 02 Jun 2019 21:43:55: #2 alternative fragment length(s) may be 4,68 bps INFO @ Sun, 02 Jun 2019 21:43:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.20_model.r WARNING @ Sun, 02 Jun 2019 21:43:55: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:43:55: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Sun, 02 Jun 2019 21:43:55: #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 21:43:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:43:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:43:59: 8000000 INFO @ Sun, 02 Jun 2019 21:44:11: 9000000 INFO @ Sun, 02 Jun 2019 21:44:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:44:21: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:44:21: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:44:21: #1 total tags in treatment: 9910838 INFO @ Sun, 02 Jun 2019 21:44:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:44:21: #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 21:44:22: #1 tags after filtering in treatment: 9910838 INFO @ Sun, 02 Jun 2019 21:44:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:44:22: #1 finished! INFO @ Sun, 02 Jun 2019 21:44:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:44:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:44:22: #2 number of paired peaks: 392 WARNING @ Sun, 02 Jun 2019 21:44:22: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Sun, 02 Jun 2019 21:44:22: start model_add_line... INFO @ Sun, 02 Jun 2019 21:44:23: start X-correlation... INFO @ Sun, 02 Jun 2019 21:44:23: end of X-cor INFO @ Sun, 02 Jun 2019 21:44:23: #2 finished! INFO @ Sun, 02 Jun 2019 21:44:23: #2 predicted fragment length is 68 bps INFO @ Sun, 02 Jun 2019 21:44:23: #2 alternative fragment length(s) may be 4,68 bps INFO @ Sun, 02 Jun 2019 21:44:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.05_model.r WARNING @ Sun, 02 Jun 2019 21:44:23: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:44:23: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Sun, 02 Jun 2019 21:44:23: #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 21:44:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:44:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:44:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:44:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:44:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.10_summits.bed INFO @ Sun, 02 Jun 2019 21:44:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (478 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:44:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:44:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:44:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.20_summits.bed INFO @ Sun, 02 Jun 2019 21:44:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:44:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:45:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:45:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:45:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020785/SRX5020785.05_summits.bed INFO @ Sun, 02 Jun 2019 21:45:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (746 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。