Job ID = 1293060 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,656,369 reads read : 12,656,369 reads written : 12,656,369 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:36 12656369 reads; of these: 12656369 (100.00%) were unpaired; of these: 114919 (0.91%) aligned 0 times 10458901 (82.64%) aligned exactly 1 time 2082549 (16.45%) aligned >1 times 99.09% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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] 884563 / 12541450 = 0.0705 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 21:43:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.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 21:43:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:43:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:43:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.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 21:43:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:43:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:43:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.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 21:43:47: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:43:47: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:43:55: 1000000 INFO @ Sun, 02 Jun 2019 21:43:58: 1000000 INFO @ Sun, 02 Jun 2019 21:43:58: 1000000 INFO @ Sun, 02 Jun 2019 21:44:03: 2000000 INFO @ Sun, 02 Jun 2019 21:44:09: 2000000 INFO @ Sun, 02 Jun 2019 21:44:09: 2000000 INFO @ Sun, 02 Jun 2019 21:44:11: 3000000 INFO @ Sun, 02 Jun 2019 21:44:19: 4000000 INFO @ Sun, 02 Jun 2019 21:44:19: 3000000 INFO @ Sun, 02 Jun 2019 21:44:20: 3000000 INFO @ Sun, 02 Jun 2019 21:44:27: 5000000 INFO @ Sun, 02 Jun 2019 21:44:30: 4000000 INFO @ Sun, 02 Jun 2019 21:44:30: 4000000 INFO @ Sun, 02 Jun 2019 21:44:35: 6000000 INFO @ Sun, 02 Jun 2019 21:44:40: 5000000 INFO @ Sun, 02 Jun 2019 21:44:40: 5000000 INFO @ Sun, 02 Jun 2019 21:44:43: 7000000 INFO @ Sun, 02 Jun 2019 21:44:50: 6000000 INFO @ Sun, 02 Jun 2019 21:44:51: 6000000 INFO @ Sun, 02 Jun 2019 21:44:51: 8000000 INFO @ Sun, 02 Jun 2019 21:44:59: 9000000 INFO @ Sun, 02 Jun 2019 21:45:01: 7000000 INFO @ Sun, 02 Jun 2019 21:45:01: 7000000 INFO @ Sun, 02 Jun 2019 21:45:07: 10000000 INFO @ Sun, 02 Jun 2019 21:45:11: 8000000 INFO @ Sun, 02 Jun 2019 21:45:11: 8000000 INFO @ Sun, 02 Jun 2019 21:45:15: 11000000 INFO @ Sun, 02 Jun 2019 21:45:20: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:45:20: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:45:20: #1 total tags in treatment: 11656887 INFO @ Sun, 02 Jun 2019 21:45:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:45:20: #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 21:45:21: #1 tags after filtering in treatment: 11656887 INFO @ Sun, 02 Jun 2019 21:45:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:45:21: #1 finished! INFO @ Sun, 02 Jun 2019 21:45:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:45:21: 9000000 INFO @ Sun, 02 Jun 2019 21:45:22: #2 number of paired peaks: 290 WARNING @ Sun, 02 Jun 2019 21:45:22: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Sun, 02 Jun 2019 21:45:22: start model_add_line... INFO @ Sun, 02 Jun 2019 21:45:22: 9000000 INFO @ Sun, 02 Jun 2019 21:45:22: start X-correlation... INFO @ Sun, 02 Jun 2019 21:45:22: end of X-cor INFO @ Sun, 02 Jun 2019 21:45:22: #2 finished! INFO @ Sun, 02 Jun 2019 21:45:22: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:45:22: #2 alternative fragment length(s) may be 3,52 bps INFO @ Sun, 02 Jun 2019 21:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.05_model.r WARNING @ Sun, 02 Jun 2019 21:45:22: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:45:22: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Sun, 02 Jun 2019 21:45:22: #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 21:45:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:45:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:45:31: 10000000 INFO @ Sun, 02 Jun 2019 21:45:32: 10000000 INFO @ Sun, 02 Jun 2019 21:45:42: 11000000 INFO @ Sun, 02 Jun 2019 21:45:42: 11000000 INFO @ Sun, 02 Jun 2019 21:45:48: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:45:48: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:45:48: #1 total tags in treatment: 11656887 INFO @ Sun, 02 Jun 2019 21:45:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:45:48: #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 21:45:48: #1 tags after filtering in treatment: 11656887 INFO @ Sun, 02 Jun 2019 21:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:45:48: #1 finished! INFO @ Sun, 02 Jun 2019 21:45:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:45:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:45:48: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:45:48: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:45:48: #1 total tags in treatment: 11656887 INFO @ Sun, 02 Jun 2019 21:45:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:45:48: #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 21:45:49: #1 tags after filtering in treatment: 11656887 INFO @ Sun, 02 Jun 2019 21:45:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:45:49: #1 finished! INFO @ Sun, 02 Jun 2019 21:45:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:45:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:45:49: #2 number of paired peaks: 290 WARNING @ Sun, 02 Jun 2019 21:45:49: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Sun, 02 Jun 2019 21:45:49: start model_add_line... INFO @ Sun, 02 Jun 2019 21:45:49: start X-correlation... INFO @ Sun, 02 Jun 2019 21:45:49: end of X-cor INFO @ Sun, 02 Jun 2019 21:45:49: #2 finished! INFO @ Sun, 02 Jun 2019 21:45:49: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:45:49: #2 alternative fragment length(s) may be 3,52 bps INFO @ Sun, 02 Jun 2019 21:45:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.20_model.r WARNING @ Sun, 02 Jun 2019 21:45:49: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:45:49: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Sun, 02 Jun 2019 21:45:49: #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 21:45:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:45:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:45:50: #2 number of paired peaks: 290 WARNING @ Sun, 02 Jun 2019 21:45:50: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Sun, 02 Jun 2019 21:45:50: start model_add_line... INFO @ Sun, 02 Jun 2019 21:45:50: start X-correlation... INFO @ Sun, 02 Jun 2019 21:45:50: end of X-cor INFO @ Sun, 02 Jun 2019 21:45:50: #2 finished! INFO @ Sun, 02 Jun 2019 21:45:50: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:45:50: #2 alternative fragment length(s) may be 3,52 bps INFO @ Sun, 02 Jun 2019 21:45:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.10_model.r WARNING @ Sun, 02 Jun 2019 21:45:50: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:45:50: #2 You may need to consider one of the other alternative d(s): 3,52 WARNING @ Sun, 02 Jun 2019 21:45:50: #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 21:45:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:45:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:45:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:46:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:46:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:46:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.05_summits.bed INFO @ Sun, 02 Jun 2019 21:46:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:46:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:46:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:46:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:46:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.20_summits.bed INFO @ Sun, 02 Jun 2019 21:46:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:46:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:46:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020823/SRX5020823.10_summits.bed INFO @ Sun, 02 Jun 2019 21:46:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (387 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。