Job ID = 1293141 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,087,212 reads read : 30,087,212 reads written : 30,087,212 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: 00:06:16 30087212 reads; of these: 30087212 (100.00%) were unpaired; of these: 7323576 (24.34%) aligned 0 times 19926911 (66.23%) aligned exactly 1 time 2836725 (9.43%) aligned >1 times 75.66% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 4246680 / 22763636 = 0.1866 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 22:24:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.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 22:24:01: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:24:01: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:24:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.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 22:24:01: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:24:01: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:24:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.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 22:24:01: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:24:01: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:24:10: 1000000 INFO @ Sun, 02 Jun 2019 22:24:10: 1000000 INFO @ Sun, 02 Jun 2019 22:24:11: 1000000 INFO @ Sun, 02 Jun 2019 22:24:18: 2000000 INFO @ Sun, 02 Jun 2019 22:24:18: 2000000 INFO @ Sun, 02 Jun 2019 22:24:20: 2000000 INFO @ Sun, 02 Jun 2019 22:24:26: 3000000 INFO @ Sun, 02 Jun 2019 22:24:26: 3000000 INFO @ Sun, 02 Jun 2019 22:24:28: 3000000 INFO @ Sun, 02 Jun 2019 22:24:34: 4000000 INFO @ Sun, 02 Jun 2019 22:24:34: 4000000 INFO @ Sun, 02 Jun 2019 22:24:36: 4000000 INFO @ Sun, 02 Jun 2019 22:24:43: 5000000 INFO @ Sun, 02 Jun 2019 22:24:43: 5000000 INFO @ Sun, 02 Jun 2019 22:24:44: 5000000 INFO @ Sun, 02 Jun 2019 22:24:51: 6000000 INFO @ Sun, 02 Jun 2019 22:24:51: 6000000 INFO @ Sun, 02 Jun 2019 22:24:52: 6000000 INFO @ Sun, 02 Jun 2019 22:25:00: 7000000 INFO @ Sun, 02 Jun 2019 22:25:00: 7000000 INFO @ Sun, 02 Jun 2019 22:25:00: 7000000 INFO @ Sun, 02 Jun 2019 22:25:08: 8000000 INFO @ Sun, 02 Jun 2019 22:25:08: 8000000 INFO @ Sun, 02 Jun 2019 22:25:08: 8000000 INFO @ Sun, 02 Jun 2019 22:25:16: 9000000 INFO @ Sun, 02 Jun 2019 22:25:16: 9000000 INFO @ Sun, 02 Jun 2019 22:25:16: 9000000 INFO @ Sun, 02 Jun 2019 22:25:24: 10000000 INFO @ Sun, 02 Jun 2019 22:25:24: 10000000 INFO @ Sun, 02 Jun 2019 22:25:24: 10000000 INFO @ Sun, 02 Jun 2019 22:25:32: 11000000 INFO @ Sun, 02 Jun 2019 22:25:33: 11000000 INFO @ Sun, 02 Jun 2019 22:25:33: 11000000 INFO @ Sun, 02 Jun 2019 22:25:41: 12000000 INFO @ Sun, 02 Jun 2019 22:25:41: 12000000 INFO @ Sun, 02 Jun 2019 22:25:41: 12000000 INFO @ Sun, 02 Jun 2019 22:25:49: 13000000 INFO @ Sun, 02 Jun 2019 22:25:50: 13000000 INFO @ Sun, 02 Jun 2019 22:25:50: 13000000 INFO @ Sun, 02 Jun 2019 22:25:57: 14000000 INFO @ Sun, 02 Jun 2019 22:25:59: 14000000 INFO @ Sun, 02 Jun 2019 22:25:59: 14000000 INFO @ Sun, 02 Jun 2019 22:26:05: 15000000 INFO @ Sun, 02 Jun 2019 22:26:07: 15000000 INFO @ Sun, 02 Jun 2019 22:26:07: 15000000 INFO @ Sun, 02 Jun 2019 22:26:13: 16000000 INFO @ Sun, 02 Jun 2019 22:26:15: 16000000 INFO @ Sun, 02 Jun 2019 22:26:16: 16000000 INFO @ Sun, 02 Jun 2019 22:26:21: 17000000 INFO @ Sun, 02 Jun 2019 22:26:22: 17000000 INFO @ Sun, 02 Jun 2019 22:26:23: 17000000 INFO @ Sun, 02 Jun 2019 22:26:29: 18000000 INFO @ Sun, 02 Jun 2019 22:26:29: 18000000 INFO @ Sun, 02 Jun 2019 22:26:31: 18000000 INFO @ Sun, 02 Jun 2019 22:26:33: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:33: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:33: #1 total tags in treatment: 18516956 INFO @ Sun, 02 Jun 2019 22:26:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:33: #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 22:26:33: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:33: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:33: #1 total tags in treatment: 18516956 INFO @ Sun, 02 Jun 2019 22:26:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:33: #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 22:26:34: #1 tags after filtering in treatment: 18516956 INFO @ Sun, 02 Jun 2019 22:26:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:34: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:34: #1 tags after filtering in treatment: 18516956 INFO @ Sun, 02 Jun 2019 22:26:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:34: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:35: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:35: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:35: #1 total tags in treatment: 18516956 INFO @ Sun, 02 Jun 2019 22:26:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:35: #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 22:26:35: #1 tags after filtering in treatment: 18516956 INFO @ Sun, 02 Jun 2019 22:26:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:35: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:35: #2 number of paired peaks: 1455 INFO @ Sun, 02 Jun 2019 22:26:35: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:35: #2 number of paired peaks: 1455 INFO @ Sun, 02 Jun 2019 22:26:35: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:36: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:36: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:36: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:36: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 22:26:36: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 02 Jun 2019 22:26:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.20_model.r WARNING @ Sun, 02 Jun 2019 22:26:36: #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 22:26:36: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 02 Jun 2019 22:26:36: #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 22:26:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:36: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:36: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:36: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:36: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 22:26:36: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 02 Jun 2019 22:26:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.05_model.r WARNING @ Sun, 02 Jun 2019 22:26:36: #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 22:26:36: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 02 Jun 2019 22:26:36: #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 22:26:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:37: #2 number of paired peaks: 1455 INFO @ Sun, 02 Jun 2019 22:26:37: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:37: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:37: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:37: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:37: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 22:26:37: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 02 Jun 2019 22:26:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.10_model.r WARNING @ Sun, 02 Jun 2019 22:26:37: #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 22:26:37: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 02 Jun 2019 22:26:37: #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 22:26:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:27:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:27:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:27:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:27:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:27:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:27:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.05_summits.bed INFO @ Sun, 02 Jun 2019 22:27:39: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (14448 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:27:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:27:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:27:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.20_summits.bed INFO @ Sun, 02 Jun 2019 22:27:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (516 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:27:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:27:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:27:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402713/SRX5402713.10_summits.bed INFO @ Sun, 02 Jun 2019 22:27:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5475 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。