Job ID = 2003481 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,245,470 reads read : 18,245,470 reads written : 18,245,470 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Multiseed full-index search: 00:26:33 18245470 reads; of these: 18245470 (100.00%) were unpaired; of these: 4664690 (25.57%) aligned 0 times 10393566 (56.97%) aligned exactly 1 time 3187214 (17.47%) aligned >1 times 74.43% overall alignment rate Time searching: 00:26:34 Overall time: 00:26:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 492758 / 13580780 = 0.0363 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 @ Fri, 05 Jul 2019 13:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 13:00:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:00:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 13:00:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:00:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:00:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 13:00:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:00:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:00:30: 1000000 INFO @ Fri, 05 Jul 2019 13:00:30: 1000000 INFO @ Fri, 05 Jul 2019 13:00:30: 1000000 INFO @ Fri, 05 Jul 2019 13:00:40: 2000000 INFO @ Fri, 05 Jul 2019 13:00:42: 2000000 INFO @ Fri, 05 Jul 2019 13:00:42: 2000000 INFO @ Fri, 05 Jul 2019 13:00:50: 3000000 INFO @ Fri, 05 Jul 2019 13:00:53: 3000000 INFO @ Fri, 05 Jul 2019 13:00:53: 3000000 INFO @ Fri, 05 Jul 2019 13:01:00: 4000000 INFO @ Fri, 05 Jul 2019 13:01:04: 4000000 INFO @ Fri, 05 Jul 2019 13:01:04: 4000000 INFO @ Fri, 05 Jul 2019 13:01:09: 5000000 INFO @ Fri, 05 Jul 2019 13:01:16: 5000000 INFO @ Fri, 05 Jul 2019 13:01:16: 5000000 INFO @ Fri, 05 Jul 2019 13:01:19: 6000000 INFO @ Fri, 05 Jul 2019 13:01:28: 6000000 INFO @ Fri, 05 Jul 2019 13:01:28: 6000000 INFO @ Fri, 05 Jul 2019 13:01:29: 7000000 INFO @ Fri, 05 Jul 2019 13:01:39: 8000000 INFO @ Fri, 05 Jul 2019 13:01:39: 7000000 INFO @ Fri, 05 Jul 2019 13:01:39: 7000000 INFO @ Fri, 05 Jul 2019 13:01:48: 9000000 INFO @ Fri, 05 Jul 2019 13:01:50: 8000000 INFO @ Fri, 05 Jul 2019 13:01:50: 8000000 INFO @ Fri, 05 Jul 2019 13:02:00: 10000000 INFO @ Fri, 05 Jul 2019 13:02:01: 9000000 INFO @ Fri, 05 Jul 2019 13:02:01: 9000000 INFO @ Fri, 05 Jul 2019 13:02:10: 10000000 INFO @ Fri, 05 Jul 2019 13:02:10: 11000000 INFO @ Fri, 05 Jul 2019 13:02:12: 10000000 INFO @ Fri, 05 Jul 2019 13:02:18: 11000000 INFO @ Fri, 05 Jul 2019 13:02:20: 12000000 INFO @ Fri, 05 Jul 2019 13:02:24: 11000000 INFO @ Fri, 05 Jul 2019 13:02:28: 12000000 INFO @ Fri, 05 Jul 2019 13:02:30: 13000000 INFO @ Fri, 05 Jul 2019 13:02:31: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 13:02:31: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 13:02:31: #1 total tags in treatment: 13088022 INFO @ Fri, 05 Jul 2019 13:02:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:02:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:02:31: #1 tags after filtering in treatment: 13087828 INFO @ Fri, 05 Jul 2019 13:02:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:02:31: #1 finished! INFO @ Fri, 05 Jul 2019 13:02:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:02:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:02:33: #2 number of paired peaks: 4783 INFO @ Fri, 05 Jul 2019 13:02:33: start model_add_line... INFO @ Fri, 05 Jul 2019 13:02:33: start X-correlation... INFO @ Fri, 05 Jul 2019 13:02:33: end of X-cor INFO @ Fri, 05 Jul 2019 13:02:33: #2 finished! INFO @ Fri, 05 Jul 2019 13:02:33: #2 predicted fragment length is 73 bps INFO @ Fri, 05 Jul 2019 13:02:33: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 05 Jul 2019 13:02:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.20_model.r WARNING @ Fri, 05 Jul 2019 13:02:33: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:02:33: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 05 Jul 2019 13:02:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 13:02:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:02:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:02:36: 12000000 INFO @ Fri, 05 Jul 2019 13:02:37: 13000000 INFO @ Fri, 05 Jul 2019 13:02:38: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 13:02:38: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 13:02:38: #1 total tags in treatment: 13088022 INFO @ Fri, 05 Jul 2019 13:02:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:02:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:02:38: #1 tags after filtering in treatment: 13087828 INFO @ Fri, 05 Jul 2019 13:02:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:02:38: #1 finished! INFO @ Fri, 05 Jul 2019 13:02:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:02:40: #2 number of paired peaks: 4783 INFO @ Fri, 05 Jul 2019 13:02:40: start model_add_line... INFO @ Fri, 05 Jul 2019 13:02:40: start X-correlation... INFO @ Fri, 05 Jul 2019 13:02:40: end of X-cor INFO @ Fri, 05 Jul 2019 13:02:40: #2 finished! INFO @ Fri, 05 Jul 2019 13:02:40: #2 predicted fragment length is 73 bps INFO @ Fri, 05 Jul 2019 13:02:40: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 05 Jul 2019 13:02:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.05_model.r WARNING @ Fri, 05 Jul 2019 13:02:40: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:02:40: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 05 Jul 2019 13:02:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 13:02:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:02:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:02:47: 13000000 INFO @ Fri, 05 Jul 2019 13:02:48: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 13:02:48: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 13:02:48: #1 total tags in treatment: 13088022 INFO @ Fri, 05 Jul 2019 13:02:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:02:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 13:02:48: #1 tags after filtering in treatment: 13087828 INFO @ Fri, 05 Jul 2019 13:02:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:02:48: #1 finished! INFO @ Fri, 05 Jul 2019 13:02:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:02:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:02:50: #2 number of paired peaks: 4783 INFO @ Fri, 05 Jul 2019 13:02:50: start model_add_line... INFO @ Fri, 05 Jul 2019 13:02:50: start X-correlation... INFO @ Fri, 05 Jul 2019 13:02:50: end of X-cor INFO @ Fri, 05 Jul 2019 13:02:50: #2 finished! INFO @ Fri, 05 Jul 2019 13:02:50: #2 predicted fragment length is 73 bps INFO @ Fri, 05 Jul 2019 13:02:50: #2 alternative fragment length(s) may be 73 bps INFO @ Fri, 05 Jul 2019 13:02:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.10_model.r WARNING @ Fri, 05 Jul 2019 13:02:50: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 13:02:50: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Fri, 05 Jul 2019 13:02:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 13:02:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:02:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:03:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:03:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:03:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:03:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.20_peaks.xls INFO @ Fri, 05 Jul 2019 13:03:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:03:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.20_summits.bed INFO @ Fri, 05 Jul 2019 13:03:35: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (294 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:03:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.05_peaks.xls INFO @ Fri, 05 Jul 2019 13:03:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:03:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.05_summits.bed INFO @ Fri, 05 Jul 2019 13:03:42: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (882 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:03:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.10_peaks.xls INFO @ Fri, 05 Jul 2019 13:03:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:03:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX189936/SRX189936.10_summits.bed INFO @ Fri, 05 Jul 2019 13:03:52: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (554 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。