Job ID = 2640417 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 45,989,171 reads read : 45,989,171 reads written : 45,989,171 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:23:23 45989171 reads; of these: 45989171 (100.00%) were unpaired; of these: 22556096 (49.05%) aligned 0 times 14169119 (30.81%) aligned exactly 1 time 9263956 (20.14%) aligned >1 times 50.95% overall alignment rate Time searching: 00:23:26 Overall time: 00:23:26 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] 8587670 / 23433075 = 0.3665 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:16:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.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 @ Sat, 24 Aug 2019 17:16:52: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:16:52: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:16:59: 1000000 INFO @ Sat, 24 Aug 2019 17:17:07: 2000000 INFO @ Sat, 24 Aug 2019 17:17:14: 3000000 INFO @ Sat, 24 Aug 2019 17:17:21: 4000000 INFO @ Sat, 24 Aug 2019 17:17:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.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 @ Sat, 24 Aug 2019 17:17:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:17:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:17:28: 5000000 INFO @ Sat, 24 Aug 2019 17:17:29: 1000000 INFO @ Sat, 24 Aug 2019 17:17:35: 6000000 INFO @ Sat, 24 Aug 2019 17:17:36: 2000000 INFO @ Sat, 24 Aug 2019 17:17:44: 7000000 INFO @ Sat, 24 Aug 2019 17:17:45: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:17:52: 8000000 INFO @ Sat, 24 Aug 2019 17:17:53: 4000000 INFO @ Sat, 24 Aug 2019 17:17:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.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 @ Sat, 24 Aug 2019 17:17:53: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:17:53: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:18:00: 9000000 INFO @ Sat, 24 Aug 2019 17:18:02: 5000000 INFO @ Sat, 24 Aug 2019 17:18:02: 1000000 INFO @ Sat, 24 Aug 2019 17:18:07: 10000000 INFO @ Sat, 24 Aug 2019 17:18:09: 6000000 INFO @ Sat, 24 Aug 2019 17:18:11: 2000000 INFO @ Sat, 24 Aug 2019 17:18:14: 11000000 INFO @ Sat, 24 Aug 2019 17:18:16: 7000000 INFO @ Sat, 24 Aug 2019 17:18:18: 3000000 INFO @ Sat, 24 Aug 2019 17:18:21: 12000000 INFO @ Sat, 24 Aug 2019 17:18:24: 8000000 INFO @ Sat, 24 Aug 2019 17:18:26: 4000000 INFO @ Sat, 24 Aug 2019 17:18:28: 13000000 INFO @ Sat, 24 Aug 2019 17:18:32: 9000000 INFO @ Sat, 24 Aug 2019 17:18:34: 5000000 INFO @ Sat, 24 Aug 2019 17:18:35: 14000000 INFO @ Sat, 24 Aug 2019 17:18:40: 10000000 INFO @ Sat, 24 Aug 2019 17:18:41: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 17:18:41: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 17:18:41: #1 total tags in treatment: 14845405 INFO @ Sat, 24 Aug 2019 17:18:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:18:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:18:42: #1 tags after filtering in treatment: 14845279 INFO @ Sat, 24 Aug 2019 17:18:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:18:42: #1 finished! INFO @ Sat, 24 Aug 2019 17:18:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:18:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:18:43: 6000000 INFO @ Sat, 24 Aug 2019 17:18:45: #2 number of paired peaks: 24727 INFO @ Sat, 24 Aug 2019 17:18:45: start model_add_line... INFO @ Sat, 24 Aug 2019 17:18:45: start X-correlation... INFO @ Sat, 24 Aug 2019 17:18:45: end of X-cor INFO @ Sat, 24 Aug 2019 17:18:45: #2 finished! INFO @ Sat, 24 Aug 2019 17:18:45: #2 predicted fragment length is 41 bps INFO @ Sat, 24 Aug 2019 17:18:45: #2 alternative fragment length(s) may be 41 bps INFO @ Sat, 24 Aug 2019 17:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.05_model.r WARNING @ Sat, 24 Aug 2019 17:18:45: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:18:45: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Sat, 24 Aug 2019 17:18:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:18:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:18:47: 11000000 INFO @ Sat, 24 Aug 2019 17:18:51: 7000000 INFO @ Sat, 24 Aug 2019 17:18:55: 12000000 INFO @ Sat, 24 Aug 2019 17:19:00: 8000000 INFO @ Sat, 24 Aug 2019 17:19:02: 13000000 INFO @ Sat, 24 Aug 2019 17:19:08: 9000000 INFO @ Sat, 24 Aug 2019 17:19:10: 14000000 INFO @ Sat, 24 Aug 2019 17:19:16: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 17:19:16: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 17:19:16: #1 total tags in treatment: 14845405 INFO @ Sat, 24 Aug 2019 17:19:16: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:19:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:19:17: #1 tags after filtering in treatment: 14845279 INFO @ Sat, 24 Aug 2019 17:19:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:19:17: #1 finished! INFO @ Sat, 24 Aug 2019 17:19:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:19:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:19:17: 10000000 INFO @ Sat, 24 Aug 2019 17:19:20: #2 number of paired peaks: 24727 INFO @ Sat, 24 Aug 2019 17:19:20: start model_add_line... INFO @ Sat, 24 Aug 2019 17:19:20: start X-correlation... INFO @ Sat, 24 Aug 2019 17:19:20: end of X-cor INFO @ Sat, 24 Aug 2019 17:19:20: #2 finished! INFO @ Sat, 24 Aug 2019 17:19:20: #2 predicted fragment length is 41 bps INFO @ Sat, 24 Aug 2019 17:19:20: #2 alternative fragment length(s) may be 41 bps INFO @ Sat, 24 Aug 2019 17:19:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.10_model.r WARNING @ Sat, 24 Aug 2019 17:19:20: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:19:20: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Sat, 24 Aug 2019 17:19:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:19:20: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:19:26: 11000000 INFO @ Sat, 24 Aug 2019 17:19:32: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:19:34: 12000000 INFO @ Sat, 24 Aug 2019 17:19:42: 13000000 INFO @ Sat, 24 Aug 2019 17:19:51: 14000000 INFO @ Sat, 24 Aug 2019 17:19:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:19:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:19:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.05_summits.bed INFO @ Sat, 24 Aug 2019 17:19:55: Done! pass1 - making usageList (109 chroms): 5 millis pass2 - checking and writing primary data (8246 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:19:58: #1 tag size is determined as 42 bps INFO @ Sat, 24 Aug 2019 17:19:58: #1 tag size = 42 INFO @ Sat, 24 Aug 2019 17:19:58: #1 total tags in treatment: 14845405 INFO @ Sat, 24 Aug 2019 17:19:58: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:19:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:19:59: #1 tags after filtering in treatment: 14845279 INFO @ Sat, 24 Aug 2019 17:19:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:19:59: #1 finished! INFO @ Sat, 24 Aug 2019 17:19:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:20:02: #2 number of paired peaks: 24727 INFO @ Sat, 24 Aug 2019 17:20:02: start model_add_line... INFO @ Sat, 24 Aug 2019 17:20:02: start X-correlation... INFO @ Sat, 24 Aug 2019 17:20:02: end of X-cor INFO @ Sat, 24 Aug 2019 17:20:02: #2 finished! INFO @ Sat, 24 Aug 2019 17:20:02: #2 predicted fragment length is 41 bps INFO @ Sat, 24 Aug 2019 17:20:02: #2 alternative fragment length(s) may be 41 bps INFO @ Sat, 24 Aug 2019 17:20:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.20_model.r WARNING @ Sat, 24 Aug 2019 17:20:02: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:20:02: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Sat, 24 Aug 2019 17:20:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 17:20:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:20:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:20:06: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:20:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:20:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:20:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.10_summits.bed INFO @ Sat, 24 Aug 2019 17:20:29: Done! pass1 - making usageList (81 chroms): 2 millis pass2 - checking and writing primary data (3053 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:20:48: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:21:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:21:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:21:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX208967/SRX208967.20_summits.bed INFO @ Sat, 24 Aug 2019 17:21:11: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (1065 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。