Job ID = 2640485 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,614,691 reads read : 39,229,382 reads written : 19,614,691 reads 0-length : 19,614,691 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: 00:00:00 Multiseed full-index search: 00:14:11 19614691 reads; of these: 19614691 (100.00%) were unpaired; of these: 402259 (2.05%) aligned 0 times 16270972 (82.95%) aligned exactly 1 time 2941460 (15.00%) aligned >1 times 97.95% overall alignment rate Time searching: 00:14:13 Overall time: 00:14:13 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] 2187936 / 19212432 = 0.1139 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.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 17:42:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:42:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:42:42: 1000000 INFO @ Sat, 24 Aug 2019 17:42:50: 2000000 INFO @ Sat, 24 Aug 2019 17:42:57: 3000000 INFO @ Sat, 24 Aug 2019 17:43:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.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 17:43:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:43:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:43:05: 4000000 INFO @ Sat, 24 Aug 2019 17:43:12: 1000000 INFO @ Sat, 24 Aug 2019 17:43:13: 5000000 INFO @ Sat, 24 Aug 2019 17:43:20: 2000000 INFO @ Sat, 24 Aug 2019 17:43:21: 6000000 INFO @ Sat, 24 Aug 2019 17:43:28: 3000000 INFO @ Sat, 24 Aug 2019 17:43:29: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:43:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.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 17:43:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:43:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:43:36: 4000000 INFO @ Sat, 24 Aug 2019 17:43:37: 8000000 INFO @ Sat, 24 Aug 2019 17:43:44: 1000000 INFO @ Sat, 24 Aug 2019 17:43:44: 5000000 INFO @ Sat, 24 Aug 2019 17:43:46: 9000000 INFO @ Sat, 24 Aug 2019 17:43:53: 6000000 INFO @ Sat, 24 Aug 2019 17:43:54: 2000000 INFO @ Sat, 24 Aug 2019 17:43:54: 10000000 INFO @ Sat, 24 Aug 2019 17:44:01: 7000000 INFO @ Sat, 24 Aug 2019 17:44:02: 11000000 INFO @ Sat, 24 Aug 2019 17:44:04: 3000000 INFO @ Sat, 24 Aug 2019 17:44:09: 8000000 INFO @ Sat, 24 Aug 2019 17:44:10: 12000000 INFO @ Sat, 24 Aug 2019 17:44:13: 4000000 INFO @ Sat, 24 Aug 2019 17:44:17: 9000000 INFO @ Sat, 24 Aug 2019 17:44:18: 13000000 INFO @ Sat, 24 Aug 2019 17:44:23: 5000000 INFO @ Sat, 24 Aug 2019 17:44:25: 10000000 INFO @ Sat, 24 Aug 2019 17:44:27: 14000000 INFO @ Sat, 24 Aug 2019 17:44:34: 6000000 INFO @ Sat, 24 Aug 2019 17:44:34: 11000000 INFO @ Sat, 24 Aug 2019 17:44:35: 15000000 INFO @ Sat, 24 Aug 2019 17:44:43: 12000000 INFO @ Sat, 24 Aug 2019 17:44:44: 16000000 INFO @ Sat, 24 Aug 2019 17:44:44: 7000000 INFO @ Sat, 24 Aug 2019 17:44:51: 13000000 INFO @ Sat, 24 Aug 2019 17:44:52: 17000000 INFO @ Sat, 24 Aug 2019 17:44:53: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:44:53: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:44:53: #1 total tags in treatment: 17024496 INFO @ Sat, 24 Aug 2019 17:44:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:44:53: #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 17:44:53: #1 tags after filtering in treatment: 17024277 INFO @ Sat, 24 Aug 2019 17:44:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:44:53: #1 finished! INFO @ Sat, 24 Aug 2019 17:44:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:44:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:44:54: 8000000 INFO @ Sat, 24 Aug 2019 17:44:59: #2 number of paired peaks: 93541 INFO @ Sat, 24 Aug 2019 17:44:59: start model_add_line... INFO @ Sat, 24 Aug 2019 17:44:59: start X-correlation... INFO @ Sat, 24 Aug 2019 17:44:59: end of X-cor INFO @ Sat, 24 Aug 2019 17:44:59: #2 finished! INFO @ Sat, 24 Aug 2019 17:44:59: #2 predicted fragment length is 182 bps INFO @ Sat, 24 Aug 2019 17:44:59: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 24 Aug 2019 17:44:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.05_model.r INFO @ Sat, 24 Aug 2019 17:44:59: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:44:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:45:00: 14000000 INFO @ Sat, 24 Aug 2019 17:45:04: 9000000 INFO @ Sat, 24 Aug 2019 17:45:08: 15000000 INFO @ Sat, 24 Aug 2019 17:45:14: 10000000 INFO @ Sat, 24 Aug 2019 17:45:16: 16000000 INFO @ Sat, 24 Aug 2019 17:45:24: 11000000 INFO @ Sat, 24 Aug 2019 17:45:25: 17000000 INFO @ Sat, 24 Aug 2019 17:45:25: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:45:25: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:45:25: #1 total tags in treatment: 17024496 INFO @ Sat, 24 Aug 2019 17:45:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:45:25: #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 17:45:25: #1 tags after filtering in treatment: 17024277 INFO @ Sat, 24 Aug 2019 17:45:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:45:25: #1 finished! INFO @ Sat, 24 Aug 2019 17:45:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:45:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:45:31: #2 number of paired peaks: 93541 INFO @ Sat, 24 Aug 2019 17:45:31: start model_add_line... INFO @ Sat, 24 Aug 2019 17:45:31: start X-correlation... INFO @ Sat, 24 Aug 2019 17:45:31: end of X-cor INFO @ Sat, 24 Aug 2019 17:45:31: #2 finished! INFO @ Sat, 24 Aug 2019 17:45:31: #2 predicted fragment length is 182 bps INFO @ Sat, 24 Aug 2019 17:45:31: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 24 Aug 2019 17:45:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.10_model.r INFO @ Sat, 24 Aug 2019 17:45:31: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:45:33: 12000000 INFO @ Sat, 24 Aug 2019 17:45:43: 13000000 INFO @ Sat, 24 Aug 2019 17:45:52: 14000000 INFO @ Sat, 24 Aug 2019 17:45:54: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:46:01: 15000000 INFO @ Sat, 24 Aug 2019 17:46:11: 16000000 INFO @ Sat, 24 Aug 2019 17:46:20: 17000000 INFO @ Sat, 24 Aug 2019 17:46:20: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:46:20: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:46:20: #1 total tags in treatment: 17024496 INFO @ Sat, 24 Aug 2019 17:46:20: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:46:20: #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 17:46:21: #1 tags after filtering in treatment: 17024277 INFO @ Sat, 24 Aug 2019 17:46:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:46:21: #1 finished! INFO @ Sat, 24 Aug 2019 17:46:21: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:46:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:46:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:46:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.05_summits.bed INFO @ Sat, 24 Aug 2019 17:46:24: Done! pass1 - making usageList (111 chroms): 9 millis pass2 - checking and writing primary data (40220 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:46:26: #2 number of paired peaks: 93541 INFO @ Sat, 24 Aug 2019 17:46:26: start model_add_line... INFO @ Sat, 24 Aug 2019 17:46:27: start X-correlation... INFO @ Sat, 24 Aug 2019 17:46:27: end of X-cor INFO @ Sat, 24 Aug 2019 17:46:27: #2 finished! INFO @ Sat, 24 Aug 2019 17:46:27: #2 predicted fragment length is 182 bps INFO @ Sat, 24 Aug 2019 17:46:27: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 24 Aug 2019 17:46:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.20_model.r INFO @ Sat, 24 Aug 2019 17:46:27: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:46:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:46:27: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:46:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:46:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:46:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.10_summits.bed INFO @ Sat, 24 Aug 2019 17:46:57: Done! pass1 - making usageList (93 chroms): 8 millis pass2 - checking and writing primary data (24758 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:47:22: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:47:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:47:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:47:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374995/SRX5374995.20_summits.bed INFO @ Sat, 24 Aug 2019 17:47:52: Done! pass1 - making usageList (59 chroms): 6 millis pass2 - checking and writing primary data (10582 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。