Job ID = 2003185 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,750,882 reads read : 35,750,882 reads written : 35,750,882 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR498449.sra.cache’: 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: 00:17:59 35750882 reads; of these: 35750882 (100.00%) were unpaired; of these: 4166078 (11.65%) aligned 0 times 23848930 (66.71%) aligned exactly 1 time 7735874 (21.64%) aligned >1 times 88.35% overall alignment rate Time searching: 00:18:01 Overall time: 00:18:01 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 12 files... [bam_rmdupse_core] 12242401 / 31584804 = 0.3876 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 12:38:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.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 12:38:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:38:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:38:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.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 12:38:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:38:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:38:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.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 12:38:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:38:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:38:23: 1000000 INFO @ Fri, 05 Jul 2019 12:38:26: 1000000 INFO @ Fri, 05 Jul 2019 12:38:27: 1000000 INFO @ Fri, 05 Jul 2019 12:38:30: 2000000 INFO @ Fri, 05 Jul 2019 12:38:37: 2000000 INFO @ Fri, 05 Jul 2019 12:38:37: 3000000 INFO @ Fri, 05 Jul 2019 12:38:38: 2000000 INFO @ Fri, 05 Jul 2019 12:38:45: 4000000 INFO @ Fri, 05 Jul 2019 12:38:47: 3000000 INFO @ Fri, 05 Jul 2019 12:38:48: 3000000 INFO @ Fri, 05 Jul 2019 12:38:53: 5000000 INFO @ Fri, 05 Jul 2019 12:38:58: 4000000 INFO @ Fri, 05 Jul 2019 12:38:59: 4000000 INFO @ Fri, 05 Jul 2019 12:39:00: 6000000 INFO @ Fri, 05 Jul 2019 12:39:08: 5000000 INFO @ Fri, 05 Jul 2019 12:39:08: 7000000 INFO @ Fri, 05 Jul 2019 12:39:09: 5000000 INFO @ Fri, 05 Jul 2019 12:39:16: 8000000 INFO @ Fri, 05 Jul 2019 12:39:16: 6000000 INFO @ Fri, 05 Jul 2019 12:39:19: 6000000 INFO @ Fri, 05 Jul 2019 12:39:23: 9000000 INFO @ Fri, 05 Jul 2019 12:39:24: 7000000 INFO @ Fri, 05 Jul 2019 12:39:28: 7000000 INFO @ Fri, 05 Jul 2019 12:39:31: 10000000 INFO @ Fri, 05 Jul 2019 12:39:32: 8000000 INFO @ Fri, 05 Jul 2019 12:39:37: 8000000 INFO @ Fri, 05 Jul 2019 12:39:38: 11000000 INFO @ Fri, 05 Jul 2019 12:39:40: 9000000 INFO @ Fri, 05 Jul 2019 12:39:45: 12000000 INFO @ Fri, 05 Jul 2019 12:39:46: 9000000 INFO @ Fri, 05 Jul 2019 12:39:48: 10000000 INFO @ Fri, 05 Jul 2019 12:39:53: 13000000 INFO @ Fri, 05 Jul 2019 12:39:55: 10000000 INFO @ Fri, 05 Jul 2019 12:39:57: 11000000 INFO @ Fri, 05 Jul 2019 12:40:00: 14000000 INFO @ Fri, 05 Jul 2019 12:40:05: 12000000 INFO @ Fri, 05 Jul 2019 12:40:05: 11000000 INFO @ Fri, 05 Jul 2019 12:40:08: 15000000 INFO @ Fri, 05 Jul 2019 12:40:13: 13000000 INFO @ Fri, 05 Jul 2019 12:40:14: 12000000 INFO @ Fri, 05 Jul 2019 12:40:15: 16000000 INFO @ Fri, 05 Jul 2019 12:40:21: 14000000 INFO @ Fri, 05 Jul 2019 12:40:23: 17000000 INFO @ Fri, 05 Jul 2019 12:40:23: 13000000 INFO @ Fri, 05 Jul 2019 12:40:30: 15000000 INFO @ Fri, 05 Jul 2019 12:40:30: 18000000 INFO @ Fri, 05 Jul 2019 12:40:32: 14000000 INFO @ Fri, 05 Jul 2019 12:40:38: 19000000 INFO @ Fri, 05 Jul 2019 12:40:38: 16000000 INFO @ Fri, 05 Jul 2019 12:40:40: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:40:40: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:40:40: #1 total tags in treatment: 19342403 INFO @ Fri, 05 Jul 2019 12:40:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:40:40: #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 12:40:41: #1 tags after filtering in treatment: 19342265 INFO @ Fri, 05 Jul 2019 12:40:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:40:41: #1 finished! INFO @ Fri, 05 Jul 2019 12:40:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:40:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:40:41: 15000000 INFO @ Fri, 05 Jul 2019 12:40:45: #2 number of paired peaks: 54501 INFO @ Fri, 05 Jul 2019 12:40:45: start model_add_line... INFO @ Fri, 05 Jul 2019 12:40:46: start X-correlation... INFO @ Fri, 05 Jul 2019 12:40:46: end of X-cor INFO @ Fri, 05 Jul 2019 12:40:46: #2 finished! INFO @ Fri, 05 Jul 2019 12:40:46: #2 predicted fragment length is 265 bps INFO @ Fri, 05 Jul 2019 12:40:46: #2 alternative fragment length(s) may be 265 bps INFO @ Fri, 05 Jul 2019 12:40:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.05_model.r INFO @ Fri, 05 Jul 2019 12:40:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:40:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:40:46: 17000000 INFO @ Fri, 05 Jul 2019 12:40:51: 16000000 INFO @ Fri, 05 Jul 2019 12:40:54: 18000000 INFO @ Fri, 05 Jul 2019 12:41:00: 17000000 INFO @ Fri, 05 Jul 2019 12:41:02: 19000000 INFO @ Fri, 05 Jul 2019 12:41:05: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:41:05: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:41:05: #1 total tags in treatment: 19342403 INFO @ Fri, 05 Jul 2019 12:41:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:41:05: #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 12:41:06: #1 tags after filtering in treatment: 19342265 INFO @ Fri, 05 Jul 2019 12:41:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:41:06: #1 finished! INFO @ Fri, 05 Jul 2019 12:41:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:41:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:41:09: 18000000 INFO @ Fri, 05 Jul 2019 12:41:10: #2 number of paired peaks: 54501 INFO @ Fri, 05 Jul 2019 12:41:10: start model_add_line... INFO @ Fri, 05 Jul 2019 12:41:11: start X-correlation... INFO @ Fri, 05 Jul 2019 12:41:11: end of X-cor INFO @ Fri, 05 Jul 2019 12:41:11: #2 finished! INFO @ Fri, 05 Jul 2019 12:41:11: #2 predicted fragment length is 265 bps INFO @ Fri, 05 Jul 2019 12:41:11: #2 alternative fragment length(s) may be 265 bps INFO @ Fri, 05 Jul 2019 12:41:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.10_model.r INFO @ Fri, 05 Jul 2019 12:41:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:41:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:41:18: 19000000 INFO @ Fri, 05 Jul 2019 12:41:21: #1 tag size is determined as 42 bps INFO @ Fri, 05 Jul 2019 12:41:21: #1 tag size = 42 INFO @ Fri, 05 Jul 2019 12:41:21: #1 total tags in treatment: 19342403 INFO @ Fri, 05 Jul 2019 12:41:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:41:21: #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 12:41:21: #1 tags after filtering in treatment: 19342265 INFO @ Fri, 05 Jul 2019 12:41:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:41:21: #1 finished! INFO @ Fri, 05 Jul 2019 12:41:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:41:26: #2 number of paired peaks: 54501 INFO @ Fri, 05 Jul 2019 12:41:26: start model_add_line... INFO @ Fri, 05 Jul 2019 12:41:26: start X-correlation... INFO @ Fri, 05 Jul 2019 12:41:26: end of X-cor INFO @ Fri, 05 Jul 2019 12:41:26: #2 finished! INFO @ Fri, 05 Jul 2019 12:41:26: #2 predicted fragment length is 265 bps INFO @ Fri, 05 Jul 2019 12:41:26: #2 alternative fragment length(s) may be 265 bps INFO @ Fri, 05 Jul 2019 12:41:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.20_model.r INFO @ Fri, 05 Jul 2019 12:41:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:41:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:41:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:42:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:42:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:42:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:42:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.05_summits.bed INFO @ Fri, 05 Jul 2019 12:42:19: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (2878 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:42:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:42:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:42:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:42:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.10_summits.bed INFO @ Fri, 05 Jul 2019 12:42:44: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (1128 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:43:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:43:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:43:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX148695/SRX148695.20_summits.bed INFO @ Fri, 05 Jul 2019 12:43:00: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (447 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。