Job ID = 2001617 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,395,443 reads read : 27,395,443 reads written : 27,395,443 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: 00:10:10 27395443 reads; of these: 27395443 (100.00%) were unpaired; of these: 711248 (2.60%) aligned 0 times 20500910 (74.83%) aligned exactly 1 time 6183285 (22.57%) aligned >1 times 97.40% overall alignment rate Time searching: 00:10:11 Overall time: 00:10:11 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] 2068511 / 26684195 = 0.0775 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 06:35:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.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 06:35:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:35:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:35:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.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 06:35:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:35:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:35:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.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 06:35:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:35:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:35:38: 1000000 INFO @ Fri, 05 Jul 2019 06:35:39: 1000000 INFO @ Fri, 05 Jul 2019 06:35:39: 1000000 INFO @ Fri, 05 Jul 2019 06:35:45: 2000000 INFO @ Fri, 05 Jul 2019 06:35:45: 2000000 INFO @ Fri, 05 Jul 2019 06:35:46: 2000000 INFO @ Fri, 05 Jul 2019 06:35:52: 3000000 INFO @ Fri, 05 Jul 2019 06:35:52: 3000000 INFO @ Fri, 05 Jul 2019 06:35:53: 3000000 INFO @ Fri, 05 Jul 2019 06:35:58: 4000000 INFO @ Fri, 05 Jul 2019 06:35:59: 4000000 INFO @ Fri, 05 Jul 2019 06:35:59: 4000000 INFO @ Fri, 05 Jul 2019 06:36:05: 5000000 INFO @ Fri, 05 Jul 2019 06:36:06: 5000000 INFO @ Fri, 05 Jul 2019 06:36:06: 5000000 INFO @ Fri, 05 Jul 2019 06:36:12: 6000000 INFO @ Fri, 05 Jul 2019 06:36:12: 6000000 INFO @ Fri, 05 Jul 2019 06:36:13: 6000000 INFO @ Fri, 05 Jul 2019 06:36:19: 7000000 INFO @ Fri, 05 Jul 2019 06:36:19: 7000000 INFO @ Fri, 05 Jul 2019 06:36:20: 7000000 INFO @ Fri, 05 Jul 2019 06:36:25: 8000000 INFO @ Fri, 05 Jul 2019 06:36:26: 8000000 INFO @ Fri, 05 Jul 2019 06:36:26: 8000000 INFO @ Fri, 05 Jul 2019 06:36:32: 9000000 INFO @ Fri, 05 Jul 2019 06:36:33: 9000000 INFO @ Fri, 05 Jul 2019 06:36:33: 9000000 INFO @ Fri, 05 Jul 2019 06:36:39: 10000000 INFO @ Fri, 05 Jul 2019 06:36:39: 10000000 INFO @ Fri, 05 Jul 2019 06:36:40: 10000000 INFO @ Fri, 05 Jul 2019 06:36:46: 11000000 INFO @ Fri, 05 Jul 2019 06:36:46: 11000000 INFO @ Fri, 05 Jul 2019 06:36:46: 11000000 INFO @ Fri, 05 Jul 2019 06:36:52: 12000000 INFO @ Fri, 05 Jul 2019 06:36:53: 12000000 INFO @ Fri, 05 Jul 2019 06:36:53: 12000000 INFO @ Fri, 05 Jul 2019 06:36:59: 13000000 INFO @ Fri, 05 Jul 2019 06:37:00: 13000000 INFO @ Fri, 05 Jul 2019 06:37:00: 13000000 INFO @ Fri, 05 Jul 2019 06:37:06: 14000000 INFO @ Fri, 05 Jul 2019 06:37:07: 14000000 INFO @ Fri, 05 Jul 2019 06:37:07: 14000000 INFO @ Fri, 05 Jul 2019 06:37:12: 15000000 INFO @ Fri, 05 Jul 2019 06:37:13: 15000000 INFO @ Fri, 05 Jul 2019 06:37:13: 15000000 INFO @ Fri, 05 Jul 2019 06:37:19: 16000000 INFO @ Fri, 05 Jul 2019 06:37:20: 16000000 INFO @ Fri, 05 Jul 2019 06:37:20: 16000000 INFO @ Fri, 05 Jul 2019 06:37:26: 17000000 INFO @ Fri, 05 Jul 2019 06:37:27: 17000000 INFO @ Fri, 05 Jul 2019 06:37:27: 17000000 INFO @ Fri, 05 Jul 2019 06:37:33: 18000000 INFO @ Fri, 05 Jul 2019 06:37:34: 18000000 INFO @ Fri, 05 Jul 2019 06:37:34: 18000000 INFO @ Fri, 05 Jul 2019 06:37:40: 19000000 INFO @ Fri, 05 Jul 2019 06:37:40: 19000000 INFO @ Fri, 05 Jul 2019 06:37:41: 19000000 INFO @ Fri, 05 Jul 2019 06:37:46: 20000000 INFO @ Fri, 05 Jul 2019 06:37:47: 20000000 INFO @ Fri, 05 Jul 2019 06:37:48: 20000000 INFO @ Fri, 05 Jul 2019 06:37:53: 21000000 INFO @ Fri, 05 Jul 2019 06:37:54: 21000000 INFO @ Fri, 05 Jul 2019 06:37:54: 21000000 INFO @ Fri, 05 Jul 2019 06:38:00: 22000000 INFO @ Fri, 05 Jul 2019 06:38:01: 22000000 INFO @ Fri, 05 Jul 2019 06:38:01: 22000000 INFO @ Fri, 05 Jul 2019 06:38:07: 23000000 INFO @ Fri, 05 Jul 2019 06:38:07: 23000000 INFO @ Fri, 05 Jul 2019 06:38:08: 23000000 INFO @ Fri, 05 Jul 2019 06:38:13: 24000000 INFO @ Fri, 05 Jul 2019 06:38:14: 24000000 INFO @ Fri, 05 Jul 2019 06:38:15: 24000000 INFO @ Fri, 05 Jul 2019 06:38:18: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:38:18: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:38:18: #1 total tags in treatment: 24615684 INFO @ Fri, 05 Jul 2019 06:38:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:38:18: #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 06:38:18: #1 tags after filtering in treatment: 24615539 INFO @ Fri, 05 Jul 2019 06:38:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:38:18: #1 finished! INFO @ Fri, 05 Jul 2019 06:38:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:38:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:38:19: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:38:19: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:38:19: #1 total tags in treatment: 24615684 INFO @ Fri, 05 Jul 2019 06:38:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:38:19: #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 06:38:19: #1 tags after filtering in treatment: 24615539 INFO @ Fri, 05 Jul 2019 06:38:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:38:19: #1 finished! INFO @ Fri, 05 Jul 2019 06:38:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:38:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:38:19: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:38:19: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:38:19: #1 total tags in treatment: 24615684 INFO @ Fri, 05 Jul 2019 06:38:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:38:19: #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 06:38:20: #1 tags after filtering in treatment: 24615539 INFO @ Fri, 05 Jul 2019 06:38:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:38:20: #1 finished! INFO @ Fri, 05 Jul 2019 06:38:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:38:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:38:24: #2 number of paired peaks: 68298 INFO @ Fri, 05 Jul 2019 06:38:24: start model_add_line... INFO @ Fri, 05 Jul 2019 06:38:24: start X-correlation... INFO @ Fri, 05 Jul 2019 06:38:24: end of X-cor INFO @ Fri, 05 Jul 2019 06:38:24: #2 finished! INFO @ Fri, 05 Jul 2019 06:38:24: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 06:38:24: #2 alternative fragment length(s) may be 3,131,504 bps INFO @ Fri, 05 Jul 2019 06:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.05_model.r INFO @ Fri, 05 Jul 2019 06:38:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:38:25: #2 number of paired peaks: 68298 INFO @ Fri, 05 Jul 2019 06:38:25: start model_add_line... INFO @ Fri, 05 Jul 2019 06:38:25: start X-correlation... INFO @ Fri, 05 Jul 2019 06:38:25: end of X-cor INFO @ Fri, 05 Jul 2019 06:38:25: #2 finished! INFO @ Fri, 05 Jul 2019 06:38:25: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 06:38:25: #2 alternative fragment length(s) may be 3,131,504 bps INFO @ Fri, 05 Jul 2019 06:38:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.20_model.r INFO @ Fri, 05 Jul 2019 06:38:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:38:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:38:25: #2 number of paired peaks: 68298 INFO @ Fri, 05 Jul 2019 06:38:25: start model_add_line... INFO @ Fri, 05 Jul 2019 06:38:26: start X-correlation... INFO @ Fri, 05 Jul 2019 06:38:26: end of X-cor INFO @ Fri, 05 Jul 2019 06:38:26: #2 finished! INFO @ Fri, 05 Jul 2019 06:38:26: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 06:38:26: #2 alternative fragment length(s) may be 3,131,504 bps INFO @ Fri, 05 Jul 2019 06:38:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.10_model.r INFO @ Fri, 05 Jul 2019 06:38:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:39:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:39:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:39:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:40:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:40:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:40:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.05_summits.bed INFO @ Fri, 05 Jul 2019 06:40:20: Done! pass1 - making usageList (77 chroms): 3 millis pass2 - checking and writing primary data (6308 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:40:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:40:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:40:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.20_summits.bed INFO @ Fri, 05 Jul 2019 06:40:21: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (173 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:40:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:40:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:40:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101939/ERX101939.10_summits.bed INFO @ Fri, 05 Jul 2019 06:40:22: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (1362 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。