Job ID = 2001689 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,245,016 reads read : 21,245,016 reads written : 21,245,016 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: 00:08:41 21245016 reads; of these: 21245016 (100.00%) were unpaired; of these: 482422 (2.27%) aligned 0 times 15810047 (74.42%) aligned exactly 1 time 4952547 (23.31%) aligned >1 times 97.73% overall alignment rate Time searching: 00:08:44 Overall time: 00:08:44 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] 1349757 / 20762594 = 0.0650 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 08:59:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.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 08:59:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:59:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:59:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.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 08:59:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:59:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:59:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.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 08:59:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:59:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:59:26: 1000000 INFO @ Fri, 05 Jul 2019 08:59:26: 1000000 INFO @ Fri, 05 Jul 2019 08:59:27: 1000000 INFO @ Fri, 05 Jul 2019 08:59:33: 2000000 INFO @ Fri, 05 Jul 2019 08:59:34: 2000000 INFO @ Fri, 05 Jul 2019 08:59:35: 2000000 INFO @ Fri, 05 Jul 2019 08:59:40: 3000000 INFO @ Fri, 05 Jul 2019 08:59:42: 3000000 INFO @ Fri, 05 Jul 2019 08:59:43: 3000000 INFO @ Fri, 05 Jul 2019 08:59:48: 4000000 INFO @ Fri, 05 Jul 2019 08:59:51: 4000000 INFO @ Fri, 05 Jul 2019 08:59:51: 4000000 INFO @ Fri, 05 Jul 2019 08:59:56: 5000000 INFO @ Fri, 05 Jul 2019 08:59:58: 5000000 INFO @ Fri, 05 Jul 2019 08:59:59: 5000000 INFO @ Fri, 05 Jul 2019 09:00:03: 6000000 INFO @ Fri, 05 Jul 2019 09:00:07: 6000000 INFO @ Fri, 05 Jul 2019 09:00:07: 6000000 INFO @ Fri, 05 Jul 2019 09:00:11: 7000000 INFO @ Fri, 05 Jul 2019 09:00:14: 7000000 INFO @ Fri, 05 Jul 2019 09:00:14: 7000000 INFO @ Fri, 05 Jul 2019 09:00:18: 8000000 INFO @ Fri, 05 Jul 2019 09:00:21: 8000000 INFO @ Fri, 05 Jul 2019 09:00:21: 8000000 INFO @ Fri, 05 Jul 2019 09:00:25: 9000000 INFO @ Fri, 05 Jul 2019 09:00:28: 9000000 INFO @ Fri, 05 Jul 2019 09:00:29: 9000000 INFO @ Fri, 05 Jul 2019 09:00:31: 10000000 INFO @ Fri, 05 Jul 2019 09:00:34: 10000000 INFO @ Fri, 05 Jul 2019 09:00:36: 10000000 INFO @ Fri, 05 Jul 2019 09:00:38: 11000000 INFO @ Fri, 05 Jul 2019 09:00:40: 11000000 INFO @ Fri, 05 Jul 2019 09:00:44: 11000000 INFO @ Fri, 05 Jul 2019 09:00:45: 12000000 INFO @ Fri, 05 Jul 2019 09:00:47: 12000000 INFO @ Fri, 05 Jul 2019 09:00:51: 13000000 INFO @ Fri, 05 Jul 2019 09:00:52: 12000000 INFO @ Fri, 05 Jul 2019 09:00:53: 13000000 INFO @ Fri, 05 Jul 2019 09:00:58: 14000000 INFO @ Fri, 05 Jul 2019 09:00:59: 14000000 INFO @ Fri, 05 Jul 2019 09:00:59: 13000000 INFO @ Fri, 05 Jul 2019 09:01:05: 15000000 INFO @ Fri, 05 Jul 2019 09:01:06: 15000000 INFO @ Fri, 05 Jul 2019 09:01:07: 14000000 INFO @ Fri, 05 Jul 2019 09:01:12: 16000000 INFO @ Fri, 05 Jul 2019 09:01:12: 16000000 INFO @ Fri, 05 Jul 2019 09:01:14: 15000000 INFO @ Fri, 05 Jul 2019 09:01:18: 17000000 INFO @ Fri, 05 Jul 2019 09:01:18: 17000000 INFO @ Fri, 05 Jul 2019 09:01:21: 16000000 INFO @ Fri, 05 Jul 2019 09:01:25: 18000000 INFO @ Fri, 05 Jul 2019 09:01:25: 18000000 INFO @ Fri, 05 Jul 2019 09:01:29: 17000000 INFO @ Fri, 05 Jul 2019 09:01:31: 19000000 INFO @ Fri, 05 Jul 2019 09:01:31: 19000000 INFO @ Fri, 05 Jul 2019 09:01:34: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:01:34: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:01:34: #1 total tags in treatment: 19412837 INFO @ Fri, 05 Jul 2019 09:01:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:01:34: #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 09:01:34: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:01:34: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:01:34: #1 total tags in treatment: 19412837 INFO @ Fri, 05 Jul 2019 09:01:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:01:34: #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 09:01:35: #1 tags after filtering in treatment: 19412673 INFO @ Fri, 05 Jul 2019 09:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:01:35: #1 finished! INFO @ Fri, 05 Jul 2019 09:01:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:01:35: #1 tags after filtering in treatment: 19412673 INFO @ Fri, 05 Jul 2019 09:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:01:35: #1 finished! INFO @ Fri, 05 Jul 2019 09:01:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:01:37: 18000000 INFO @ Fri, 05 Jul 2019 09:01:40: #2 number of paired peaks: 64642 INFO @ Fri, 05 Jul 2019 09:01:40: start model_add_line... INFO @ Fri, 05 Jul 2019 09:01:40: #2 number of paired peaks: 64642 INFO @ Fri, 05 Jul 2019 09:01:40: start model_add_line... INFO @ Fri, 05 Jul 2019 09:01:40: start X-correlation... INFO @ Fri, 05 Jul 2019 09:01:40: start X-correlation... INFO @ Fri, 05 Jul 2019 09:01:40: end of X-cor INFO @ Fri, 05 Jul 2019 09:01:40: #2 finished! INFO @ Fri, 05 Jul 2019 09:01:40: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 09:01:40: #2 alternative fragment length(s) may be 4,131,501 bps INFO @ Fri, 05 Jul 2019 09:01:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.10_model.r INFO @ Fri, 05 Jul 2019 09:01:40: end of X-cor INFO @ Fri, 05 Jul 2019 09:01:40: #2 finished! INFO @ Fri, 05 Jul 2019 09:01:40: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 09:01:40: #2 alternative fragment length(s) may be 4,131,501 bps INFO @ Fri, 05 Jul 2019 09:01:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.05_model.r INFO @ Fri, 05 Jul 2019 09:01:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:01:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:01:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:01:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:01:44: 19000000 INFO @ Fri, 05 Jul 2019 09:01:47: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:01:47: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:01:47: #1 total tags in treatment: 19412837 INFO @ Fri, 05 Jul 2019 09:01:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:01:47: #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 09:01:47: #1 tags after filtering in treatment: 19412673 INFO @ Fri, 05 Jul 2019 09:01:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:01:47: #1 finished! INFO @ Fri, 05 Jul 2019 09:01:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:01:52: #2 number of paired peaks: 64642 INFO @ Fri, 05 Jul 2019 09:01:52: start model_add_line... INFO @ Fri, 05 Jul 2019 09:01:52: start X-correlation... INFO @ Fri, 05 Jul 2019 09:01:52: end of X-cor INFO @ Fri, 05 Jul 2019 09:01:52: #2 finished! INFO @ Fri, 05 Jul 2019 09:01:52: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 09:01:52: #2 alternative fragment length(s) may be 4,131,501 bps INFO @ Fri, 05 Jul 2019 09:01:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.20_model.r INFO @ Fri, 05 Jul 2019 09:01:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:01:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:02:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:02:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:03:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:03:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:03:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:03:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.05_summits.bed INFO @ Fri, 05 Jul 2019 09:03:24: Done! pass1 - making usageList (67 chroms): 3 millis pass2 - checking and writing primary data (4948 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:03:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:03:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:03:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.10_summits.bed INFO @ Fri, 05 Jul 2019 09:03:27: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (984 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:03:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:03:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:03:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102002/ERX102002.20_summits.bed INFO @ Fri, 05 Jul 2019 09:03:37: Done! pass1 - making usageList (24 chroms): 9 millis pass2 - checking and writing primary data (116 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。