Job ID = 2001156 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,646,594 reads read : 16,646,594 reads written : 16,646,594 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: 00:04:12 16646594 reads; of these: 16646594 (100.00%) were unpaired; of these: 377682 (2.27%) aligned 0 times 14632980 (87.90%) aligned exactly 1 time 1635932 (9.83%) aligned >1 times 97.73% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 7495449 / 16268912 = 0.4607 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 04:01:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.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 04:01:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:01:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:01:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.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 04:01:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:01:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.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 04:01:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:01:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:01:20: 1000000 INFO @ Fri, 05 Jul 2019 04:01:21: 1000000 INFO @ Fri, 05 Jul 2019 04:01:22: 1000000 INFO @ Fri, 05 Jul 2019 04:01:29: 2000000 INFO @ Fri, 05 Jul 2019 04:01:31: 2000000 INFO @ Fri, 05 Jul 2019 04:01:32: 2000000 INFO @ Fri, 05 Jul 2019 04:01:37: 3000000 INFO @ Fri, 05 Jul 2019 04:01:42: 3000000 INFO @ Fri, 05 Jul 2019 04:01:43: 3000000 INFO @ Fri, 05 Jul 2019 04:01:45: 4000000 INFO @ Fri, 05 Jul 2019 04:01:52: 4000000 INFO @ Fri, 05 Jul 2019 04:01:53: 4000000 INFO @ Fri, 05 Jul 2019 04:01:53: 5000000 INFO @ Fri, 05 Jul 2019 04:02:02: 6000000 INFO @ Fri, 05 Jul 2019 04:02:03: 5000000 INFO @ Fri, 05 Jul 2019 04:02:03: 5000000 INFO @ Fri, 05 Jul 2019 04:02:10: 7000000 INFO @ Fri, 05 Jul 2019 04:02:13: 6000000 INFO @ Fri, 05 Jul 2019 04:02:13: 6000000 INFO @ Fri, 05 Jul 2019 04:02:18: 8000000 INFO @ Fri, 05 Jul 2019 04:02:23: 7000000 INFO @ Fri, 05 Jul 2019 04:02:24: 7000000 INFO @ Fri, 05 Jul 2019 04:02:24: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:02:24: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:02:24: #1 total tags in treatment: 8773463 INFO @ Fri, 05 Jul 2019 04:02:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:02:24: #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 04:02:25: #1 tags after filtering in treatment: 8773157 INFO @ Fri, 05 Jul 2019 04:02:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:02:25: #1 finished! INFO @ Fri, 05 Jul 2019 04:02:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:02:27: #2 number of paired peaks: 46112 INFO @ Fri, 05 Jul 2019 04:02:27: start model_add_line... INFO @ Fri, 05 Jul 2019 04:02:28: start X-correlation... INFO @ Fri, 05 Jul 2019 04:02:28: end of X-cor INFO @ Fri, 05 Jul 2019 04:02:28: #2 finished! INFO @ Fri, 05 Jul 2019 04:02:28: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 04:02:28: #2 alternative fragment length(s) may be 3,140 bps INFO @ Fri, 05 Jul 2019 04:02:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.05_model.r INFO @ Fri, 05 Jul 2019 04:02:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:02:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:02:33: 8000000 INFO @ Fri, 05 Jul 2019 04:02:34: 8000000 INFO @ Fri, 05 Jul 2019 04:02:41: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:02:41: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:02:41: #1 total tags in treatment: 8773463 INFO @ Fri, 05 Jul 2019 04:02:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:02:41: #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 04:02:41: #1 tags after filtering in treatment: 8773157 INFO @ Fri, 05 Jul 2019 04:02:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:02:41: #1 finished! INFO @ Fri, 05 Jul 2019 04:02:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:02:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:02:41: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:02:41: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:02:41: #1 total tags in treatment: 8773463 INFO @ Fri, 05 Jul 2019 04:02:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:02:41: #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 04:02:41: #1 tags after filtering in treatment: 8773157 INFO @ Fri, 05 Jul 2019 04:02:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:02:41: #1 finished! INFO @ Fri, 05 Jul 2019 04:02:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:02:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:02:44: #2 number of paired peaks: 46112 INFO @ Fri, 05 Jul 2019 04:02:44: start model_add_line... INFO @ Fri, 05 Jul 2019 04:02:44: start X-correlation... INFO @ Fri, 05 Jul 2019 04:02:44: #2 number of paired peaks: 46112 INFO @ Fri, 05 Jul 2019 04:02:44: start model_add_line... INFO @ Fri, 05 Jul 2019 04:02:44: end of X-cor INFO @ Fri, 05 Jul 2019 04:02:44: #2 finished! INFO @ Fri, 05 Jul 2019 04:02:44: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 04:02:44: #2 alternative fragment length(s) may be 3,140 bps INFO @ Fri, 05 Jul 2019 04:02:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.10_model.r INFO @ Fri, 05 Jul 2019 04:02:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:02:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:02:44: start X-correlation... INFO @ Fri, 05 Jul 2019 04:02:44: end of X-cor INFO @ Fri, 05 Jul 2019 04:02:44: #2 finished! INFO @ Fri, 05 Jul 2019 04:02:44: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 04:02:44: #2 alternative fragment length(s) may be 3,140 bps INFO @ Fri, 05 Jul 2019 04:02:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.20_model.r INFO @ Fri, 05 Jul 2019 04:02:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:02:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:02:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:03:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:03:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.05_summits.bed INFO @ Fri, 05 Jul 2019 04:03:12: Done! INFO @ Fri, 05 Jul 2019 04:03:12: #3 Call peaks for each chromosome... pass1 - making usageList (122 chroms): 9 millis pass2 - checking and writing primary data (40164 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:03:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:03:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:03:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:03:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:03:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.20_summits.bed INFO @ Fri, 05 Jul 2019 04:03:28: Done! INFO @ Fri, 05 Jul 2019 04:03:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.10_peaks.narrowPeak pass1 - making usageList (66 chroms): 6 millis pass2 - checking and writing primary data (16683 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:03:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101846/ERX101846.10_summits.bed INFO @ Fri, 05 Jul 2019 04:03:29: Done! pass1 - making usageList (96 chroms): 11 millis pass2 - checking and writing primary data (29658 records, 4 fields): 47 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。