Job ID = 2001175 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,706,427 reads read : 25,706,427 reads written : 25,706,427 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: 00:05:49 25706427 reads; of these: 25706427 (100.00%) were unpaired; of these: 862244 (3.35%) aligned 0 times 21725721 (84.51%) aligned exactly 1 time 3118462 (12.13%) aligned >1 times 96.65% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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] 10685060 / 24844183 = 0.4301 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 04:23:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.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 04:23:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:23:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:23:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.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 04:23:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:23:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:23:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.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 04:23:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:23:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:24:01: 1000000 INFO @ Fri, 05 Jul 2019 04:24:02: 1000000 INFO @ Fri, 05 Jul 2019 04:24:02: 1000000 INFO @ Fri, 05 Jul 2019 04:24:10: 2000000 INFO @ Fri, 05 Jul 2019 04:24:10: 2000000 INFO @ Fri, 05 Jul 2019 04:24:11: 2000000 INFO @ Fri, 05 Jul 2019 04:24:17: 3000000 INFO @ Fri, 05 Jul 2019 04:24:20: 3000000 INFO @ Fri, 05 Jul 2019 04:24:21: 3000000 INFO @ Fri, 05 Jul 2019 04:24:26: 4000000 INFO @ Fri, 05 Jul 2019 04:24:29: 4000000 INFO @ Fri, 05 Jul 2019 04:24:30: 4000000 INFO @ Fri, 05 Jul 2019 04:24:33: 5000000 INFO @ Fri, 05 Jul 2019 04:24:38: 5000000 INFO @ Fri, 05 Jul 2019 04:24:39: 5000000 INFO @ Fri, 05 Jul 2019 04:24:41: 6000000 INFO @ Fri, 05 Jul 2019 04:24:46: 6000000 INFO @ Fri, 05 Jul 2019 04:24:47: 6000000 INFO @ Fri, 05 Jul 2019 04:24:48: 7000000 INFO @ Fri, 05 Jul 2019 04:24:55: 7000000 INFO @ Fri, 05 Jul 2019 04:24:55: 7000000 INFO @ Fri, 05 Jul 2019 04:24:56: 8000000 INFO @ Fri, 05 Jul 2019 04:25:04: 9000000 INFO @ Fri, 05 Jul 2019 04:25:04: 8000000 INFO @ Fri, 05 Jul 2019 04:25:05: 8000000 INFO @ Fri, 05 Jul 2019 04:25:12: 10000000 INFO @ Fri, 05 Jul 2019 04:25:13: 9000000 INFO @ Fri, 05 Jul 2019 04:25:13: 9000000 INFO @ Fri, 05 Jul 2019 04:25:20: 11000000 INFO @ Fri, 05 Jul 2019 04:25:21: 10000000 INFO @ Fri, 05 Jul 2019 04:25:21: 10000000 INFO @ Fri, 05 Jul 2019 04:25:27: 12000000 INFO @ Fri, 05 Jul 2019 04:25:30: 11000000 INFO @ Fri, 05 Jul 2019 04:25:30: 11000000 INFO @ Fri, 05 Jul 2019 04:25:35: 13000000 INFO @ Fri, 05 Jul 2019 04:25:38: 12000000 INFO @ Fri, 05 Jul 2019 04:25:39: 12000000 INFO @ Fri, 05 Jul 2019 04:25:43: 14000000 INFO @ Fri, 05 Jul 2019 04:25:45: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:25:45: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:25:45: #1 total tags in treatment: 14159123 INFO @ Fri, 05 Jul 2019 04:25:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:25:45: #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 04:25:45: #1 tags after filtering in treatment: 14158876 INFO @ Fri, 05 Jul 2019 04:25:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:25:45: #1 finished! INFO @ Fri, 05 Jul 2019 04:25:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:25:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:25:47: 13000000 INFO @ Fri, 05 Jul 2019 04:25:48: 13000000 INFO @ Fri, 05 Jul 2019 04:25:49: #2 number of paired peaks: 53281 INFO @ Fri, 05 Jul 2019 04:25:49: start model_add_line... INFO @ Fri, 05 Jul 2019 04:25:49: start X-correlation... INFO @ Fri, 05 Jul 2019 04:25:49: end of X-cor INFO @ Fri, 05 Jul 2019 04:25:49: #2 finished! INFO @ Fri, 05 Jul 2019 04:25:49: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 04:25:49: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 05 Jul 2019 04:25:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.20_model.r INFO @ Fri, 05 Jul 2019 04:25:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:25:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:25:56: 14000000 INFO @ Fri, 05 Jul 2019 04:25:56: 14000000 INFO @ Fri, 05 Jul 2019 04:25:57: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:25:57: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:25:57: #1 total tags in treatment: 14159123 INFO @ Fri, 05 Jul 2019 04:25:57: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:25:57: #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 04:25:58: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:25:58: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:25:58: #1 total tags in treatment: 14159123 INFO @ Fri, 05 Jul 2019 04:25:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:25:58: #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 04:25:58: #1 tags after filtering in treatment: 14158876 INFO @ Fri, 05 Jul 2019 04:25:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:25:58: #1 finished! INFO @ Fri, 05 Jul 2019 04:25:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:25:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:25:58: #1 tags after filtering in treatment: 14158876 INFO @ Fri, 05 Jul 2019 04:25:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:25:58: #1 finished! INFO @ Fri, 05 Jul 2019 04:25:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:25:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:26:02: #2 number of paired peaks: 53281 INFO @ Fri, 05 Jul 2019 04:26:02: start model_add_line... INFO @ Fri, 05 Jul 2019 04:26:02: #2 number of paired peaks: 53281 INFO @ Fri, 05 Jul 2019 04:26:02: start model_add_line... INFO @ Fri, 05 Jul 2019 04:26:02: start X-correlation... INFO @ Fri, 05 Jul 2019 04:26:02: end of X-cor INFO @ Fri, 05 Jul 2019 04:26:02: #2 finished! INFO @ Fri, 05 Jul 2019 04:26:02: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 04:26:02: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 05 Jul 2019 04:26:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.05_model.r INFO @ Fri, 05 Jul 2019 04:26:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:26:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:26:02: start X-correlation... INFO @ Fri, 05 Jul 2019 04:26:02: end of X-cor INFO @ Fri, 05 Jul 2019 04:26:02: #2 finished! INFO @ Fri, 05 Jul 2019 04:26:02: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 04:26:02: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 05 Jul 2019 04:26:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.10_model.r INFO @ Fri, 05 Jul 2019 04:26:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:26:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:26:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:26:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:26:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:26:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:26:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:26:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.20_summits.bed INFO @ Fri, 05 Jul 2019 04:26:58: Done! pass1 - making usageList (72 chroms): 8 millis pass2 - checking and writing primary data (18088 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:27:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:27:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:27:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.10_summits.bed INFO @ Fri, 05 Jul 2019 04:27:15: Done! INFO @ Fri, 05 Jul 2019 04:27:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:27:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.05_peaks.narrowPeak pass1 - making usageList (103 chroms): 9 millis pass2 - checking and writing primary data (30311 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:27:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101863/ERX101863.05_summits.bed INFO @ Fri, 05 Jul 2019 04:27:16: Done! pass1 - making usageList (123 chroms): 9 millis pass2 - checking and writing primary data (40310 records, 4 fields): 55 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。