Job ID = 2002133 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,013,629 reads read : 22,013,629 reads written : 22,013,629 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:14 22013629 reads; of these: 22013629 (100.00%) were unpaired; of these: 625850 (2.84%) aligned 0 times 16364445 (74.34%) aligned exactly 1 time 5023334 (22.82%) aligned >1 times 97.16% overall alignment rate Time searching: 00:14:15 Overall time: 00:14:15 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] 1378862 / 21387779 = 0.0645 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 10:25:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.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 10:25:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:25:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:25:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.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 10:25:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:25:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:25:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.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 10:25:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:25:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:25:36: 1000000 INFO @ Fri, 05 Jul 2019 10:25:37: 1000000 INFO @ Fri, 05 Jul 2019 10:25:37: 1000000 INFO @ Fri, 05 Jul 2019 10:25:44: 2000000 INFO @ Fri, 05 Jul 2019 10:25:45: 2000000 INFO @ Fri, 05 Jul 2019 10:25:46: 2000000 INFO @ Fri, 05 Jul 2019 10:25:52: 3000000 INFO @ Fri, 05 Jul 2019 10:25:53: 3000000 INFO @ Fri, 05 Jul 2019 10:25:55: 3000000 INFO @ Fri, 05 Jul 2019 10:26:00: 4000000 INFO @ Fri, 05 Jul 2019 10:26:01: 4000000 INFO @ Fri, 05 Jul 2019 10:26:04: 4000000 INFO @ Fri, 05 Jul 2019 10:26:08: 5000000 INFO @ Fri, 05 Jul 2019 10:26:08: 5000000 INFO @ Fri, 05 Jul 2019 10:26:12: 5000000 INFO @ Fri, 05 Jul 2019 10:26:15: 6000000 INFO @ Fri, 05 Jul 2019 10:26:16: 6000000 INFO @ Fri, 05 Jul 2019 10:26:21: 6000000 INFO @ Fri, 05 Jul 2019 10:26:23: 7000000 INFO @ Fri, 05 Jul 2019 10:26:24: 7000000 INFO @ Fri, 05 Jul 2019 10:26:30: 7000000 INFO @ Fri, 05 Jul 2019 10:26:31: 8000000 INFO @ Fri, 05 Jul 2019 10:26:32: 8000000 INFO @ Fri, 05 Jul 2019 10:26:39: 8000000 INFO @ Fri, 05 Jul 2019 10:26:39: 9000000 INFO @ Fri, 05 Jul 2019 10:26:39: 9000000 INFO @ Fri, 05 Jul 2019 10:26:47: 10000000 INFO @ Fri, 05 Jul 2019 10:26:47: 10000000 INFO @ Fri, 05 Jul 2019 10:26:47: 9000000 INFO @ Fri, 05 Jul 2019 10:26:55: 11000000 INFO @ Fri, 05 Jul 2019 10:26:55: 11000000 INFO @ Fri, 05 Jul 2019 10:26:56: 10000000 INFO @ Fri, 05 Jul 2019 10:27:04: 12000000 INFO @ Fri, 05 Jul 2019 10:27:05: 12000000 INFO @ Fri, 05 Jul 2019 10:27:06: 11000000 INFO @ Fri, 05 Jul 2019 10:27:12: 13000000 INFO @ Fri, 05 Jul 2019 10:27:14: 13000000 INFO @ Fri, 05 Jul 2019 10:27:15: 12000000 INFO @ Fri, 05 Jul 2019 10:27:20: 14000000 INFO @ Fri, 05 Jul 2019 10:27:22: 14000000 INFO @ Fri, 05 Jul 2019 10:27:23: 13000000 INFO @ Fri, 05 Jul 2019 10:27:29: 15000000 INFO @ Fri, 05 Jul 2019 10:27:30: 15000000 INFO @ Fri, 05 Jul 2019 10:27:32: 14000000 INFO @ Fri, 05 Jul 2019 10:27:37: 16000000 INFO @ Fri, 05 Jul 2019 10:27:37: 16000000 INFO @ Fri, 05 Jul 2019 10:27:41: 15000000 INFO @ Fri, 05 Jul 2019 10:27:45: 17000000 INFO @ Fri, 05 Jul 2019 10:27:45: 17000000 INFO @ Fri, 05 Jul 2019 10:27:49: 16000000 INFO @ Fri, 05 Jul 2019 10:27:52: 18000000 INFO @ Fri, 05 Jul 2019 10:27:53: 18000000 INFO @ Fri, 05 Jul 2019 10:27:58: 17000000 INFO @ Fri, 05 Jul 2019 10:28:01: 19000000 INFO @ Fri, 05 Jul 2019 10:28:01: 19000000 INFO @ Fri, 05 Jul 2019 10:28:07: 18000000 INFO @ Fri, 05 Jul 2019 10:28:09: 20000000 INFO @ Fri, 05 Jul 2019 10:28:09: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:28:09: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:28:09: #1 total tags in treatment: 20008917 INFO @ Fri, 05 Jul 2019 10:28:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:28:09: #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 10:28:09: 20000000 INFO @ Fri, 05 Jul 2019 10:28:09: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:28:09: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:28:09: #1 total tags in treatment: 20008917 INFO @ Fri, 05 Jul 2019 10:28:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:28:09: #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 10:28:10: #1 tags after filtering in treatment: 20008737 INFO @ Fri, 05 Jul 2019 10:28:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:28:10: #1 finished! INFO @ Fri, 05 Jul 2019 10:28:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:28:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:28:10: #1 tags after filtering in treatment: 20008737 INFO @ Fri, 05 Jul 2019 10:28:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:28:10: #1 finished! INFO @ Fri, 05 Jul 2019 10:28:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:28:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:28:15: #2 number of paired peaks: 71384 INFO @ Fri, 05 Jul 2019 10:28:15: start model_add_line... INFO @ Fri, 05 Jul 2019 10:28:15: start X-correlation... INFO @ Fri, 05 Jul 2019 10:28:15: end of X-cor INFO @ Fri, 05 Jul 2019 10:28:15: #2 finished! INFO @ Fri, 05 Jul 2019 10:28:15: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 10:28:15: #2 alternative fragment length(s) may be 3,127,286,496 bps INFO @ Fri, 05 Jul 2019 10:28:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.10_model.r INFO @ Fri, 05 Jul 2019 10:28:15: #2 number of paired peaks: 71384 INFO @ Fri, 05 Jul 2019 10:28:15: start model_add_line... INFO @ Fri, 05 Jul 2019 10:28:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:28:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:28:15: start X-correlation... INFO @ Fri, 05 Jul 2019 10:28:15: end of X-cor INFO @ Fri, 05 Jul 2019 10:28:15: #2 finished! INFO @ Fri, 05 Jul 2019 10:28:15: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 10:28:15: #2 alternative fragment length(s) may be 3,127,286,496 bps INFO @ Fri, 05 Jul 2019 10:28:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.20_model.r INFO @ Fri, 05 Jul 2019 10:28:15: 19000000 INFO @ Fri, 05 Jul 2019 10:28:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:28:24: 20000000 INFO @ Fri, 05 Jul 2019 10:28:25: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:28:25: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:28:25: #1 total tags in treatment: 20008917 INFO @ Fri, 05 Jul 2019 10:28:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:28:25: #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 10:28:25: #1 tags after filtering in treatment: 20008737 INFO @ Fri, 05 Jul 2019 10:28:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:28:25: #1 finished! INFO @ Fri, 05 Jul 2019 10:28:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:28:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:28:30: #2 number of paired peaks: 71384 INFO @ Fri, 05 Jul 2019 10:28:30: start model_add_line... INFO @ Fri, 05 Jul 2019 10:28:30: start X-correlation... INFO @ Fri, 05 Jul 2019 10:28:30: end of X-cor INFO @ Fri, 05 Jul 2019 10:28:30: #2 finished! INFO @ Fri, 05 Jul 2019 10:28:30: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 10:28:30: #2 alternative fragment length(s) may be 3,127,286,496 bps INFO @ Fri, 05 Jul 2019 10:28:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.05_model.r INFO @ Fri, 05 Jul 2019 10:28:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:28:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:29:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:29:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:29:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:29:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:29:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:29:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.10_summits.bed INFO @ Fri, 05 Jul 2019 10:29:51: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (916 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 10:29:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.20_peaks.xls CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:29:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:29:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.20_summits.bed INFO @ Fri, 05 Jul 2019 10:29:54: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (109 records, 4 fields): 340 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:30:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:30:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:30:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102034/ERX102034.05_summits.bed INFO @ Fri, 05 Jul 2019 10:30:05: Done! pass1 - making usageList (61 chroms): 3 millis pass2 - checking and writing primary data (4432 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。