Job ID = 2002170 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,080,081 reads read : 29,080,081 reads written : 29,080,081 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: 00:11:03 29080081 reads; of these: 29080081 (100.00%) were unpaired; of these: 773892 (2.66%) aligned 0 times 19835483 (68.21%) aligned exactly 1 time 8470706 (29.13%) aligned >1 times 97.34% overall alignment rate Time searching: 00:11:06 Overall time: 00:11:06 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] 2110737 / 28306189 = 0.0746 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 11:31:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.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 11:31:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:31:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:31:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.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 11:31:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:31:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:31:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.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 11:31:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:31:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:32:01: 1000000 INFO @ Fri, 05 Jul 2019 11:32:02: 1000000 INFO @ Fri, 05 Jul 2019 11:32:03: 1000000 INFO @ Fri, 05 Jul 2019 11:32:08: 2000000 INFO @ Fri, 05 Jul 2019 11:32:09: 2000000 INFO @ Fri, 05 Jul 2019 11:32:11: 2000000 INFO @ Fri, 05 Jul 2019 11:32:14: 3000000 INFO @ Fri, 05 Jul 2019 11:32:16: 3000000 INFO @ Fri, 05 Jul 2019 11:32:19: 3000000 INFO @ Fri, 05 Jul 2019 11:32:20: 4000000 INFO @ Fri, 05 Jul 2019 11:32:24: 4000000 INFO @ Fri, 05 Jul 2019 11:32:26: 4000000 INFO @ Fri, 05 Jul 2019 11:32:27: 5000000 INFO @ Fri, 05 Jul 2019 11:32:32: 5000000 INFO @ Fri, 05 Jul 2019 11:32:33: 6000000 INFO @ Fri, 05 Jul 2019 11:32:34: 5000000 INFO @ Fri, 05 Jul 2019 11:32:40: 7000000 INFO @ Fri, 05 Jul 2019 11:32:40: 6000000 INFO @ Fri, 05 Jul 2019 11:32:42: 6000000 INFO @ Fri, 05 Jul 2019 11:32:46: 8000000 INFO @ Fri, 05 Jul 2019 11:32:48: 7000000 INFO @ Fri, 05 Jul 2019 11:32:50: 7000000 INFO @ Fri, 05 Jul 2019 11:32:53: 9000000 INFO @ Fri, 05 Jul 2019 11:32:56: 8000000 INFO @ Fri, 05 Jul 2019 11:32:57: 8000000 INFO @ Fri, 05 Jul 2019 11:32:59: 10000000 INFO @ Fri, 05 Jul 2019 11:33:04: 9000000 INFO @ Fri, 05 Jul 2019 11:33:05: 9000000 INFO @ Fri, 05 Jul 2019 11:33:06: 11000000 INFO @ Fri, 05 Jul 2019 11:33:12: 10000000 INFO @ Fri, 05 Jul 2019 11:33:12: 12000000 INFO @ Fri, 05 Jul 2019 11:33:13: 10000000 INFO @ Fri, 05 Jul 2019 11:33:19: 13000000 INFO @ Fri, 05 Jul 2019 11:33:20: 11000000 INFO @ Fri, 05 Jul 2019 11:33:20: 11000000 INFO @ Fri, 05 Jul 2019 11:33:25: 14000000 INFO @ Fri, 05 Jul 2019 11:33:28: 12000000 INFO @ Fri, 05 Jul 2019 11:33:28: 12000000 INFO @ Fri, 05 Jul 2019 11:33:31: 15000000 INFO @ Fri, 05 Jul 2019 11:33:35: 13000000 INFO @ Fri, 05 Jul 2019 11:33:36: 13000000 INFO @ Fri, 05 Jul 2019 11:33:38: 16000000 INFO @ Fri, 05 Jul 2019 11:33:43: 14000000 INFO @ Fri, 05 Jul 2019 11:33:44: 14000000 INFO @ Fri, 05 Jul 2019 11:33:44: 17000000 INFO @ Fri, 05 Jul 2019 11:33:51: 18000000 INFO @ Fri, 05 Jul 2019 11:33:52: 15000000 INFO @ Fri, 05 Jul 2019 11:33:52: 15000000 INFO @ Fri, 05 Jul 2019 11:33:57: 19000000 INFO @ Fri, 05 Jul 2019 11:34:00: 16000000 INFO @ Fri, 05 Jul 2019 11:34:00: 16000000 INFO @ Fri, 05 Jul 2019 11:34:04: 20000000 INFO @ Fri, 05 Jul 2019 11:34:08: 17000000 INFO @ Fri, 05 Jul 2019 11:34:08: 17000000 INFO @ Fri, 05 Jul 2019 11:34:10: 21000000 INFO @ Fri, 05 Jul 2019 11:34:16: 18000000 INFO @ Fri, 05 Jul 2019 11:34:16: 18000000 INFO @ Fri, 05 Jul 2019 11:34:17: 22000000 INFO @ Fri, 05 Jul 2019 11:34:23: 23000000 INFO @ Fri, 05 Jul 2019 11:34:23: 19000000 INFO @ Fri, 05 Jul 2019 11:34:24: 19000000 INFO @ Fri, 05 Jul 2019 11:34:30: 24000000 INFO @ Fri, 05 Jul 2019 11:34:31: 20000000 INFO @ Fri, 05 Jul 2019 11:34:32: 20000000 INFO @ Fri, 05 Jul 2019 11:34:36: 25000000 INFO @ Fri, 05 Jul 2019 11:34:39: 21000000 INFO @ Fri, 05 Jul 2019 11:34:40: 21000000 INFO @ Fri, 05 Jul 2019 11:34:43: 26000000 INFO @ Fri, 05 Jul 2019 11:34:44: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:34:44: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:34:44: #1 total tags in treatment: 26195452 INFO @ Fri, 05 Jul 2019 11:34:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:34:44: #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 11:34:45: #1 tags after filtering in treatment: 26195347 INFO @ Fri, 05 Jul 2019 11:34:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:34:45: #1 finished! INFO @ Fri, 05 Jul 2019 11:34:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:34:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:34:47: 22000000 INFO @ Fri, 05 Jul 2019 11:34:49: 22000000 INFO @ Fri, 05 Jul 2019 11:34:49: #2 number of paired peaks: 20371 INFO @ Fri, 05 Jul 2019 11:34:49: start model_add_line... INFO @ Fri, 05 Jul 2019 11:34:49: start X-correlation... INFO @ Fri, 05 Jul 2019 11:34:49: end of X-cor INFO @ Fri, 05 Jul 2019 11:34:49: #2 finished! INFO @ Fri, 05 Jul 2019 11:34:49: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 11:34:49: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 11:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.10_model.r INFO @ Fri, 05 Jul 2019 11:34:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:34:55: 23000000 INFO @ Fri, 05 Jul 2019 11:34:56: 23000000 INFO @ Fri, 05 Jul 2019 11:35:02: 24000000 INFO @ Fri, 05 Jul 2019 11:35:04: 24000000 INFO @ Fri, 05 Jul 2019 11:35:10: 25000000 INFO @ Fri, 05 Jul 2019 11:35:12: 25000000 INFO @ Fri, 05 Jul 2019 11:35:18: 26000000 INFO @ Fri, 05 Jul 2019 11:35:20: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:35:20: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:35:20: #1 total tags in treatment: 26195452 INFO @ Fri, 05 Jul 2019 11:35:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:35:20: #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 11:35:20: 26000000 INFO @ Fri, 05 Jul 2019 11:35:20: #1 tags after filtering in treatment: 26195347 INFO @ Fri, 05 Jul 2019 11:35:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:35:20: #1 finished! INFO @ Fri, 05 Jul 2019 11:35:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:35:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:35:22: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:35:22: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:35:22: #1 total tags in treatment: 26195452 INFO @ Fri, 05 Jul 2019 11:35:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:35:22: #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 11:35:22: #1 tags after filtering in treatment: 26195347 INFO @ Fri, 05 Jul 2019 11:35:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:35:22: #1 finished! INFO @ Fri, 05 Jul 2019 11:35:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:35:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:35:24: #2 number of paired peaks: 20371 INFO @ Fri, 05 Jul 2019 11:35:24: start model_add_line... INFO @ Fri, 05 Jul 2019 11:35:24: start X-correlation... INFO @ Fri, 05 Jul 2019 11:35:24: end of X-cor INFO @ Fri, 05 Jul 2019 11:35:24: #2 finished! INFO @ Fri, 05 Jul 2019 11:35:24: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 11:35:24: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 11:35:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.20_model.r INFO @ Fri, 05 Jul 2019 11:35:24: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:35:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:35:26: #2 number of paired peaks: 20371 INFO @ Fri, 05 Jul 2019 11:35:26: start model_add_line... INFO @ Fri, 05 Jul 2019 11:35:26: start X-correlation... INFO @ Fri, 05 Jul 2019 11:35:26: end of X-cor INFO @ Fri, 05 Jul 2019 11:35:26: #2 finished! INFO @ Fri, 05 Jul 2019 11:35:26: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 11:35:26: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 11:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.05_model.r INFO @ Fri, 05 Jul 2019 11:35:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:36:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:36:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:36:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:36:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:36:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:36:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.10_summits.bed INFO @ Fri, 05 Jul 2019 11:36:54: Done! pass1 - making usageList (82 chroms): 3 millis pass2 - checking and writing primary data (13308 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:37:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:37:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:37:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.20_summits.bed INFO @ Fri, 05 Jul 2019 11:37:29: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (8164 records, 4 fields): 15 millis INFO @ Fri, 05 Jul 2019 11:37:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:37:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:37:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210229/ERX210229.05_summits.bed INFO @ Fri, 05 Jul 2019 11:37:31: Done! pass1 - making usageList (101 chroms): 4 millis pass2 - checking and writing primary data (19409 records, 4 fields): 29 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。