Job ID = 2001168 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,107,382 reads read : 26,107,382 reads written : 26,107,382 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: 00:12:00 26107382 reads; of these: 26107382 (100.00%) were unpaired; of these: 438585 (1.68%) aligned 0 times 18856251 (72.23%) aligned exactly 1 time 6812546 (26.09%) aligned >1 times 98.32% overall alignment rate Time searching: 00:12:02 Overall time: 00:12:02 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] 1358674 / 25668797 = 0.0529 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 04:25:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.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 04:25:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:25:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:25:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.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 04:25:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:25:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:25:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.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 04:25:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:25:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:26:05: 1000000 INFO @ Fri, 05 Jul 2019 04:26:05: 1000000 INFO @ Fri, 05 Jul 2019 04:26:06: 1000000 INFO @ Fri, 05 Jul 2019 04:26:15: 2000000 INFO @ Fri, 05 Jul 2019 04:26:17: 2000000 INFO @ Fri, 05 Jul 2019 04:26:18: 2000000 INFO @ Fri, 05 Jul 2019 04:26:23: 3000000 INFO @ Fri, 05 Jul 2019 04:26:28: 3000000 INFO @ Fri, 05 Jul 2019 04:26:28: 3000000 INFO @ Fri, 05 Jul 2019 04:26:32: 4000000 INFO @ Fri, 05 Jul 2019 04:26:39: 4000000 INFO @ Fri, 05 Jul 2019 04:26:39: 4000000 INFO @ Fri, 05 Jul 2019 04:26:42: 5000000 INFO @ Fri, 05 Jul 2019 04:26:50: 5000000 INFO @ Fri, 05 Jul 2019 04:26:50: 5000000 INFO @ Fri, 05 Jul 2019 04:26:51: 6000000 INFO @ Fri, 05 Jul 2019 04:27:00: 7000000 INFO @ Fri, 05 Jul 2019 04:27:01: 6000000 INFO @ Fri, 05 Jul 2019 04:27:01: 6000000 INFO @ Fri, 05 Jul 2019 04:27:09: 8000000 INFO @ Fri, 05 Jul 2019 04:27:11: 7000000 INFO @ Fri, 05 Jul 2019 04:27:12: 7000000 INFO @ Fri, 05 Jul 2019 04:27:19: 9000000 INFO @ Fri, 05 Jul 2019 04:27:22: 8000000 INFO @ Fri, 05 Jul 2019 04:27:22: 8000000 INFO @ Fri, 05 Jul 2019 04:27:28: 10000000 INFO @ Fri, 05 Jul 2019 04:27:32: 9000000 INFO @ Fri, 05 Jul 2019 04:27:33: 9000000 INFO @ Fri, 05 Jul 2019 04:27:37: 11000000 INFO @ Fri, 05 Jul 2019 04:27:44: 10000000 INFO @ Fri, 05 Jul 2019 04:27:44: 10000000 INFO @ Fri, 05 Jul 2019 04:27:46: 12000000 INFO @ Fri, 05 Jul 2019 04:27:55: 11000000 INFO @ Fri, 05 Jul 2019 04:27:55: 11000000 INFO @ Fri, 05 Jul 2019 04:27:55: 13000000 INFO @ Fri, 05 Jul 2019 04:28:04: 14000000 INFO @ Fri, 05 Jul 2019 04:28:05: 12000000 INFO @ Fri, 05 Jul 2019 04:28:06: 12000000 INFO @ Fri, 05 Jul 2019 04:28:15: 15000000 INFO @ Fri, 05 Jul 2019 04:28:16: 13000000 INFO @ Fri, 05 Jul 2019 04:28:16: 13000000 INFO @ Fri, 05 Jul 2019 04:28:24: 16000000 INFO @ Fri, 05 Jul 2019 04:28:27: 14000000 INFO @ Fri, 05 Jul 2019 04:28:27: 14000000 INFO @ Fri, 05 Jul 2019 04:28:35: 17000000 INFO @ Fri, 05 Jul 2019 04:28:37: 15000000 INFO @ Fri, 05 Jul 2019 04:28:38: 15000000 INFO @ Fri, 05 Jul 2019 04:28:44: 18000000 INFO @ Fri, 05 Jul 2019 04:28:48: 16000000 INFO @ Fri, 05 Jul 2019 04:28:49: 16000000 INFO @ Fri, 05 Jul 2019 04:28:53: 19000000 INFO @ Fri, 05 Jul 2019 04:28:58: 17000000 INFO @ Fri, 05 Jul 2019 04:28:59: 17000000 INFO @ Fri, 05 Jul 2019 04:29:02: 20000000 INFO @ Fri, 05 Jul 2019 04:29:09: 18000000 INFO @ Fri, 05 Jul 2019 04:29:10: 18000000 INFO @ Fri, 05 Jul 2019 04:29:11: 21000000 INFO @ Fri, 05 Jul 2019 04:29:19: 19000000 INFO @ Fri, 05 Jul 2019 04:29:19: 22000000 INFO @ Fri, 05 Jul 2019 04:29:21: 19000000 INFO @ Fri, 05 Jul 2019 04:29:29: 23000000 INFO @ Fri, 05 Jul 2019 04:29:30: 20000000 INFO @ Fri, 05 Jul 2019 04:29:32: 20000000 INFO @ Fri, 05 Jul 2019 04:29:39: 24000000 INFO @ Fri, 05 Jul 2019 04:29:41: 21000000 INFO @ Fri, 05 Jul 2019 04:29:42: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:29:42: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:29:42: #1 total tags in treatment: 24310123 INFO @ Fri, 05 Jul 2019 04:29:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:29:42: #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 04:29:43: #1 tags after filtering in treatment: 24309974 INFO @ Fri, 05 Jul 2019 04:29:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:29:43: #1 finished! INFO @ Fri, 05 Jul 2019 04:29:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:29:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:29:43: 21000000 INFO @ Fri, 05 Jul 2019 04:29:48: #2 number of paired peaks: 44106 INFO @ Fri, 05 Jul 2019 04:29:48: start model_add_line... INFO @ Fri, 05 Jul 2019 04:29:48: start X-correlation... INFO @ Fri, 05 Jul 2019 04:29:48: end of X-cor INFO @ Fri, 05 Jul 2019 04:29:48: #2 finished! INFO @ Fri, 05 Jul 2019 04:29:48: #2 predicted fragment length is 123 bps INFO @ Fri, 05 Jul 2019 04:29:48: #2 alternative fragment length(s) may be 123,293,484 bps INFO @ Fri, 05 Jul 2019 04:29:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.20_model.r INFO @ Fri, 05 Jul 2019 04:29:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:29:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:29:51: 22000000 INFO @ Fri, 05 Jul 2019 04:29:53: 22000000 INFO @ Fri, 05 Jul 2019 04:30:01: 23000000 INFO @ Fri, 05 Jul 2019 04:30:03: 23000000 INFO @ Fri, 05 Jul 2019 04:30:12: 24000000 INFO @ Fri, 05 Jul 2019 04:30:14: 24000000 INFO @ Fri, 05 Jul 2019 04:30:16: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:30:16: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:30:16: #1 total tags in treatment: 24310123 INFO @ Fri, 05 Jul 2019 04:30:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:30:16: #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 04:30:16: #1 tags after filtering in treatment: 24309974 INFO @ Fri, 05 Jul 2019 04:30:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:30:16: #1 finished! INFO @ Fri, 05 Jul 2019 04:30:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:30:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:30:17: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:30:17: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:30:17: #1 total tags in treatment: 24310123 INFO @ Fri, 05 Jul 2019 04:30:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:30:17: #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 04:30:18: #1 tags after filtering in treatment: 24309974 INFO @ Fri, 05 Jul 2019 04:30:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:30:18: #1 finished! INFO @ Fri, 05 Jul 2019 04:30:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:30:21: #2 number of paired peaks: 44106 INFO @ Fri, 05 Jul 2019 04:30:21: start model_add_line... INFO @ Fri, 05 Jul 2019 04:30:22: start X-correlation... INFO @ Fri, 05 Jul 2019 04:30:22: end of X-cor INFO @ Fri, 05 Jul 2019 04:30:22: #2 finished! INFO @ Fri, 05 Jul 2019 04:30:22: #2 predicted fragment length is 123 bps INFO @ Fri, 05 Jul 2019 04:30:22: #2 alternative fragment length(s) may be 123,293,484 bps INFO @ Fri, 05 Jul 2019 04:30:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.05_model.r INFO @ Fri, 05 Jul 2019 04:30:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:30:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:30:23: #2 number of paired peaks: 44106 INFO @ Fri, 05 Jul 2019 04:30:23: start model_add_line... INFO @ Fri, 05 Jul 2019 04:30:23: start X-correlation... INFO @ Fri, 05 Jul 2019 04:30:23: end of X-cor INFO @ Fri, 05 Jul 2019 04:30:23: #2 finished! INFO @ Fri, 05 Jul 2019 04:30:23: #2 predicted fragment length is 123 bps INFO @ Fri, 05 Jul 2019 04:30:23: #2 alternative fragment length(s) may be 123,293,484 bps INFO @ Fri, 05 Jul 2019 04:30:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.10_model.r INFO @ Fri, 05 Jul 2019 04:30:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:30:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:31:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:31:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:31:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:31:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:31:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:31:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.20_summits.bed INFO @ Fri, 05 Jul 2019 04:31:53: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:32:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:32:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:32:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.05_summits.bed INFO @ Fri, 05 Jul 2019 04:32:28: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (1775 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:32:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:32:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:32:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101857/ERX101857.10_summits.bed INFO @ Fri, 05 Jul 2019 04:32:30: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (418 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。