Job ID = 2001606 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 69,699,523 reads read : 69,699,523 reads written : 69,699,523 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: 00:42:40 69699523 reads; of these: 69699523 (100.00%) were unpaired; of these: 1634444 (2.34%) aligned 0 times 60550047 (86.87%) aligned exactly 1 time 7515032 (10.78%) aligned >1 times 97.66% overall alignment rate Time searching: 00:42:43 Overall time: 00:42:43 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 28 files... [bam_rmdupse_core] 36048993 / 68065079 = 0.5296 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 07:25:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.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 07:25:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:25:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:25:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.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 07:25:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:25:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:25:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.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 07:25:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:25:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:25:41: 1000000 INFO @ Fri, 05 Jul 2019 07:25:42: 1000000 INFO @ Fri, 05 Jul 2019 07:25:43: 1000000 INFO @ Fri, 05 Jul 2019 07:25:50: 2000000 INFO @ Fri, 05 Jul 2019 07:25:51: 2000000 INFO @ Fri, 05 Jul 2019 07:25:51: 2000000 INFO @ Fri, 05 Jul 2019 07:25:58: 3000000 INFO @ Fri, 05 Jul 2019 07:25:59: 3000000 INFO @ Fri, 05 Jul 2019 07:25:59: 3000000 INFO @ Fri, 05 Jul 2019 07:26:07: 4000000 INFO @ Fri, 05 Jul 2019 07:26:08: 4000000 INFO @ Fri, 05 Jul 2019 07:26:08: 4000000 INFO @ Fri, 05 Jul 2019 07:26:15: 5000000 INFO @ Fri, 05 Jul 2019 07:26:16: 5000000 INFO @ Fri, 05 Jul 2019 07:26:17: 5000000 INFO @ Fri, 05 Jul 2019 07:26:24: 6000000 INFO @ Fri, 05 Jul 2019 07:26:24: 6000000 INFO @ Fri, 05 Jul 2019 07:26:25: 6000000 INFO @ Fri, 05 Jul 2019 07:26:32: 7000000 INFO @ Fri, 05 Jul 2019 07:26:33: 7000000 INFO @ Fri, 05 Jul 2019 07:26:34: 7000000 INFO @ Fri, 05 Jul 2019 07:26:40: 8000000 INFO @ Fri, 05 Jul 2019 07:26:41: 8000000 INFO @ Fri, 05 Jul 2019 07:26:42: 8000000 INFO @ Fri, 05 Jul 2019 07:26:49: 9000000 INFO @ Fri, 05 Jul 2019 07:26:50: 9000000 INFO @ Fri, 05 Jul 2019 07:26:51: 9000000 INFO @ Fri, 05 Jul 2019 07:26:57: 10000000 INFO @ Fri, 05 Jul 2019 07:26:59: 10000000 INFO @ Fri, 05 Jul 2019 07:27:00: 10000000 INFO @ Fri, 05 Jul 2019 07:27:05: 11000000 INFO @ Fri, 05 Jul 2019 07:27:07: 11000000 INFO @ Fri, 05 Jul 2019 07:27:08: 11000000 INFO @ Fri, 05 Jul 2019 07:27:13: 12000000 INFO @ Fri, 05 Jul 2019 07:27:16: 12000000 INFO @ Fri, 05 Jul 2019 07:27:17: 12000000 INFO @ Fri, 05 Jul 2019 07:27:21: 13000000 INFO @ Fri, 05 Jul 2019 07:27:25: 13000000 INFO @ Fri, 05 Jul 2019 07:27:26: 13000000 INFO @ Fri, 05 Jul 2019 07:27:30: 14000000 INFO @ Fri, 05 Jul 2019 07:27:34: 14000000 INFO @ Fri, 05 Jul 2019 07:27:35: 14000000 INFO @ Fri, 05 Jul 2019 07:27:38: 15000000 INFO @ Fri, 05 Jul 2019 07:27:42: 15000000 INFO @ Fri, 05 Jul 2019 07:27:43: 15000000 INFO @ Fri, 05 Jul 2019 07:27:46: 16000000 INFO @ Fri, 05 Jul 2019 07:27:49: 16000000 INFO @ Fri, 05 Jul 2019 07:27:51: 16000000 INFO @ Fri, 05 Jul 2019 07:27:54: 17000000 INFO @ Fri, 05 Jul 2019 07:27:57: 17000000 INFO @ Fri, 05 Jul 2019 07:28:00: 17000000 INFO @ Fri, 05 Jul 2019 07:28:02: 18000000 INFO @ Fri, 05 Jul 2019 07:28:06: 18000000 INFO @ Fri, 05 Jul 2019 07:28:08: 18000000 INFO @ Fri, 05 Jul 2019 07:28:11: 19000000 INFO @ Fri, 05 Jul 2019 07:28:14: 19000000 INFO @ Fri, 05 Jul 2019 07:28:17: 19000000 INFO @ Fri, 05 Jul 2019 07:28:19: 20000000 INFO @ Fri, 05 Jul 2019 07:28:22: 20000000 INFO @ Fri, 05 Jul 2019 07:28:27: 21000000 INFO @ Fri, 05 Jul 2019 07:28:27: 20000000 INFO @ Fri, 05 Jul 2019 07:28:29: 21000000 INFO @ Fri, 05 Jul 2019 07:28:35: 22000000 INFO @ Fri, 05 Jul 2019 07:28:36: 21000000 INFO @ Fri, 05 Jul 2019 07:28:37: 22000000 INFO @ Fri, 05 Jul 2019 07:28:43: 23000000 INFO @ Fri, 05 Jul 2019 07:28:45: 23000000 INFO @ Fri, 05 Jul 2019 07:28:45: 22000000 INFO @ Fri, 05 Jul 2019 07:28:51: 24000000 INFO @ Fri, 05 Jul 2019 07:28:53: 24000000 INFO @ Fri, 05 Jul 2019 07:28:55: 23000000 INFO @ Fri, 05 Jul 2019 07:28:59: 25000000 INFO @ Fri, 05 Jul 2019 07:29:00: 25000000 INFO @ Fri, 05 Jul 2019 07:29:04: 24000000 INFO @ Fri, 05 Jul 2019 07:29:07: 26000000 INFO @ Fri, 05 Jul 2019 07:29:08: 26000000 INFO @ Fri, 05 Jul 2019 07:29:14: 25000000 INFO @ Fri, 05 Jul 2019 07:29:15: 27000000 INFO @ Fri, 05 Jul 2019 07:29:16: 27000000 INFO @ Fri, 05 Jul 2019 07:29:23: 28000000 INFO @ Fri, 05 Jul 2019 07:29:24: 28000000 INFO @ Fri, 05 Jul 2019 07:29:24: 26000000 INFO @ Fri, 05 Jul 2019 07:29:31: 29000000 INFO @ Fri, 05 Jul 2019 07:29:31: 29000000 INFO @ Fri, 05 Jul 2019 07:29:33: 27000000 INFO @ Fri, 05 Jul 2019 07:29:39: 30000000 INFO @ Fri, 05 Jul 2019 07:29:39: 30000000 INFO @ Fri, 05 Jul 2019 07:29:43: 28000000 INFO @ Fri, 05 Jul 2019 07:29:47: 31000000 INFO @ Fri, 05 Jul 2019 07:29:47: 31000000 INFO @ Fri, 05 Jul 2019 07:29:53: 29000000 INFO @ Fri, 05 Jul 2019 07:29:55: 32000000 INFO @ Fri, 05 Jul 2019 07:29:55: 32000000 INFO @ Fri, 05 Jul 2019 07:29:56: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:29:56: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:29:56: #1 total tags in treatment: 32016086 INFO @ Fri, 05 Jul 2019 07:29:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:29:56: #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 07:29:56: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:29:56: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:29:56: #1 total tags in treatment: 32016086 INFO @ Fri, 05 Jul 2019 07:29:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:29:56: #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 07:29:56: #1 tags after filtering in treatment: 32015893 INFO @ Fri, 05 Jul 2019 07:29:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:29:56: #1 finished! INFO @ Fri, 05 Jul 2019 07:29:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:29:56: #1 tags after filtering in treatment: 32015893 INFO @ Fri, 05 Jul 2019 07:29:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:29:56: #1 finished! INFO @ Fri, 05 Jul 2019 07:29:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:30:03: 30000000 INFO @ Fri, 05 Jul 2019 07:30:06: #2 number of paired peaks: 107973 INFO @ Fri, 05 Jul 2019 07:30:06: start model_add_line... INFO @ Fri, 05 Jul 2019 07:30:06: #2 number of paired peaks: 107973 INFO @ Fri, 05 Jul 2019 07:30:06: start model_add_line... INFO @ Fri, 05 Jul 2019 07:30:07: start X-correlation... INFO @ Fri, 05 Jul 2019 07:30:07: end of X-cor INFO @ Fri, 05 Jul 2019 07:30:07: #2 finished! INFO @ Fri, 05 Jul 2019 07:30:07: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 07:30:07: #2 alternative fragment length(s) may be 4,129 bps INFO @ Fri, 05 Jul 2019 07:30:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.20_model.r INFO @ Fri, 05 Jul 2019 07:30:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:30:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:30:07: start X-correlation... INFO @ Fri, 05 Jul 2019 07:30:07: end of X-cor INFO @ Fri, 05 Jul 2019 07:30:07: #2 finished! INFO @ Fri, 05 Jul 2019 07:30:07: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 07:30:07: #2 alternative fragment length(s) may be 4,129 bps INFO @ Fri, 05 Jul 2019 07:30:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.05_model.r INFO @ Fri, 05 Jul 2019 07:30:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:30:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:30:12: 31000000 INFO @ Fri, 05 Jul 2019 07:30:22: 32000000 INFO @ Fri, 05 Jul 2019 07:30:22: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 07:30:22: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 07:30:22: #1 total tags in treatment: 32016086 INFO @ Fri, 05 Jul 2019 07:30:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:30:22: #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 07:30:23: #1 tags after filtering in treatment: 32015893 INFO @ Fri, 05 Jul 2019 07:30:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:30:23: #1 finished! INFO @ Fri, 05 Jul 2019 07:30:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:30:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:30:32: #2 number of paired peaks: 107973 INFO @ Fri, 05 Jul 2019 07:30:32: start model_add_line... INFO @ Fri, 05 Jul 2019 07:30:33: start X-correlation... INFO @ Fri, 05 Jul 2019 07:30:33: end of X-cor INFO @ Fri, 05 Jul 2019 07:30:33: #2 finished! INFO @ Fri, 05 Jul 2019 07:30:33: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 07:30:33: #2 alternative fragment length(s) may be 4,129 bps INFO @ Fri, 05 Jul 2019 07:30:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.10_model.r INFO @ Fri, 05 Jul 2019 07:30:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:30:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:31:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:31:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:32:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:32:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:32:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:32:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.20_summits.bed INFO @ Fri, 05 Jul 2019 07:32:33: Done! pass1 - making usageList (112 chroms): 11 millis pass2 - checking and writing primary data (31157 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:32:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:32:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:32:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.05_summits.bed INFO @ Fri, 05 Jul 2019 07:32:42: Done! pass1 - making usageList (169 chroms): 20 millis pass2 - checking and writing primary data (72112 records, 4 fields): 99 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:33:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:33:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:33:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101933/ERX101933.10_summits.bed INFO @ Fri, 05 Jul 2019 07:33:08: Done! pass1 - making usageList (145 chroms): 15 millis pass2 - checking and writing primary data (52766 records, 4 fields): 70 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。