Job ID = 2002535 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,868,729 reads read : 26,868,729 reads written : 26,868,729 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:32 26868729 reads; of these: 26868729 (100.00%) were unpaired; of these: 530847 (1.98%) aligned 0 times 21724786 (80.86%) aligned exactly 1 time 4613096 (17.17%) aligned >1 times 98.02% overall alignment rate Time searching: 00:23:32 Overall time: 00:23:32 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 12 files... [bam_rmdupse_core] 952528 / 26337882 = 0.0362 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 12:38:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.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 12:38:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:38:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:38:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.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 12:38:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:38:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:38:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.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 12:38:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:38:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:39:00: 1000000 INFO @ Fri, 05 Jul 2019 12:39:02: 1000000 INFO @ Fri, 05 Jul 2019 12:39:03: 1000000 INFO @ Fri, 05 Jul 2019 12:39:07: 2000000 INFO @ Fri, 05 Jul 2019 12:39:10: 2000000 INFO @ Fri, 05 Jul 2019 12:39:11: 2000000 INFO @ Fri, 05 Jul 2019 12:39:14: 3000000 INFO @ Fri, 05 Jul 2019 12:39:18: 3000000 INFO @ Fri, 05 Jul 2019 12:39:20: 3000000 INFO @ Fri, 05 Jul 2019 12:39:21: 4000000 INFO @ Fri, 05 Jul 2019 12:39:27: 4000000 INFO @ Fri, 05 Jul 2019 12:39:28: 5000000 INFO @ Fri, 05 Jul 2019 12:39:28: 4000000 INFO @ Fri, 05 Jul 2019 12:39:35: 6000000 INFO @ Fri, 05 Jul 2019 12:39:35: 5000000 INFO @ Fri, 05 Jul 2019 12:39:36: 5000000 INFO @ Fri, 05 Jul 2019 12:39:42: 7000000 INFO @ Fri, 05 Jul 2019 12:39:43: 6000000 INFO @ Fri, 05 Jul 2019 12:39:45: 6000000 INFO @ Fri, 05 Jul 2019 12:39:49: 8000000 INFO @ Fri, 05 Jul 2019 12:39:52: 7000000 INFO @ Fri, 05 Jul 2019 12:39:53: 7000000 INFO @ Fri, 05 Jul 2019 12:39:55: 9000000 INFO @ Fri, 05 Jul 2019 12:40:00: 8000000 INFO @ Fri, 05 Jul 2019 12:40:01: 8000000 INFO @ Fri, 05 Jul 2019 12:40:02: 10000000 INFO @ Fri, 05 Jul 2019 12:40:08: 9000000 INFO @ Fri, 05 Jul 2019 12:40:09: 11000000 INFO @ Fri, 05 Jul 2019 12:40:09: 9000000 INFO @ Fri, 05 Jul 2019 12:40:16: 12000000 INFO @ Fri, 05 Jul 2019 12:40:16: 10000000 INFO @ Fri, 05 Jul 2019 12:40:18: 10000000 INFO @ Fri, 05 Jul 2019 12:40:23: 13000000 INFO @ Fri, 05 Jul 2019 12:40:25: 11000000 INFO @ Fri, 05 Jul 2019 12:40:26: 11000000 INFO @ Fri, 05 Jul 2019 12:40:30: 14000000 INFO @ Fri, 05 Jul 2019 12:40:33: 12000000 INFO @ Fri, 05 Jul 2019 12:40:34: 12000000 INFO @ Fri, 05 Jul 2019 12:40:37: 15000000 INFO @ Fri, 05 Jul 2019 12:40:41: 13000000 INFO @ Fri, 05 Jul 2019 12:40:42: 13000000 INFO @ Fri, 05 Jul 2019 12:40:44: 16000000 INFO @ Fri, 05 Jul 2019 12:40:50: 14000000 INFO @ Fri, 05 Jul 2019 12:40:51: 14000000 INFO @ Fri, 05 Jul 2019 12:40:51: 17000000 INFO @ Fri, 05 Jul 2019 12:40:58: 18000000 INFO @ Fri, 05 Jul 2019 12:40:58: 15000000 INFO @ Fri, 05 Jul 2019 12:41:00: 15000000 INFO @ Fri, 05 Jul 2019 12:41:05: 19000000 INFO @ Fri, 05 Jul 2019 12:41:07: 16000000 INFO @ Fri, 05 Jul 2019 12:41:08: 16000000 INFO @ Fri, 05 Jul 2019 12:41:12: 20000000 INFO @ Fri, 05 Jul 2019 12:41:15: 17000000 INFO @ Fri, 05 Jul 2019 12:41:16: 17000000 INFO @ Fri, 05 Jul 2019 12:41:19: 21000000 INFO @ Fri, 05 Jul 2019 12:41:24: 18000000 INFO @ Fri, 05 Jul 2019 12:41:25: 18000000 INFO @ Fri, 05 Jul 2019 12:41:26: 22000000 INFO @ Fri, 05 Jul 2019 12:41:32: 19000000 INFO @ Fri, 05 Jul 2019 12:41:33: 19000000 INFO @ Fri, 05 Jul 2019 12:41:33: 23000000 INFO @ Fri, 05 Jul 2019 12:41:40: 20000000 INFO @ Fri, 05 Jul 2019 12:41:41: 24000000 INFO @ Fri, 05 Jul 2019 12:41:41: 20000000 INFO @ Fri, 05 Jul 2019 12:41:48: 25000000 INFO @ Fri, 05 Jul 2019 12:41:48: 21000000 INFO @ Fri, 05 Jul 2019 12:41:50: 21000000 INFO @ Fri, 05 Jul 2019 12:41:51: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:41:51: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:41:51: #1 total tags in treatment: 25385354 INFO @ Fri, 05 Jul 2019 12:41:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:41:51: #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 12:41:52: #1 tags after filtering in treatment: 25385182 INFO @ Fri, 05 Jul 2019 12:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:41:52: #1 finished! INFO @ Fri, 05 Jul 2019 12:41:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:41:57: 22000000 INFO @ Fri, 05 Jul 2019 12:41:58: 22000000 INFO @ Fri, 05 Jul 2019 12:41:59: #2 number of paired peaks: 108071 INFO @ Fri, 05 Jul 2019 12:41:59: start model_add_line... INFO @ Fri, 05 Jul 2019 12:41:59: start X-correlation... INFO @ Fri, 05 Jul 2019 12:41:59: end of X-cor INFO @ Fri, 05 Jul 2019 12:41:59: #2 finished! INFO @ Fri, 05 Jul 2019 12:41:59: #2 predicted fragment length is 234 bps INFO @ Fri, 05 Jul 2019 12:41:59: #2 alternative fragment length(s) may be 234 bps INFO @ Fri, 05 Jul 2019 12:41:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.05_model.r INFO @ Fri, 05 Jul 2019 12:41:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:42:05: 23000000 INFO @ Fri, 05 Jul 2019 12:42:06: 23000000 INFO @ Fri, 05 Jul 2019 12:42:13: 24000000 INFO @ Fri, 05 Jul 2019 12:42:14: 24000000 INFO @ Fri, 05 Jul 2019 12:42:22: 25000000 INFO @ Fri, 05 Jul 2019 12:42:23: 25000000 INFO @ Fri, 05 Jul 2019 12:42:25: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:42:25: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:42:25: #1 total tags in treatment: 25385354 INFO @ Fri, 05 Jul 2019 12:42:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:42:25: #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 12:42:26: #1 tags after filtering in treatment: 25385182 INFO @ Fri, 05 Jul 2019 12:42:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:42:26: #1 finished! INFO @ Fri, 05 Jul 2019 12:42:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:42:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:42:27: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:42:27: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:42:27: #1 total tags in treatment: 25385354 INFO @ Fri, 05 Jul 2019 12:42:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:42:27: #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 12:42:27: #1 tags after filtering in treatment: 25385182 INFO @ Fri, 05 Jul 2019 12:42:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:42:27: #1 finished! INFO @ Fri, 05 Jul 2019 12:42:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:42:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:42:33: #2 number of paired peaks: 108071 INFO @ Fri, 05 Jul 2019 12:42:33: start model_add_line... INFO @ Fri, 05 Jul 2019 12:42:34: start X-correlation... INFO @ Fri, 05 Jul 2019 12:42:34: end of X-cor INFO @ Fri, 05 Jul 2019 12:42:34: #2 finished! INFO @ Fri, 05 Jul 2019 12:42:34: #2 predicted fragment length is 234 bps INFO @ Fri, 05 Jul 2019 12:42:34: #2 alternative fragment length(s) may be 234 bps INFO @ Fri, 05 Jul 2019 12:42:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.10_model.r INFO @ Fri, 05 Jul 2019 12:42:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:42:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:42:34: #2 number of paired peaks: 108071 INFO @ Fri, 05 Jul 2019 12:42:34: start model_add_line... INFO @ Fri, 05 Jul 2019 12:42:35: start X-correlation... INFO @ Fri, 05 Jul 2019 12:42:35: end of X-cor INFO @ Fri, 05 Jul 2019 12:42:35: #2 finished! INFO @ Fri, 05 Jul 2019 12:42:35: #2 predicted fragment length is 234 bps INFO @ Fri, 05 Jul 2019 12:42:35: #2 alternative fragment length(s) may be 234 bps INFO @ Fri, 05 Jul 2019 12:42:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.20_model.r INFO @ Fri, 05 Jul 2019 12:42:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:42:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:43:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:43:57: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:43:58: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:44:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:44:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:44:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.05_summits.bed INFO @ Fri, 05 Jul 2019 12:44:09: Done! pass1 - making usageList (114 chroms): 11 millis pass2 - checking and writing primary data (33415 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:44:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:44:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:44:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.20_summits.bed INFO @ Fri, 05 Jul 2019 12:44:41: Done! pass1 - making usageList (49 chroms): 5 millis pass2 - checking and writing primary data (9236 records, 4 fields): 16 millis INFO @ Fri, 05 Jul 2019 12:44:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:44:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:44:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX531051/ERX531051.10_summits.bed INFO @ Fri, 05 Jul 2019 12:44:43: Done! pass1 - making usageList (93 chroms): 4 millis pass2 - checking and writing primary data (20081 records, 4 fields): 42 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。