Job ID = 2001598 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,186,673 reads read : 25,186,673 reads written : 25,186,673 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: 00:10:04 25186673 reads; of these: 25186673 (100.00%) were unpaired; of these: 535357 (2.13%) aligned 0 times 18754197 (74.46%) aligned exactly 1 time 5897119 (23.41%) aligned >1 times 97.87% overall alignment rate Time searching: 00:10:05 Overall time: 00:10:05 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] 1543381 / 24651316 = 0.0626 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 06:02:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.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 06:02:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:02:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:02:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.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 06:02:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:02:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:02:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.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 06:02:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:02:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:02:58: 1000000 INFO @ Fri, 05 Jul 2019 06:02:59: 1000000 INFO @ Fri, 05 Jul 2019 06:03:01: 1000000 INFO @ Fri, 05 Jul 2019 06:03:07: 2000000 INFO @ Fri, 05 Jul 2019 06:03:08: 2000000 INFO @ Fri, 05 Jul 2019 06:03:10: 2000000 INFO @ Fri, 05 Jul 2019 06:03:16: 3000000 INFO @ Fri, 05 Jul 2019 06:03:17: 3000000 INFO @ Fri, 05 Jul 2019 06:03:20: 3000000 INFO @ Fri, 05 Jul 2019 06:03:25: 4000000 INFO @ Fri, 05 Jul 2019 06:03:26: 4000000 INFO @ Fri, 05 Jul 2019 06:03:29: 4000000 INFO @ Fri, 05 Jul 2019 06:03:33: 5000000 INFO @ Fri, 05 Jul 2019 06:03:34: 5000000 INFO @ Fri, 05 Jul 2019 06:03:39: 5000000 INFO @ Fri, 05 Jul 2019 06:03:42: 6000000 INFO @ Fri, 05 Jul 2019 06:03:43: 6000000 INFO @ Fri, 05 Jul 2019 06:03:48: 6000000 INFO @ Fri, 05 Jul 2019 06:03:51: 7000000 INFO @ Fri, 05 Jul 2019 06:03:52: 7000000 INFO @ Fri, 05 Jul 2019 06:03:57: 7000000 INFO @ Fri, 05 Jul 2019 06:04:00: 8000000 INFO @ Fri, 05 Jul 2019 06:04:01: 8000000 INFO @ Fri, 05 Jul 2019 06:04:07: 8000000 INFO @ Fri, 05 Jul 2019 06:04:09: 9000000 INFO @ Fri, 05 Jul 2019 06:04:10: 9000000 INFO @ Fri, 05 Jul 2019 06:04:16: 9000000 INFO @ Fri, 05 Jul 2019 06:04:17: 10000000 INFO @ Fri, 05 Jul 2019 06:04:18: 10000000 INFO @ Fri, 05 Jul 2019 06:04:25: 10000000 INFO @ Fri, 05 Jul 2019 06:04:26: 11000000 INFO @ Fri, 05 Jul 2019 06:04:27: 11000000 INFO @ Fri, 05 Jul 2019 06:04:35: 11000000 INFO @ Fri, 05 Jul 2019 06:04:35: 12000000 INFO @ Fri, 05 Jul 2019 06:04:36: 12000000 INFO @ Fri, 05 Jul 2019 06:04:44: 13000000 INFO @ Fri, 05 Jul 2019 06:04:44: 12000000 INFO @ Fri, 05 Jul 2019 06:04:45: 13000000 INFO @ Fri, 05 Jul 2019 06:04:53: 14000000 INFO @ Fri, 05 Jul 2019 06:04:54: 13000000 INFO @ Fri, 05 Jul 2019 06:04:54: 14000000 INFO @ Fri, 05 Jul 2019 06:05:02: 15000000 INFO @ Fri, 05 Jul 2019 06:05:03: 15000000 INFO @ Fri, 05 Jul 2019 06:05:03: 14000000 INFO @ Fri, 05 Jul 2019 06:05:10: 16000000 INFO @ Fri, 05 Jul 2019 06:05:11: 16000000 INFO @ Fri, 05 Jul 2019 06:05:13: 15000000 INFO @ Fri, 05 Jul 2019 06:05:19: 17000000 INFO @ Fri, 05 Jul 2019 06:05:20: 17000000 INFO @ Fri, 05 Jul 2019 06:05:22: 16000000 INFO @ Fri, 05 Jul 2019 06:05:28: 18000000 INFO @ Fri, 05 Jul 2019 06:05:29: 18000000 INFO @ Fri, 05 Jul 2019 06:05:31: 17000000 INFO @ Fri, 05 Jul 2019 06:05:36: 19000000 INFO @ Fri, 05 Jul 2019 06:05:37: 19000000 INFO @ Fri, 05 Jul 2019 06:05:40: 18000000 INFO @ Fri, 05 Jul 2019 06:05:45: 20000000 INFO @ Fri, 05 Jul 2019 06:05:46: 20000000 INFO @ Fri, 05 Jul 2019 06:05:50: 19000000 INFO @ Fri, 05 Jul 2019 06:05:54: 21000000 INFO @ Fri, 05 Jul 2019 06:05:54: 21000000 INFO @ Fri, 05 Jul 2019 06:05:59: 20000000 INFO @ Fri, 05 Jul 2019 06:06:02: 22000000 INFO @ Fri, 05 Jul 2019 06:06:03: 22000000 INFO @ Fri, 05 Jul 2019 06:06:08: 21000000 INFO @ Fri, 05 Jul 2019 06:06:11: 23000000 INFO @ Fri, 05 Jul 2019 06:06:11: 23000000 INFO @ Fri, 05 Jul 2019 06:06:12: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:06:12: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:06:12: #1 total tags in treatment: 23107935 INFO @ Fri, 05 Jul 2019 06:06:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:06:12: #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 06:06:12: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:06:12: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:06:12: #1 total tags in treatment: 23107935 INFO @ Fri, 05 Jul 2019 06:06:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:06:12: #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 06:06:13: #1 tags after filtering in treatment: 23107775 INFO @ Fri, 05 Jul 2019 06:06:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:06:13: #1 finished! INFO @ Fri, 05 Jul 2019 06:06:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:06:13: #1 tags after filtering in treatment: 23107775 INFO @ Fri, 05 Jul 2019 06:06:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:06:13: #1 finished! INFO @ Fri, 05 Jul 2019 06:06:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:06:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:06:16: 22000000 INFO @ Fri, 05 Jul 2019 06:06:17: #2 number of paired peaks: 56421 INFO @ Fri, 05 Jul 2019 06:06:17: start model_add_line... INFO @ Fri, 05 Jul 2019 06:06:18: start X-correlation... INFO @ Fri, 05 Jul 2019 06:06:18: end of X-cor INFO @ Fri, 05 Jul 2019 06:06:18: #2 finished! INFO @ Fri, 05 Jul 2019 06:06:18: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 06:06:18: #2 alternative fragment length(s) may be 2,130,497 bps INFO @ Fri, 05 Jul 2019 06:06:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.05_model.r INFO @ Fri, 05 Jul 2019 06:06:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:06:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:06:18: #2 number of paired peaks: 56421 INFO @ Fri, 05 Jul 2019 06:06:18: start model_add_line... INFO @ Fri, 05 Jul 2019 06:06:18: start X-correlation... INFO @ Fri, 05 Jul 2019 06:06:18: end of X-cor INFO @ Fri, 05 Jul 2019 06:06:18: #2 finished! INFO @ Fri, 05 Jul 2019 06:06:18: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 06:06:18: #2 alternative fragment length(s) may be 2,130,497 bps INFO @ Fri, 05 Jul 2019 06:06:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.10_model.r INFO @ Fri, 05 Jul 2019 06:06:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:06:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:06:26: 23000000 INFO @ Fri, 05 Jul 2019 06:06:27: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:06:27: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:06:27: #1 total tags in treatment: 23107935 INFO @ Fri, 05 Jul 2019 06:06:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:06:27: #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 06:06:27: #1 tags after filtering in treatment: 23107775 INFO @ Fri, 05 Jul 2019 06:06:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:06:27: #1 finished! INFO @ Fri, 05 Jul 2019 06:06:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:06:32: #2 number of paired peaks: 56421 INFO @ Fri, 05 Jul 2019 06:06:32: start model_add_line... INFO @ Fri, 05 Jul 2019 06:06:32: start X-correlation... INFO @ Fri, 05 Jul 2019 06:06:32: end of X-cor INFO @ Fri, 05 Jul 2019 06:06:32: #2 finished! INFO @ Fri, 05 Jul 2019 06:06:32: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 06:06:32: #2 alternative fragment length(s) may be 2,130,497 bps INFO @ Fri, 05 Jul 2019 06:06:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.20_model.r INFO @ Fri, 05 Jul 2019 06:06:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:06:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:07:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:07:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:07:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:08:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:08:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:08:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.05_summits.bed INFO @ Fri, 05 Jul 2019 06:08:11: Done! INFO @ Fri, 05 Jul 2019 06:08:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:08:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:08:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.10_summits.bed INFO @ Fri, 05 Jul 2019 06:08:11: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (879 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (60 chroms): 2 millis pass2 - checking and writing primary data (4182 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:08:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:08:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:08:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101926/ERX101926.20_summits.bed INFO @ Fri, 05 Jul 2019 06:08:26: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (98 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。