Job ID = 2001150 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,494,065 reads read : 20,494,065 reads written : 20,494,065 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: 00:04:45 20494065 reads; of these: 20494065 (100.00%) were unpaired; of these: 639943 (3.12%) aligned 0 times 17912354 (87.40%) aligned exactly 1 time 1941768 (9.47%) aligned >1 times 96.88% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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] 8802988 / 19854122 = 0.4434 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 03:54:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.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 03:54:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:54:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:54:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.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 03:54:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:54:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:54:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.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 03:54:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:54:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:54:50: 1000000 INFO @ Fri, 05 Jul 2019 03:54:50: 1000000 INFO @ Fri, 05 Jul 2019 03:54:51: 1000000 INFO @ Fri, 05 Jul 2019 03:54:58: 2000000 INFO @ Fri, 05 Jul 2019 03:54:59: 2000000 INFO @ Fri, 05 Jul 2019 03:55:00: 2000000 INFO @ Fri, 05 Jul 2019 03:55:06: 3000000 INFO @ Fri, 05 Jul 2019 03:55:08: 3000000 INFO @ Fri, 05 Jul 2019 03:55:09: 3000000 INFO @ Fri, 05 Jul 2019 03:55:16: 4000000 INFO @ Fri, 05 Jul 2019 03:55:17: 4000000 INFO @ Fri, 05 Jul 2019 03:55:19: 4000000 INFO @ Fri, 05 Jul 2019 03:55:25: 5000000 INFO @ Fri, 05 Jul 2019 03:55:27: 5000000 INFO @ Fri, 05 Jul 2019 03:55:28: 5000000 INFO @ Fri, 05 Jul 2019 03:55:35: 6000000 INFO @ Fri, 05 Jul 2019 03:55:37: 6000000 INFO @ Fri, 05 Jul 2019 03:55:38: 6000000 INFO @ Fri, 05 Jul 2019 03:55:43: 7000000 INFO @ Fri, 05 Jul 2019 03:55:46: 7000000 INFO @ Fri, 05 Jul 2019 03:55:48: 7000000 INFO @ Fri, 05 Jul 2019 03:55:51: 8000000 INFO @ Fri, 05 Jul 2019 03:55:54: 8000000 INFO @ Fri, 05 Jul 2019 03:55:56: 8000000 INFO @ Fri, 05 Jul 2019 03:55:58: 9000000 INFO @ Fri, 05 Jul 2019 03:56:03: 9000000 INFO @ Fri, 05 Jul 2019 03:56:05: 9000000 INFO @ Fri, 05 Jul 2019 03:56:06: 10000000 INFO @ Fri, 05 Jul 2019 03:56:11: 10000000 INFO @ Fri, 05 Jul 2019 03:56:13: 10000000 INFO @ Fri, 05 Jul 2019 03:56:14: 11000000 INFO @ Fri, 05 Jul 2019 03:56:14: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:56:14: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:56:14: #1 total tags in treatment: 11051134 INFO @ Fri, 05 Jul 2019 03:56:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:56:14: #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 03:56:14: #1 tags after filtering in treatment: 11050858 INFO @ Fri, 05 Jul 2019 03:56:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:56:14: #1 finished! INFO @ Fri, 05 Jul 2019 03:56:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:56:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:56:17: #2 number of paired peaks: 39449 INFO @ Fri, 05 Jul 2019 03:56:17: start model_add_line... INFO @ Fri, 05 Jul 2019 03:56:18: start X-correlation... INFO @ Fri, 05 Jul 2019 03:56:18: end of X-cor INFO @ Fri, 05 Jul 2019 03:56:18: #2 finished! INFO @ Fri, 05 Jul 2019 03:56:18: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 03:56:18: #2 alternative fragment length(s) may be 4,131 bps INFO @ Fri, 05 Jul 2019 03:56:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.05_model.r INFO @ Fri, 05 Jul 2019 03:56:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:56:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:56:19: 11000000 INFO @ Fri, 05 Jul 2019 03:56:19: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:56:19: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:56:19: #1 total tags in treatment: 11051134 INFO @ Fri, 05 Jul 2019 03:56:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:56:19: #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 03:56:20: #1 tags after filtering in treatment: 11050858 INFO @ Fri, 05 Jul 2019 03:56:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:56:20: #1 finished! INFO @ Fri, 05 Jul 2019 03:56:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:56:21: 11000000 INFO @ Fri, 05 Jul 2019 03:56:21: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:56:21: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:56:21: #1 total tags in treatment: 11051134 INFO @ Fri, 05 Jul 2019 03:56:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:56:21: #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 03:56:22: #1 tags after filtering in treatment: 11050858 INFO @ Fri, 05 Jul 2019 03:56:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:56:22: #1 finished! INFO @ Fri, 05 Jul 2019 03:56:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:56:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:56:23: #2 number of paired peaks: 39449 INFO @ Fri, 05 Jul 2019 03:56:23: start model_add_line... INFO @ Fri, 05 Jul 2019 03:56:23: start X-correlation... INFO @ Fri, 05 Jul 2019 03:56:23: end of X-cor INFO @ Fri, 05 Jul 2019 03:56:23: #2 finished! INFO @ Fri, 05 Jul 2019 03:56:23: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 03:56:23: #2 alternative fragment length(s) may be 4,131 bps INFO @ Fri, 05 Jul 2019 03:56:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.10_model.r INFO @ Fri, 05 Jul 2019 03:56:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:56:25: #2 number of paired peaks: 39449 INFO @ Fri, 05 Jul 2019 03:56:25: start model_add_line... INFO @ Fri, 05 Jul 2019 03:56:25: start X-correlation... INFO @ Fri, 05 Jul 2019 03:56:25: end of X-cor INFO @ Fri, 05 Jul 2019 03:56:25: #2 finished! INFO @ Fri, 05 Jul 2019 03:56:25: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 03:56:25: #2 alternative fragment length(s) may be 4,131 bps INFO @ Fri, 05 Jul 2019 03:56:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.20_model.r INFO @ Fri, 05 Jul 2019 03:56:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:56:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:56:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:56:57: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:56:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 03:57:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.05_peaks.xls INFO @ Fri, 05 Jul 2019 03:57:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:57:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.05_summits.bed INFO @ Fri, 05 Jul 2019 03:57:14: Done! pass1 - making usageList (128 chroms): 9 millis pass2 - checking and writing primary data (41499 records, 4 fields): 62 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 03:57:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.10_peaks.xls INFO @ Fri, 05 Jul 2019 03:57:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:57:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.10_summits.bed INFO @ Fri, 05 Jul 2019 03:57:16: Done! pass1 - making usageList (104 chroms): 7 millis pass2 - checking and writing primary data (32925 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 03:57:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.20_peaks.xls INFO @ Fri, 05 Jul 2019 03:57:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 03:57:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101840/ERX101840.20_summits.bed INFO @ Fri, 05 Jul 2019 03:57:18: Done! pass1 - making usageList (78 chroms): 5 millis pass2 - checking and writing primary data (23014 records, 4 fields): 38 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。