Job ID = 2002164 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,895,798 reads read : 21,895,798 reads written : 21,895,798 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR458089.sra.cache’: 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: 00:08:27 21895798 reads; of these: 21895798 (100.00%) were unpaired; of these: 734640 (3.36%) aligned 0 times 15525977 (70.91%) aligned exactly 1 time 5635181 (25.74%) aligned >1 times 96.64% overall alignment rate Time searching: 00:08:30 Overall time: 00:08:30 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] 1604192 / 21161158 = 0.0758 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 10:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.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 10:56:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:56:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.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 10:56:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:56:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:56:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.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 10:56:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:56:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:56:21: 1000000 INFO @ Fri, 05 Jul 2019 10:56:24: 1000000 INFO @ Fri, 05 Jul 2019 10:56:25: 1000000 INFO @ Fri, 05 Jul 2019 10:56:28: 2000000 INFO @ Fri, 05 Jul 2019 10:56:31: 2000000 INFO @ Fri, 05 Jul 2019 10:56:32: 2000000 INFO @ Fri, 05 Jul 2019 10:56:35: 3000000 INFO @ Fri, 05 Jul 2019 10:56:39: 3000000 INFO @ Fri, 05 Jul 2019 10:56:40: 3000000 INFO @ Fri, 05 Jul 2019 10:56:42: 4000000 INFO @ Fri, 05 Jul 2019 10:56:47: 4000000 INFO @ Fri, 05 Jul 2019 10:56:47: 4000000 INFO @ Fri, 05 Jul 2019 10:56:48: 5000000 INFO @ Fri, 05 Jul 2019 10:56:54: 5000000 INFO @ Fri, 05 Jul 2019 10:56:55: 6000000 INFO @ Fri, 05 Jul 2019 10:56:55: 5000000 INFO @ Fri, 05 Jul 2019 10:57:01: 6000000 INFO @ Fri, 05 Jul 2019 10:57:02: 7000000 INFO @ Fri, 05 Jul 2019 10:57:03: 6000000 INFO @ Fri, 05 Jul 2019 10:57:08: 7000000 INFO @ Fri, 05 Jul 2019 10:57:08: 8000000 INFO @ Fri, 05 Jul 2019 10:57:11: 7000000 INFO @ Fri, 05 Jul 2019 10:57:14: 8000000 INFO @ Fri, 05 Jul 2019 10:57:15: 9000000 INFO @ Fri, 05 Jul 2019 10:57:18: 8000000 INFO @ Fri, 05 Jul 2019 10:57:21: 9000000 INFO @ Fri, 05 Jul 2019 10:57:21: 10000000 INFO @ Fri, 05 Jul 2019 10:57:26: 9000000 INFO @ Fri, 05 Jul 2019 10:57:28: 11000000 INFO @ Fri, 05 Jul 2019 10:57:28: 10000000 INFO @ Fri, 05 Jul 2019 10:57:33: 10000000 INFO @ Fri, 05 Jul 2019 10:57:35: 12000000 INFO @ Fri, 05 Jul 2019 10:57:35: 11000000 INFO @ Fri, 05 Jul 2019 10:57:41: 11000000 INFO @ Fri, 05 Jul 2019 10:57:41: 13000000 INFO @ Fri, 05 Jul 2019 10:57:42: 12000000 INFO @ Fri, 05 Jul 2019 10:57:48: 14000000 INFO @ Fri, 05 Jul 2019 10:57:49: 12000000 INFO @ Fri, 05 Jul 2019 10:57:49: 13000000 INFO @ Fri, 05 Jul 2019 10:57:54: 15000000 INFO @ Fri, 05 Jul 2019 10:57:56: 14000000 INFO @ Fri, 05 Jul 2019 10:57:56: 13000000 INFO @ Fri, 05 Jul 2019 10:58:01: 16000000 INFO @ Fri, 05 Jul 2019 10:58:03: 15000000 INFO @ Fri, 05 Jul 2019 10:58:04: 14000000 INFO @ Fri, 05 Jul 2019 10:58:08: 17000000 INFO @ Fri, 05 Jul 2019 10:58:10: 16000000 INFO @ Fri, 05 Jul 2019 10:58:11: 15000000 INFO @ Fri, 05 Jul 2019 10:58:14: 18000000 INFO @ Fri, 05 Jul 2019 10:58:17: 17000000 INFO @ Fri, 05 Jul 2019 10:58:19: 16000000 INFO @ Fri, 05 Jul 2019 10:58:21: 19000000 INFO @ Fri, 05 Jul 2019 10:58:24: 18000000 INFO @ Fri, 05 Jul 2019 10:58:25: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:58:25: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:58:25: #1 total tags in treatment: 19556966 INFO @ Fri, 05 Jul 2019 10:58:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:58:25: #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 10:58:26: #1 tags after filtering in treatment: 19556820 INFO @ Fri, 05 Jul 2019 10:58:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:58:26: #1 finished! INFO @ Fri, 05 Jul 2019 10:58:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:58:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:58:27: 17000000 INFO @ Fri, 05 Jul 2019 10:58:29: #2 number of paired peaks: 37049 INFO @ Fri, 05 Jul 2019 10:58:29: start model_add_line... INFO @ Fri, 05 Jul 2019 10:58:29: start X-correlation... INFO @ Fri, 05 Jul 2019 10:58:29: end of X-cor INFO @ Fri, 05 Jul 2019 10:58:29: #2 finished! INFO @ Fri, 05 Jul 2019 10:58:29: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 10:58:29: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 10:58:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.05_model.r INFO @ Fri, 05 Jul 2019 10:58:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:58:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:58:31: 19000000 INFO @ Fri, 05 Jul 2019 10:58:34: 18000000 INFO @ Fri, 05 Jul 2019 10:58:35: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:58:35: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:58:35: #1 total tags in treatment: 19556966 INFO @ Fri, 05 Jul 2019 10:58:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:58:35: #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 10:58:35: #1 tags after filtering in treatment: 19556820 INFO @ Fri, 05 Jul 2019 10:58:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:58:35: #1 finished! INFO @ Fri, 05 Jul 2019 10:58:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:58:39: #2 number of paired peaks: 37049 INFO @ Fri, 05 Jul 2019 10:58:39: start model_add_line... INFO @ Fri, 05 Jul 2019 10:58:39: start X-correlation... INFO @ Fri, 05 Jul 2019 10:58:39: end of X-cor INFO @ Fri, 05 Jul 2019 10:58:39: #2 finished! INFO @ Fri, 05 Jul 2019 10:58:39: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 10:58:39: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 10:58:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.20_model.r INFO @ Fri, 05 Jul 2019 10:58:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:58:42: 19000000 INFO @ Fri, 05 Jul 2019 10:58:46: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:58:46: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:58:46: #1 total tags in treatment: 19556966 INFO @ Fri, 05 Jul 2019 10:58:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:58:46: #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 10:58:47: #1 tags after filtering in treatment: 19556820 INFO @ Fri, 05 Jul 2019 10:58:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:58:47: #1 finished! INFO @ Fri, 05 Jul 2019 10:58:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:58:51: #2 number of paired peaks: 37049 INFO @ Fri, 05 Jul 2019 10:58:51: start model_add_line... INFO @ Fri, 05 Jul 2019 10:58:51: start X-correlation... INFO @ Fri, 05 Jul 2019 10:58:51: end of X-cor INFO @ Fri, 05 Jul 2019 10:58:51: #2 finished! INFO @ Fri, 05 Jul 2019 10:58:51: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 10:58:51: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 10:58:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.10_model.r INFO @ Fri, 05 Jul 2019 10:58:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:58:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:59:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:59:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:59:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:00:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:00:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.05_summits.bed INFO @ Fri, 05 Jul 2019 11:00:07: Done! pass1 - making usageList (104 chroms): 7 millis pass2 - checking and writing primary data (33193 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:00:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:00:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:00:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.20_summits.bed INFO @ Fri, 05 Jul 2019 11:00:14: Done! pass1 - making usageList (53 chroms): 4 millis pass2 - checking and writing primary data (13774 records, 4 fields): 160 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:00:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:00:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190367/ERX190367.10_summits.bed INFO @ Fri, 05 Jul 2019 11:00:26: Done! pass1 - making usageList (78 chroms): 5 millis pass2 - checking and writing primary data (22907 records, 4 fields): 31 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。