Job ID = 2002161 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,322,423 reads read : 20,322,423 reads written : 20,322,423 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR458088.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: 00:00:04 Time loading forward index: 00:00:06 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:36 20322423 reads; of these: 20322423 (100.00%) were unpaired; of these: 5125092 (25.22%) aligned 0 times 11903974 (58.58%) aligned exactly 1 time 3293357 (16.21%) aligned >1 times 74.78% overall alignment rate Time searching: 00:07:46 Overall time: 00:07:46 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] 2388688 / 15197331 = 0.1572 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 10:53:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.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 10:53:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:53:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:53:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.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 10:53:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:53:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.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 10:53:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:53:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:53:16: 1000000 INFO @ Fri, 05 Jul 2019 10:53:18: 1000000 INFO @ Fri, 05 Jul 2019 10:53:18: 1000000 INFO @ Fri, 05 Jul 2019 10:53:23: 2000000 INFO @ Fri, 05 Jul 2019 10:53:26: 2000000 INFO @ Fri, 05 Jul 2019 10:53:27: 2000000 INFO @ Fri, 05 Jul 2019 10:53:29: 3000000 INFO @ Fri, 05 Jul 2019 10:53:33: 3000000 INFO @ Fri, 05 Jul 2019 10:53:35: 3000000 INFO @ Fri, 05 Jul 2019 10:53:36: 4000000 INFO @ Fri, 05 Jul 2019 10:53:40: 4000000 INFO @ Fri, 05 Jul 2019 10:53:42: 5000000 INFO @ Fri, 05 Jul 2019 10:53:43: 4000000 INFO @ Fri, 05 Jul 2019 10:53:47: 5000000 INFO @ Fri, 05 Jul 2019 10:53:49: 6000000 INFO @ Fri, 05 Jul 2019 10:53:50: 5000000 INFO @ Fri, 05 Jul 2019 10:53:54: 6000000 INFO @ Fri, 05 Jul 2019 10:53:55: 7000000 INFO @ Fri, 05 Jul 2019 10:53:58: 6000000 INFO @ Fri, 05 Jul 2019 10:54:01: 7000000 INFO @ Fri, 05 Jul 2019 10:54:02: 8000000 INFO @ Fri, 05 Jul 2019 10:54:06: 7000000 INFO @ Fri, 05 Jul 2019 10:54:08: 8000000 INFO @ Fri, 05 Jul 2019 10:54:08: 9000000 INFO @ Fri, 05 Jul 2019 10:54:14: 8000000 INFO @ Fri, 05 Jul 2019 10:54:14: 9000000 INFO @ Fri, 05 Jul 2019 10:54:15: 10000000 INFO @ Fri, 05 Jul 2019 10:54:21: 11000000 INFO @ Fri, 05 Jul 2019 10:54:21: 9000000 INFO @ Fri, 05 Jul 2019 10:54:21: 10000000 INFO @ Fri, 05 Jul 2019 10:54:28: 12000000 INFO @ Fri, 05 Jul 2019 10:54:28: 11000000 INFO @ Fri, 05 Jul 2019 10:54:29: 10000000 INFO @ Fri, 05 Jul 2019 10:54:35: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 10:54:35: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 10:54:35: #1 total tags in treatment: 12808643 INFO @ Fri, 05 Jul 2019 10:54:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:54:35: #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 10:54:35: #1 tags after filtering in treatment: 12808442 INFO @ Fri, 05 Jul 2019 10:54:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:54:35: #1 finished! INFO @ Fri, 05 Jul 2019 10:54:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:54:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:54:36: 12000000 INFO @ Fri, 05 Jul 2019 10:54:37: 11000000 INFO @ Fri, 05 Jul 2019 10:54:38: #2 number of paired peaks: 54460 INFO @ Fri, 05 Jul 2019 10:54:38: start model_add_line... INFO @ Fri, 05 Jul 2019 10:54:39: start X-correlation... INFO @ Fri, 05 Jul 2019 10:54:39: end of X-cor INFO @ Fri, 05 Jul 2019 10:54:39: #2 finished! INFO @ Fri, 05 Jul 2019 10:54:39: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 10:54:39: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 10:54:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.10_model.r INFO @ Fri, 05 Jul 2019 10:54:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:54:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:54:42: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 10:54:42: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 10:54:42: #1 total tags in treatment: 12808643 INFO @ Fri, 05 Jul 2019 10:54:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:54:42: #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 10:54:42: #1 tags after filtering in treatment: 12808442 INFO @ Fri, 05 Jul 2019 10:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:54:42: #1 finished! INFO @ Fri, 05 Jul 2019 10:54:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:54:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:54:45: 12000000 INFO @ Fri, 05 Jul 2019 10:54:46: #2 number of paired peaks: 54460 INFO @ Fri, 05 Jul 2019 10:54:46: start model_add_line... INFO @ Fri, 05 Jul 2019 10:54:46: start X-correlation... INFO @ Fri, 05 Jul 2019 10:54:46: end of X-cor INFO @ Fri, 05 Jul 2019 10:54:46: #2 finished! INFO @ Fri, 05 Jul 2019 10:54:46: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 10:54:46: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 10:54:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.20_model.r INFO @ Fri, 05 Jul 2019 10:54:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:54:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:54:51: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 10:54:51: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 10:54:51: #1 total tags in treatment: 12808643 INFO @ Fri, 05 Jul 2019 10:54:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:54:51: #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 10:54:51: #1 tags after filtering in treatment: 12808442 INFO @ Fri, 05 Jul 2019 10:54:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:54:51: #1 finished! INFO @ Fri, 05 Jul 2019 10:54:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:54:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:54:55: #2 number of paired peaks: 54460 INFO @ Fri, 05 Jul 2019 10:54:55: start model_add_line... INFO @ Fri, 05 Jul 2019 10:54:55: start X-correlation... INFO @ Fri, 05 Jul 2019 10:54:55: end of X-cor INFO @ Fri, 05 Jul 2019 10:54:55: #2 finished! INFO @ Fri, 05 Jul 2019 10:54:55: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 10:54:55: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 05 Jul 2019 10:54:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.05_model.r INFO @ Fri, 05 Jul 2019 10:54:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:55:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:55:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:55:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:55:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:55:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:55:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.10_summits.bed INFO @ Fri, 05 Jul 2019 10:55:42: Done! pass1 - making usageList (122 chroms): 10 millis pass2 - checking and writing primary data (28537 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:55:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:55:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:55:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.20_summits.bed INFO @ Fri, 05 Jul 2019 10:55:48: Done! pass1 - making usageList (97 chroms): 7 millis pass2 - checking and writing primary data (16961 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:55:58: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:55:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:55:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX190365/ERX190365.05_summits.bed INFO @ Fri, 05 Jul 2019 10:55:59: Done! pass1 - making usageList (147 chroms): 8 millis pass2 - checking and writing primary data (42019 records, 4 fields): 59 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。