Job ID = 2001662 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,304,621 reads read : 27,304,621 reads written : 27,304,621 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: 00:00:01 Multiseed full-index search: 00:05:42 27304621 reads; of these: 27304621 (100.00%) were unpaired; of these: 650858 (2.38%) aligned 0 times 24041384 (88.05%) aligned exactly 1 time 2612379 (9.57%) aligned >1 times 97.62% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 12097522 / 26653763 = 0.4539 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 07:51:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.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 07:51:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:51:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:51:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.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 07:51:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:51:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:51:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.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 07:51:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 07:51:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 07:51:55: 1000000 INFO @ Fri, 05 Jul 2019 07:51:55: 1000000 INFO @ Fri, 05 Jul 2019 07:51:57: 1000000 INFO @ Fri, 05 Jul 2019 07:52:01: 2000000 INFO @ Fri, 05 Jul 2019 07:52:01: 2000000 INFO @ Fri, 05 Jul 2019 07:52:04: 2000000 INFO @ Fri, 05 Jul 2019 07:52:08: 3000000 INFO @ Fri, 05 Jul 2019 07:52:08: 3000000 INFO @ Fri, 05 Jul 2019 07:52:12: 3000000 INFO @ Fri, 05 Jul 2019 07:52:14: 4000000 INFO @ Fri, 05 Jul 2019 07:52:15: 4000000 INFO @ Fri, 05 Jul 2019 07:52:19: 4000000 INFO @ Fri, 05 Jul 2019 07:52:20: 5000000 INFO @ Fri, 05 Jul 2019 07:52:22: 5000000 INFO @ Fri, 05 Jul 2019 07:52:26: 6000000 INFO @ Fri, 05 Jul 2019 07:52:26: 5000000 INFO @ Fri, 05 Jul 2019 07:52:28: 6000000 INFO @ Fri, 05 Jul 2019 07:52:32: 7000000 INFO @ Fri, 05 Jul 2019 07:52:34: 6000000 INFO @ Fri, 05 Jul 2019 07:52:35: 7000000 INFO @ Fri, 05 Jul 2019 07:52:38: 8000000 INFO @ Fri, 05 Jul 2019 07:52:41: 7000000 INFO @ Fri, 05 Jul 2019 07:52:42: 8000000 INFO @ Fri, 05 Jul 2019 07:52:44: 9000000 INFO @ Fri, 05 Jul 2019 07:52:49: 8000000 INFO @ Fri, 05 Jul 2019 07:52:49: 9000000 INFO @ Fri, 05 Jul 2019 07:52:50: 10000000 INFO @ Fri, 05 Jul 2019 07:52:55: 10000000 INFO @ Fri, 05 Jul 2019 07:52:56: 9000000 INFO @ Fri, 05 Jul 2019 07:52:56: 11000000 INFO @ Fri, 05 Jul 2019 07:53:02: 11000000 INFO @ Fri, 05 Jul 2019 07:53:02: 12000000 INFO @ Fri, 05 Jul 2019 07:53:03: 10000000 INFO @ Fri, 05 Jul 2019 07:53:08: 13000000 INFO @ Fri, 05 Jul 2019 07:53:09: 12000000 INFO @ Fri, 05 Jul 2019 07:53:11: 11000000 INFO @ Fri, 05 Jul 2019 07:53:15: 14000000 INFO @ Fri, 05 Jul 2019 07:53:15: 13000000 INFO @ Fri, 05 Jul 2019 07:53:18: 12000000 INFO @ Fri, 05 Jul 2019 07:53:19: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:53:19: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:53:19: #1 total tags in treatment: 14556241 INFO @ Fri, 05 Jul 2019 07:53:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:53:19: #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 07:53:19: #1 tags after filtering in treatment: 14555954 INFO @ Fri, 05 Jul 2019 07:53:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:53:19: #1 finished! INFO @ Fri, 05 Jul 2019 07:53:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:53:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:53:22: 14000000 INFO @ Fri, 05 Jul 2019 07:53:23: #2 number of paired peaks: 52559 INFO @ Fri, 05 Jul 2019 07:53:23: start model_add_line... INFO @ Fri, 05 Jul 2019 07:53:23: start X-correlation... INFO @ Fri, 05 Jul 2019 07:53:23: end of X-cor INFO @ Fri, 05 Jul 2019 07:53:23: #2 finished! INFO @ Fri, 05 Jul 2019 07:53:23: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 07:53:23: #2 alternative fragment length(s) may be 4,120 bps INFO @ Fri, 05 Jul 2019 07:53:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.10_model.r INFO @ Fri, 05 Jul 2019 07:53:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:53:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:53:25: 13000000 INFO @ Fri, 05 Jul 2019 07:53:25: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:53:25: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:53:25: #1 total tags in treatment: 14556241 INFO @ Fri, 05 Jul 2019 07:53:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:53:25: #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 07:53:26: #1 tags after filtering in treatment: 14555954 INFO @ Fri, 05 Jul 2019 07:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:53:26: #1 finished! INFO @ Fri, 05 Jul 2019 07:53:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:53:30: #2 number of paired peaks: 52559 INFO @ Fri, 05 Jul 2019 07:53:30: start model_add_line... INFO @ Fri, 05 Jul 2019 07:53:30: start X-correlation... INFO @ Fri, 05 Jul 2019 07:53:30: end of X-cor INFO @ Fri, 05 Jul 2019 07:53:30: #2 finished! INFO @ Fri, 05 Jul 2019 07:53:30: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 07:53:30: #2 alternative fragment length(s) may be 4,120 bps INFO @ Fri, 05 Jul 2019 07:53:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.05_model.r INFO @ Fri, 05 Jul 2019 07:53:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:53:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:53:32: 14000000 INFO @ Fri, 05 Jul 2019 07:53:37: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 07:53:37: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 07:53:37: #1 total tags in treatment: 14556241 INFO @ Fri, 05 Jul 2019 07:53:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 07:53:37: #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 07:53:37: #1 tags after filtering in treatment: 14555954 INFO @ Fri, 05 Jul 2019 07:53:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 07:53:37: #1 finished! INFO @ Fri, 05 Jul 2019 07:53:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 07:53:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 07:53:41: #2 number of paired peaks: 52559 INFO @ Fri, 05 Jul 2019 07:53:41: start model_add_line... INFO @ Fri, 05 Jul 2019 07:53:41: start X-correlation... INFO @ Fri, 05 Jul 2019 07:53:41: end of X-cor INFO @ Fri, 05 Jul 2019 07:53:41: #2 finished! INFO @ Fri, 05 Jul 2019 07:53:41: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 07:53:41: #2 alternative fragment length(s) may be 4,120 bps INFO @ Fri, 05 Jul 2019 07:53:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.20_model.r INFO @ Fri, 05 Jul 2019 07:53:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 07:53:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 07:54:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:54:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:54:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 07:54:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.10_peaks.xls INFO @ Fri, 05 Jul 2019 07:54:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:54:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.10_summits.bed INFO @ Fri, 05 Jul 2019 07:54:35: Done! pass1 - making usageList (126 chroms): 12 millis pass2 - checking and writing primary data (40386 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:54:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.05_peaks.xls INFO @ Fri, 05 Jul 2019 07:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.05_summits.bed INFO @ Fri, 05 Jul 2019 07:54:41: Done! pass1 - making usageList (149 chroms): 10 millis pass2 - checking and writing primary data (50981 records, 4 fields): 69 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 07:54:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.20_peaks.xls INFO @ Fri, 05 Jul 2019 07:54:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 07:54:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101977/ERX101977.20_summits.bed INFO @ Fri, 05 Jul 2019 07:54:48: Done! pass1 - making usageList (90 chroms): 5 millis pass2 - checking and writing primary data (27246 records, 4 fields): 70 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。