Job ID = 2640408 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,650,531 reads read : 3,650,531 reads written : 3,650,531 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR399326.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: 00:00:02 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:01:38 3650531 reads; of these: 3650531 (100.00%) were unpaired; of these: 91242 (2.50%) aligned 0 times 2630335 (72.05%) aligned exactly 1 time 928954 (25.45%) aligned >1 times 97.50% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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_rmdupse_core] 631665 / 3559289 = 0.1775 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 16:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.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 @ Sat, 24 Aug 2019 16:15:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:15:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:15:23: 1000000 INFO @ Sat, 24 Aug 2019 16:15:32: 2000000 INFO @ Sat, 24 Aug 2019 16:15:40: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:15:40: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:15:40: #1 total tags in treatment: 2927624 INFO @ Sat, 24 Aug 2019 16:15:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:15:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:15:40: #1 tags after filtering in treatment: 2927315 INFO @ Sat, 24 Aug 2019 16:15:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:15:40: #1 finished! INFO @ Sat, 24 Aug 2019 16:15:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:15:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:15:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.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 @ Sat, 24 Aug 2019 16:15:43: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:15:43: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:15:45: #2 number of paired peaks: 31801 INFO @ Sat, 24 Aug 2019 16:15:45: start model_add_line... INFO @ Sat, 24 Aug 2019 16:15:45: start X-correlation... INFO @ Sat, 24 Aug 2019 16:15:45: end of X-cor INFO @ Sat, 24 Aug 2019 16:15:45: #2 finished! INFO @ Sat, 24 Aug 2019 16:15:45: #2 predicted fragment length is 294 bps INFO @ Sat, 24 Aug 2019 16:15:45: #2 alternative fragment length(s) may be 294 bps INFO @ Sat, 24 Aug 2019 16:15:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.05_model.r INFO @ Sat, 24 Aug 2019 16:15:45: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:15:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:15:53: 1000000 INFO @ Sat, 24 Aug 2019 16:15:55: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.05_peaks.xls INFO @ Sat, 24 Aug 2019 16:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.05_summits.bed INFO @ Sat, 24 Aug 2019 16:16:00: Done! pass1 - making usageList (24 chroms): 2 millis pass2 - checking and writing primary data (204 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:16:03: 2000000 INFO @ Sat, 24 Aug 2019 16:16:10: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:16:10: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:16:10: #1 total tags in treatment: 2927624 INFO @ Sat, 24 Aug 2019 16:16:10: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:16:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:16:10: #1 tags after filtering in treatment: 2927315 INFO @ Sat, 24 Aug 2019 16:16:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:16:10: #1 finished! INFO @ Sat, 24 Aug 2019 16:16:10: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:16:10: #2 looking for paired plus/minus strand peaks... BedGraph に変換中... INFO @ Sat, 24 Aug 2019 16:16:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.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 @ Sat, 24 Aug 2019 16:16:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:16:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:16:14: #2 number of paired peaks: 31801 INFO @ Sat, 24 Aug 2019 16:16:14: start model_add_line... INFO @ Sat, 24 Aug 2019 16:16:15: start X-correlation... INFO @ Sat, 24 Aug 2019 16:16:15: end of X-cor INFO @ Sat, 24 Aug 2019 16:16:15: #2 finished! INFO @ Sat, 24 Aug 2019 16:16:15: #2 predicted fragment length is 294 bps INFO @ Sat, 24 Aug 2019 16:16:15: #2 alternative fragment length(s) may be 294 bps INFO @ Sat, 24 Aug 2019 16:16:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.10_model.r INFO @ Sat, 24 Aug 2019 16:16:15: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:16:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:16:22: 1000000 INFO @ Sat, 24 Aug 2019 16:16:24: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:16:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.10_peaks.xls INFO @ Sat, 24 Aug 2019 16:16:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:16:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.10_summits.bed INFO @ Sat, 24 Aug 2019 16:16:29: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (84 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:16:31: 2000000 INFO @ Sat, 24 Aug 2019 16:16:39: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:16:39: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:16:39: #1 total tags in treatment: 2927624 INFO @ Sat, 24 Aug 2019 16:16:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:16:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:16:39: #1 tags after filtering in treatment: 2927315 INFO @ Sat, 24 Aug 2019 16:16:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:16:39: #1 finished! INFO @ Sat, 24 Aug 2019 16:16:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:16:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:16:43: #2 number of paired peaks: 31801 INFO @ Sat, 24 Aug 2019 16:16:43: start model_add_line... INFO @ Sat, 24 Aug 2019 16:16:43: start X-correlation... INFO @ Sat, 24 Aug 2019 16:16:43: end of X-cor INFO @ Sat, 24 Aug 2019 16:16:43: #2 finished! INFO @ Sat, 24 Aug 2019 16:16:43: #2 predicted fragment length is 294 bps INFO @ Sat, 24 Aug 2019 16:16:43: #2 alternative fragment length(s) may be 294 bps INFO @ Sat, 24 Aug 2019 16:16:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.20_model.r INFO @ Sat, 24 Aug 2019 16:16:43: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:16:53: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:16:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.20_peaks.xls INFO @ Sat, 24 Aug 2019 16:16:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:16:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116048/SRX116048.20_summits.bed INFO @ Sat, 24 Aug 2019 16:16:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。