Job ID = 1290635 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,930,630 reads read : 11,930,630 reads written : 11,930,630 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:59 11930630 reads; of these: 11930630 (100.00%) were unpaired; of these: 2216020 (18.57%) aligned 0 times 7120040 (59.68%) aligned exactly 1 time 2594570 (21.75%) aligned >1 times 81.43% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1472413 / 9714610 = 0.1516 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 @ Sat, 01 Jun 2019 21:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 01 Jun 2019 21:51:21: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:21: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 01 Jun 2019 21:51:21: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:21: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 01 Jun 2019 21:51:21: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:21: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:30: 1000000 INFO @ Sat, 01 Jun 2019 21:51:33: 1000000 INFO @ Sat, 01 Jun 2019 21:51:33: 1000000 INFO @ Sat, 01 Jun 2019 21:51:38: 2000000 INFO @ Sat, 01 Jun 2019 21:51:44: 2000000 INFO @ Sat, 01 Jun 2019 21:51:45: 2000000 INFO @ Sat, 01 Jun 2019 21:51:46: 3000000 INFO @ Sat, 01 Jun 2019 21:51:54: 4000000 INFO @ Sat, 01 Jun 2019 21:51:56: 3000000 INFO @ Sat, 01 Jun 2019 21:51:56: 3000000 INFO @ Sat, 01 Jun 2019 21:52:02: 5000000 INFO @ Sat, 01 Jun 2019 21:52:08: 4000000 INFO @ Sat, 01 Jun 2019 21:52:09: 4000000 INFO @ Sat, 01 Jun 2019 21:52:10: 6000000 INFO @ Sat, 01 Jun 2019 21:52:18: 7000000 INFO @ Sat, 01 Jun 2019 21:52:20: 5000000 INFO @ Sat, 01 Jun 2019 21:52:21: 5000000 INFO @ Sat, 01 Jun 2019 21:52:25: 8000000 INFO @ Sat, 01 Jun 2019 21:52:27: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 21:52:27: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 21:52:27: #1 total tags in treatment: 8242197 INFO @ Sat, 01 Jun 2019 21:52:27: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:28: #1 tags after filtering in treatment: 8242197 INFO @ Sat, 01 Jun 2019 21:52:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:28: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:28: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:29: #2 number of paired peaks: 1459 INFO @ Sat, 01 Jun 2019 21:52:29: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:29: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:29: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:29: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:29: #2 predicted fragment length is 130 bps INFO @ Sat, 01 Jun 2019 21:52:29: #2 alternative fragment length(s) may be 3,130 bps INFO @ Sat, 01 Jun 2019 21:52:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.10_model.r INFO @ Sat, 01 Jun 2019 21:52:29: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:30: 6000000 INFO @ Sat, 01 Jun 2019 21:52:31: 6000000 INFO @ Sat, 01 Jun 2019 21:52:39: 7000000 INFO @ Sat, 01 Jun 2019 21:52:40: 7000000 INFO @ Sat, 01 Jun 2019 21:52:48: 8000000 INFO @ Sat, 01 Jun 2019 21:52:48: 8000000 INFO @ Sat, 01 Jun 2019 21:52:50: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 21:52:50: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 21:52:50: #1 total tags in treatment: 8242197 INFO @ Sat, 01 Jun 2019 21:52:50: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:50: #1 tags after filtering in treatment: 8242197 INFO @ Sat, 01 Jun 2019 21:52:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:50: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:50: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:50: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 21:52:50: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 21:52:50: #1 total tags in treatment: 8242197 INFO @ Sat, 01 Jun 2019 21:52:50: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:51: #1 tags after filtering in treatment: 8242197 INFO @ Sat, 01 Jun 2019 21:52:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:51: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:51: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:51: #2 number of paired peaks: 1459 INFO @ Sat, 01 Jun 2019 21:52:51: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:51: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:51: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:51: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:51: #2 predicted fragment length is 130 bps INFO @ Sat, 01 Jun 2019 21:52:51: #2 alternative fragment length(s) may be 3,130 bps INFO @ Sat, 01 Jun 2019 21:52:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.20_model.r INFO @ Sat, 01 Jun 2019 21:52:51: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:52: #2 number of paired peaks: 1459 INFO @ Sat, 01 Jun 2019 21:52:52: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:52: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:52: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:52: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:52: #2 predicted fragment length is 130 bps INFO @ Sat, 01 Jun 2019 21:52:52: #2 alternative fragment length(s) may be 3,130 bps INFO @ Sat, 01 Jun 2019 21:52:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.05_model.r INFO @ Sat, 01 Jun 2019 21:52:52: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:55: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.10_summits.bed INFO @ Sat, 01 Jun 2019 21:53:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (527 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:17: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:17: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.05_summits.bed INFO @ Sat, 01 Jun 2019 21:53:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1512 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4456932/SRX4456932.20_summits.bed INFO @ Sat, 01 Jun 2019 21:53:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (229 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。