Job ID = 1301554 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,914,441 reads read : 8,914,441 reads written : 8,914,441 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: 00:02:01 8914441 reads; of these: 8914441 (100.00%) were unpaired; of these: 892009 (10.01%) aligned 0 times 7638031 (85.68%) aligned exactly 1 time 384401 (4.31%) aligned >1 times 89.99% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 2285173 / 8022432 = 0.2848 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 @ Mon, 03 Jun 2019 20:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 20:00:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:00:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 20:00:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:00:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 20:00:18: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:00:18: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:00:28: 1000000 INFO @ Mon, 03 Jun 2019 20:00:28: 1000000 INFO @ Mon, 03 Jun 2019 20:00:29: 1000000 INFO @ Mon, 03 Jun 2019 20:00:37: 2000000 INFO @ Mon, 03 Jun 2019 20:00:37: 2000000 INFO @ Mon, 03 Jun 2019 20:00:38: 2000000 INFO @ Mon, 03 Jun 2019 20:00:46: 3000000 INFO @ Mon, 03 Jun 2019 20:00:46: 3000000 INFO @ Mon, 03 Jun 2019 20:00:48: 3000000 INFO @ Mon, 03 Jun 2019 20:00:55: 4000000 INFO @ Mon, 03 Jun 2019 20:00:55: 4000000 INFO @ Mon, 03 Jun 2019 20:00:58: 4000000 INFO @ Mon, 03 Jun 2019 20:01:04: 5000000 INFO @ Mon, 03 Jun 2019 20:01:04: 5000000 INFO @ Mon, 03 Jun 2019 20:01:08: 5000000 INFO @ Mon, 03 Jun 2019 20:01:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:01:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:01:11: #1 total tags in treatment: 5737259 INFO @ Mon, 03 Jun 2019 20:01:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:01:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:01:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:01:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:01:11: #1 total tags in treatment: 5737259 INFO @ Mon, 03 Jun 2019 20:01:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:01:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:01:11: #1 tags after filtering in treatment: 5737259 INFO @ Mon, 03 Jun 2019 20:01:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:01:11: #1 finished! INFO @ Mon, 03 Jun 2019 20:01:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:01:11: #1 tags after filtering in treatment: 5737259 INFO @ Mon, 03 Jun 2019 20:01:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:01:11: #1 finished! INFO @ Mon, 03 Jun 2019 20:01:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:01:12: #2 number of paired peaks: 13245 INFO @ Mon, 03 Jun 2019 20:01:12: start model_add_line... INFO @ Mon, 03 Jun 2019 20:01:12: #2 number of paired peaks: 13245 INFO @ Mon, 03 Jun 2019 20:01:12: start model_add_line... INFO @ Mon, 03 Jun 2019 20:01:12: start X-correlation... INFO @ Mon, 03 Jun 2019 20:01:13: start X-correlation... INFO @ Mon, 03 Jun 2019 20:01:13: end of X-cor INFO @ Mon, 03 Jun 2019 20:01:13: #2 finished! INFO @ Mon, 03 Jun 2019 20:01:13: #2 predicted fragment length is 208 bps INFO @ Mon, 03 Jun 2019 20:01:13: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 03 Jun 2019 20:01:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.10_model.r INFO @ Mon, 03 Jun 2019 20:01:13: end of X-cor INFO @ Mon, 03 Jun 2019 20:01:13: #2 finished! INFO @ Mon, 03 Jun 2019 20:01:13: #2 predicted fragment length is 208 bps INFO @ Mon, 03 Jun 2019 20:01:13: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 03 Jun 2019 20:01:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.20_model.r INFO @ Mon, 03 Jun 2019 20:01:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:01:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:01:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:01:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:01:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:01:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:01:14: #1 total tags in treatment: 5737259 INFO @ Mon, 03 Jun 2019 20:01:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:01:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:01:15: #1 tags after filtering in treatment: 5737259 INFO @ Mon, 03 Jun 2019 20:01:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:01:15: #1 finished! INFO @ Mon, 03 Jun 2019 20:01:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:01:16: #2 number of paired peaks: 13245 INFO @ Mon, 03 Jun 2019 20:01:16: start model_add_line... INFO @ Mon, 03 Jun 2019 20:01:16: start X-correlation... INFO @ Mon, 03 Jun 2019 20:01:16: end of X-cor INFO @ Mon, 03 Jun 2019 20:01:16: #2 finished! INFO @ Mon, 03 Jun 2019 20:01:16: #2 predicted fragment length is 208 bps INFO @ Mon, 03 Jun 2019 20:01:16: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 03 Jun 2019 20:01:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.05_model.r INFO @ Mon, 03 Jun 2019 20:01:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:01:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:01:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:01:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:01:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:01:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:01:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:01:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.20_summits.bed INFO @ Mon, 03 Jun 2019 20:01:41: Done! INFO @ Mon, 03 Jun 2019 20:01:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.10_peaks.xls pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (5503 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:01:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:01:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.10_summits.bed INFO @ Mon, 03 Jun 2019 20:01:41: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7191 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485222/SRX485222.05_summits.bed INFO @ Mon, 03 Jun 2019 20:01:45: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7885 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。