Job ID = 1294913 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,005,474 reads read : 14,005,474 reads written : 14,005,474 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: 00:04:08 14005474 reads; of these: 14005474 (100.00%) were unpaired; of these: 1122436 (8.01%) aligned 0 times 11939141 (85.25%) aligned exactly 1 time 943897 (6.74%) aligned >1 times 91.99% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2088213 / 12883038 = 0.1621 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 10:54:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.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 10:54:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:54:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:54:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.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 10:54:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:54:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:54:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.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 10:54:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:54:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:55:03: 1000000 INFO @ Mon, 03 Jun 2019 10:55:04: 1000000 INFO @ Mon, 03 Jun 2019 10:55:04: 1000000 INFO @ Mon, 03 Jun 2019 10:55:11: 2000000 INFO @ Mon, 03 Jun 2019 10:55:12: 2000000 INFO @ Mon, 03 Jun 2019 10:55:12: 2000000 INFO @ Mon, 03 Jun 2019 10:55:19: 3000000 INFO @ Mon, 03 Jun 2019 10:55:20: 3000000 INFO @ Mon, 03 Jun 2019 10:55:20: 3000000 INFO @ Mon, 03 Jun 2019 10:55:26: 4000000 INFO @ Mon, 03 Jun 2019 10:55:27: 4000000 INFO @ Mon, 03 Jun 2019 10:55:27: 4000000 INFO @ Mon, 03 Jun 2019 10:55:34: 5000000 INFO @ Mon, 03 Jun 2019 10:55:35: 5000000 INFO @ Mon, 03 Jun 2019 10:55:35: 5000000 INFO @ Mon, 03 Jun 2019 10:55:41: 6000000 INFO @ Mon, 03 Jun 2019 10:55:42: 6000000 INFO @ Mon, 03 Jun 2019 10:55:42: 6000000 INFO @ Mon, 03 Jun 2019 10:55:48: 7000000 INFO @ Mon, 03 Jun 2019 10:55:49: 7000000 INFO @ Mon, 03 Jun 2019 10:55:49: 7000000 INFO @ Mon, 03 Jun 2019 10:55:56: 8000000 INFO @ Mon, 03 Jun 2019 10:55:56: 8000000 INFO @ Mon, 03 Jun 2019 10:55:57: 8000000 INFO @ Mon, 03 Jun 2019 10:56:03: 9000000 INFO @ Mon, 03 Jun 2019 10:56:04: 9000000 INFO @ Mon, 03 Jun 2019 10:56:04: 9000000 INFO @ Mon, 03 Jun 2019 10:56:11: 10000000 INFO @ Mon, 03 Jun 2019 10:56:12: 10000000 INFO @ Mon, 03 Jun 2019 10:56:12: 10000000 INFO @ Mon, 03 Jun 2019 10:56:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:56:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:56:17: #1 total tags in treatment: 10794825 INFO @ Mon, 03 Jun 2019 10:56:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:56:17: #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 10:56:17: #1 tags after filtering in treatment: 10794825 INFO @ Mon, 03 Jun 2019 10:56:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:56:17: #1 finished! INFO @ Mon, 03 Jun 2019 10:56:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:56:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:56:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:56:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:56:18: #1 total tags in treatment: 10794825 INFO @ Mon, 03 Jun 2019 10:56:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:56:18: #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 10:56:18: #1 tags after filtering in treatment: 10794825 INFO @ Mon, 03 Jun 2019 10:56:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:56:18: #1 finished! INFO @ Mon, 03 Jun 2019 10:56:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:56:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:56:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:56:18: #1 total tags in treatment: 10794825 INFO @ Mon, 03 Jun 2019 10:56:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:56:18: #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 10:56:18: #1 tags after filtering in treatment: 10794825 INFO @ Mon, 03 Jun 2019 10:56:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:56:18: #1 finished! INFO @ Mon, 03 Jun 2019 10:56:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:56:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:56:18: #2 number of paired peaks: 5695 INFO @ Mon, 03 Jun 2019 10:56:18: start model_add_line... INFO @ Mon, 03 Jun 2019 10:56:19: start X-correlation... INFO @ Mon, 03 Jun 2019 10:56:19: end of X-cor INFO @ Mon, 03 Jun 2019 10:56:19: #2 finished! INFO @ Mon, 03 Jun 2019 10:56:19: #2 predicted fragment length is 250 bps INFO @ Mon, 03 Jun 2019 10:56:19: #2 alternative fragment length(s) may be 250 bps INFO @ Mon, 03 Jun 2019 10:56:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.05_model.r INFO @ Mon, 03 Jun 2019 10:56:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:56:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:56:19: #2 number of paired peaks: 5695 INFO @ Mon, 03 Jun 2019 10:56:19: start model_add_line... INFO @ Mon, 03 Jun 2019 10:56:20: start X-correlation... INFO @ Mon, 03 Jun 2019 10:56:20: end of X-cor INFO @ Mon, 03 Jun 2019 10:56:20: #2 finished! INFO @ Mon, 03 Jun 2019 10:56:20: #2 predicted fragment length is 250 bps INFO @ Mon, 03 Jun 2019 10:56:20: #2 alternative fragment length(s) may be 250 bps INFO @ Mon, 03 Jun 2019 10:56:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.10_model.r INFO @ Mon, 03 Jun 2019 10:56:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:56:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:56:20: #2 number of paired peaks: 5695 INFO @ Mon, 03 Jun 2019 10:56:20: start model_add_line... INFO @ Mon, 03 Jun 2019 10:56:20: start X-correlation... INFO @ Mon, 03 Jun 2019 10:56:20: end of X-cor INFO @ Mon, 03 Jun 2019 10:56:20: #2 finished! INFO @ Mon, 03 Jun 2019 10:56:20: #2 predicted fragment length is 250 bps INFO @ Mon, 03 Jun 2019 10:56:20: #2 alternative fragment length(s) may be 250 bps INFO @ Mon, 03 Jun 2019 10:56:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.20_model.r INFO @ Mon, 03 Jun 2019 10:56:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:56:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:56:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:56:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:56:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:57:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:57:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.20_summits.bed INFO @ Mon, 03 Jun 2019 10:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.05_summits.bed INFO @ Mon, 03 Jun 2019 10:57:15: Done! INFO @ Mon, 03 Jun 2019 10:57:15: Done! pass1 - making usageList (12 chroms): 3 millis pass2 - checking and writing primary data (6078 records, 4 fields): 9 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (17980 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:57:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:57:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:57:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287986/SRX287986.10_summits.bed INFO @ Mon, 03 Jun 2019 10:57:17: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (11666 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。