Job ID = 1293824 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,017,458 reads read : 5,017,458 reads written : 5,017,458 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:24 5017458 reads; of these: 5017458 (100.00%) were unpaired; of these: 226585 (4.52%) aligned 0 times 3680330 (73.35%) aligned exactly 1 time 1110543 (22.13%) aligned >1 times 95.48% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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] 214680 / 4790873 = 0.0448 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 02:40:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.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 02:40:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:40:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:40:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.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 02:40:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:40:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:40:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.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 02:40:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:40:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:40:54: 1000000 INFO @ Mon, 03 Jun 2019 02:40:55: 1000000 INFO @ Mon, 03 Jun 2019 02:40:55: 1000000 INFO @ Mon, 03 Jun 2019 02:41:01: 2000000 INFO @ Mon, 03 Jun 2019 02:41:01: 2000000 INFO @ Mon, 03 Jun 2019 02:41:02: 2000000 INFO @ Mon, 03 Jun 2019 02:41:07: 3000000 INFO @ Mon, 03 Jun 2019 02:41:07: 3000000 INFO @ Mon, 03 Jun 2019 02:41:08: 3000000 INFO @ Mon, 03 Jun 2019 02:41:13: 4000000 INFO @ Mon, 03 Jun 2019 02:41:13: 4000000 INFO @ Mon, 03 Jun 2019 02:41:15: 4000000 INFO @ Mon, 03 Jun 2019 02:41:16: #1 tag size is determined as 30 bps INFO @ Mon, 03 Jun 2019 02:41:16: #1 tag size = 30 INFO @ Mon, 03 Jun 2019 02:41:16: #1 total tags in treatment: 4576193 INFO @ Mon, 03 Jun 2019 02:41:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:41:16: #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 02:41:17: #1 tags after filtering in treatment: 4576193 INFO @ Mon, 03 Jun 2019 02:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:41:17: #1 finished! INFO @ Mon, 03 Jun 2019 02:41:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:41:17: #1 tag size is determined as 30 bps INFO @ Mon, 03 Jun 2019 02:41:17: #1 tag size = 30 INFO @ Mon, 03 Jun 2019 02:41:17: #1 total tags in treatment: 4576193 INFO @ Mon, 03 Jun 2019 02:41:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:41:17: #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 02:41:17: #1 tags after filtering in treatment: 4576193 INFO @ Mon, 03 Jun 2019 02:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:41:17: #1 finished! INFO @ Mon, 03 Jun 2019 02:41:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:41:17: #2 number of paired peaks: 1022 INFO @ Mon, 03 Jun 2019 02:41:17: start model_add_line... INFO @ Mon, 03 Jun 2019 02:41:17: start X-correlation... INFO @ Mon, 03 Jun 2019 02:41:17: end of X-cor INFO @ Mon, 03 Jun 2019 02:41:17: #2 finished! INFO @ Mon, 03 Jun 2019 02:41:17: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 02:41:17: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 03 Jun 2019 02:41:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.20_model.r INFO @ Mon, 03 Jun 2019 02:41:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:41:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:41:17: #2 number of paired peaks: 1022 INFO @ Mon, 03 Jun 2019 02:41:17: start model_add_line... INFO @ Mon, 03 Jun 2019 02:41:17: start X-correlation... INFO @ Mon, 03 Jun 2019 02:41:18: end of X-cor INFO @ Mon, 03 Jun 2019 02:41:18: #2 finished! INFO @ Mon, 03 Jun 2019 02:41:18: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 02:41:18: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 03 Jun 2019 02:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.05_model.r INFO @ Mon, 03 Jun 2019 02:41:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:41:19: #1 tag size is determined as 30 bps INFO @ Mon, 03 Jun 2019 02:41:19: #1 tag size = 30 INFO @ Mon, 03 Jun 2019 02:41:19: #1 total tags in treatment: 4576193 INFO @ Mon, 03 Jun 2019 02:41:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:41:19: #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 02:41:19: #1 tags after filtering in treatment: 4576193 INFO @ Mon, 03 Jun 2019 02:41:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:41:19: #1 finished! INFO @ Mon, 03 Jun 2019 02:41:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:41:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:41:19: #2 number of paired peaks: 1022 INFO @ Mon, 03 Jun 2019 02:41:19: start model_add_line... INFO @ Mon, 03 Jun 2019 02:41:19: start X-correlation... INFO @ Mon, 03 Jun 2019 02:41:19: end of X-cor INFO @ Mon, 03 Jun 2019 02:41:19: #2 finished! INFO @ Mon, 03 Jun 2019 02:41:19: #2 predicted fragment length is 85 bps INFO @ Mon, 03 Jun 2019 02:41:19: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 03 Jun 2019 02:41:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.10_model.r INFO @ Mon, 03 Jun 2019 02:41:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:41:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:41:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:41:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:41:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:41:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:41:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:41:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.20_summits.bed INFO @ Mon, 03 Jun 2019 02:41:38: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (684 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:41:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:41:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:41:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.05_summits.bed INFO @ Mon, 03 Jun 2019 02:41:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2117 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:41:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:41:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:41:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX124482/SRX124482.10_summits.bed INFO @ Mon, 03 Jun 2019 02:41:41: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1360 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。