Job ID = 2590828 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,495,495 reads read : 46,990,990 reads written : 23,495,495 reads 0-length : 23,495,495 rm: cannot remove ‘[DSE]RR*’: 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: 00:08:18 23495495 reads; of these: 23495495 (100.00%) were unpaired; of these: 2210385 (9.41%) aligned 0 times 16396532 (69.79%) aligned exactly 1 time 4888578 (20.81%) aligned >1 times 90.59% overall alignment rate Time searching: 00:08:18 Overall time: 00:08:18 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 12 files... [bam_rmdupse_core] 9714719 / 21285110 = 0.4564 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, 12 Aug 2019 23:43:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.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, 12 Aug 2019 23:43:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:43:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:43:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.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, 12 Aug 2019 23:43:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:43:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:43:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.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, 12 Aug 2019 23:43:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:43:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:43:17: 1000000 INFO @ Mon, 12 Aug 2019 23:43:18: 1000000 INFO @ Mon, 12 Aug 2019 23:43:19: 1000000 INFO @ Mon, 12 Aug 2019 23:43:24: 2000000 INFO @ Mon, 12 Aug 2019 23:43:24: 2000000 INFO @ Mon, 12 Aug 2019 23:43:26: 2000000 INFO @ Mon, 12 Aug 2019 23:43:30: 3000000 INFO @ Mon, 12 Aug 2019 23:43:31: 3000000 INFO @ Mon, 12 Aug 2019 23:43:33: 3000000 INFO @ Mon, 12 Aug 2019 23:43:37: 4000000 INFO @ Mon, 12 Aug 2019 23:43:38: 4000000 INFO @ Mon, 12 Aug 2019 23:43:39: 4000000 INFO @ Mon, 12 Aug 2019 23:43:43: 5000000 INFO @ Mon, 12 Aug 2019 23:43:45: 5000000 INFO @ Mon, 12 Aug 2019 23:43:46: 5000000 INFO @ Mon, 12 Aug 2019 23:43:49: 6000000 INFO @ Mon, 12 Aug 2019 23:43:51: 6000000 INFO @ Mon, 12 Aug 2019 23:43:53: 6000000 INFO @ Mon, 12 Aug 2019 23:43:55: 7000000 INFO @ Mon, 12 Aug 2019 23:43:58: 7000000 INFO @ Mon, 12 Aug 2019 23:43:59: 7000000 INFO @ Mon, 12 Aug 2019 23:44:01: 8000000 INFO @ Mon, 12 Aug 2019 23:44:05: 8000000 INFO @ Mon, 12 Aug 2019 23:44:06: 8000000 INFO @ Mon, 12 Aug 2019 23:44:08: 9000000 INFO @ Mon, 12 Aug 2019 23:44:11: 9000000 INFO @ Mon, 12 Aug 2019 23:44:13: 9000000 INFO @ Mon, 12 Aug 2019 23:44:14: 10000000 INFO @ Mon, 12 Aug 2019 23:44:18: 10000000 INFO @ Mon, 12 Aug 2019 23:44:19: 10000000 INFO @ Mon, 12 Aug 2019 23:44:20: 11000000 INFO @ Mon, 12 Aug 2019 23:44:23: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:44:23: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:44:23: #1 total tags in treatment: 11570391 INFO @ Mon, 12 Aug 2019 23:44:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:44:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:44:24: #1 tags after filtering in treatment: 11570391 INFO @ Mon, 12 Aug 2019 23:44:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:44:24: #1 finished! INFO @ Mon, 12 Aug 2019 23:44:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:44:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:44:25: 11000000 INFO @ Mon, 12 Aug 2019 23:44:25: #2 number of paired peaks: 3037 INFO @ Mon, 12 Aug 2019 23:44:25: start model_add_line... INFO @ Mon, 12 Aug 2019 23:44:25: start X-correlation... INFO @ Mon, 12 Aug 2019 23:44:25: end of X-cor INFO @ Mon, 12 Aug 2019 23:44:25: #2 finished! INFO @ Mon, 12 Aug 2019 23:44:25: #2 predicted fragment length is 212 bps INFO @ Mon, 12 Aug 2019 23:44:25: #2 alternative fragment length(s) may be 212 bps INFO @ Mon, 12 Aug 2019 23:44:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.10_model.r INFO @ Mon, 12 Aug 2019 23:44:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:44:26: 11000000 INFO @ Mon, 12 Aug 2019 23:44:28: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:44:28: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:44:28: #1 total tags in treatment: 11570391 INFO @ Mon, 12 Aug 2019 23:44:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:44:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:44:29: #1 tags after filtering in treatment: 11570391 INFO @ Mon, 12 Aug 2019 23:44:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:44:29: #1 finished! INFO @ Mon, 12 Aug 2019 23:44:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:44:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:44:30: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:44:30: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:44:30: #1 total tags in treatment: 11570391 INFO @ Mon, 12 Aug 2019 23:44:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:44:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:44:30: #2 number of paired peaks: 3037 INFO @ Mon, 12 Aug 2019 23:44:30: start model_add_line... INFO @ Mon, 12 Aug 2019 23:44:30: #1 tags after filtering in treatment: 11570391 INFO @ Mon, 12 Aug 2019 23:44:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:44:30: #1 finished! INFO @ Mon, 12 Aug 2019 23:44:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:44:30: start X-correlation... INFO @ Mon, 12 Aug 2019 23:44:30: end of X-cor INFO @ Mon, 12 Aug 2019 23:44:30: #2 finished! INFO @ Mon, 12 Aug 2019 23:44:30: #2 predicted fragment length is 212 bps INFO @ Mon, 12 Aug 2019 23:44:30: #2 alternative fragment length(s) may be 212 bps INFO @ Mon, 12 Aug 2019 23:44:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.05_model.r INFO @ Mon, 12 Aug 2019 23:44:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:44:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:44:31: #2 number of paired peaks: 3037 INFO @ Mon, 12 Aug 2019 23:44:31: start model_add_line... INFO @ Mon, 12 Aug 2019 23:44:32: start X-correlation... INFO @ Mon, 12 Aug 2019 23:44:32: end of X-cor INFO @ Mon, 12 Aug 2019 23:44:32: #2 finished! INFO @ Mon, 12 Aug 2019 23:44:32: #2 predicted fragment length is 212 bps INFO @ Mon, 12 Aug 2019 23:44:32: #2 alternative fragment length(s) may be 212 bps INFO @ Mon, 12 Aug 2019 23:44:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.20_model.r INFO @ Mon, 12 Aug 2019 23:44:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:44:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:45:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:45:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:45:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:45:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:45:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:45:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.10_summits.bed INFO @ Mon, 12 Aug 2019 23:45:21: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7109 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:45:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:45:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:45:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.05_summits.bed INFO @ Mon, 12 Aug 2019 23:45:27: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (10017 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:45:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:45:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:45:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011067/SRX5011067.20_summits.bed INFO @ Mon, 12 Aug 2019 23:45:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4453 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。