Job ID = 2590678 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,117,571 reads read : 64,235,142 reads written : 32,117,571 reads 0-length : 32,117,571 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: 00:11:44 32117571 reads; of these: 32117571 (100.00%) were unpaired; of these: 3730266 (11.61%) aligned 0 times 21118451 (65.75%) aligned exactly 1 time 7268854 (22.63%) aligned >1 times 88.39% overall alignment rate Time searching: 00:11:44 Overall time: 00:11:44 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] 14432512 / 28387305 = 0.5084 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 23:30:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.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 23:30:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:30:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:30:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.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 23:30:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:30:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:30:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.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 23:30:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:30:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:30:27: 1000000 INFO @ Mon, 12 Aug 2019 23:30:29: 1000000 INFO @ Mon, 12 Aug 2019 23:30:33: 1000000 INFO @ Mon, 12 Aug 2019 23:30:35: 2000000 INFO @ Mon, 12 Aug 2019 23:30:37: 2000000 INFO @ Mon, 12 Aug 2019 23:30:42: 3000000 INFO @ Mon, 12 Aug 2019 23:30:43: 2000000 INFO @ Mon, 12 Aug 2019 23:30:45: 3000000 INFO @ Mon, 12 Aug 2019 23:30:50: 4000000 INFO @ Mon, 12 Aug 2019 23:30:52: 4000000 INFO @ Mon, 12 Aug 2019 23:30:54: 3000000 INFO @ Mon, 12 Aug 2019 23:30:58: 5000000 INFO @ Mon, 12 Aug 2019 23:31:00: 5000000 INFO @ Mon, 12 Aug 2019 23:31:04: 4000000 INFO @ Mon, 12 Aug 2019 23:31:05: 6000000 INFO @ Mon, 12 Aug 2019 23:31:08: 6000000 INFO @ Mon, 12 Aug 2019 23:31:13: 7000000 INFO @ Mon, 12 Aug 2019 23:31:14: 5000000 INFO @ Mon, 12 Aug 2019 23:31:16: 7000000 INFO @ Mon, 12 Aug 2019 23:31:20: 8000000 INFO @ Mon, 12 Aug 2019 23:31:24: 8000000 INFO @ Mon, 12 Aug 2019 23:31:25: 6000000 INFO @ Mon, 12 Aug 2019 23:31:28: 9000000 INFO @ Mon, 12 Aug 2019 23:31:31: 9000000 INFO @ Mon, 12 Aug 2019 23:31:35: 7000000 INFO @ Mon, 12 Aug 2019 23:31:35: 10000000 INFO @ Mon, 12 Aug 2019 23:31:39: 10000000 INFO @ Mon, 12 Aug 2019 23:31:43: 11000000 INFO @ Mon, 12 Aug 2019 23:31:45: 8000000 INFO @ Mon, 12 Aug 2019 23:31:46: 11000000 INFO @ Mon, 12 Aug 2019 23:31:51: 12000000 INFO @ Mon, 12 Aug 2019 23:31:54: 12000000 INFO @ Mon, 12 Aug 2019 23:31:56: 9000000 INFO @ Mon, 12 Aug 2019 23:31:59: 13000000 INFO @ Mon, 12 Aug 2019 23:32:01: 13000000 INFO @ Mon, 12 Aug 2019 23:32:06: 10000000 INFO @ Mon, 12 Aug 2019 23:32:06: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:32:06: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:32:06: #1 total tags in treatment: 13954793 INFO @ Mon, 12 Aug 2019 23:32:06: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:32:06: #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 23:32:07: #1 tags after filtering in treatment: 13954793 INFO @ Mon, 12 Aug 2019 23:32:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:32:07: #1 finished! INFO @ Mon, 12 Aug 2019 23:32:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:32:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:32:08: #2 number of paired peaks: 1623 INFO @ Mon, 12 Aug 2019 23:32:08: start model_add_line... INFO @ Mon, 12 Aug 2019 23:32:08: start X-correlation... INFO @ Mon, 12 Aug 2019 23:32:08: end of X-cor INFO @ Mon, 12 Aug 2019 23:32:08: #2 finished! INFO @ Mon, 12 Aug 2019 23:32:08: #2 predicted fragment length is 195 bps INFO @ Mon, 12 Aug 2019 23:32:08: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 12 Aug 2019 23:32:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.05_model.r INFO @ Mon, 12 Aug 2019 23:32:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:32:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:32:09: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:32:09: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:32:09: #1 total tags in treatment: 13954793 INFO @ Mon, 12 Aug 2019 23:32:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:32:09: #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 23:32:09: #1 tags after filtering in treatment: 13954793 INFO @ Mon, 12 Aug 2019 23:32:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:32:09: #1 finished! INFO @ Mon, 12 Aug 2019 23:32:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:32:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:32:10: #2 number of paired peaks: 1623 INFO @ Mon, 12 Aug 2019 23:32:10: start model_add_line... INFO @ Mon, 12 Aug 2019 23:32:10: start X-correlation... INFO @ Mon, 12 Aug 2019 23:32:10: end of X-cor INFO @ Mon, 12 Aug 2019 23:32:10: #2 finished! INFO @ Mon, 12 Aug 2019 23:32:10: #2 predicted fragment length is 195 bps INFO @ Mon, 12 Aug 2019 23:32:10: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 12 Aug 2019 23:32:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.10_model.r INFO @ Mon, 12 Aug 2019 23:32:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:32:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:32:16: 11000000 INFO @ Mon, 12 Aug 2019 23:32:27: 12000000 INFO @ Mon, 12 Aug 2019 23:32:37: 13000000 INFO @ Mon, 12 Aug 2019 23:32:46: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:32:46: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:32:46: #1 total tags in treatment: 13954793 INFO @ Mon, 12 Aug 2019 23:32:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:32:46: #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 23:32:46: #1 tags after filtering in treatment: 13954793 INFO @ Mon, 12 Aug 2019 23:32:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:32:46: #1 finished! INFO @ Mon, 12 Aug 2019 23:32:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:32:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:32:48: #2 number of paired peaks: 1623 INFO @ Mon, 12 Aug 2019 23:32:48: start model_add_line... INFO @ Mon, 12 Aug 2019 23:32:48: start X-correlation... INFO @ Mon, 12 Aug 2019 23:32:48: end of X-cor INFO @ Mon, 12 Aug 2019 23:32:48: #2 finished! INFO @ Mon, 12 Aug 2019 23:32:48: #2 predicted fragment length is 195 bps INFO @ Mon, 12 Aug 2019 23:32:48: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 12 Aug 2019 23:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.20_model.r INFO @ Mon, 12 Aug 2019 23:32:48: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:32:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:32:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:32:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:33:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:33:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:33:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.05_summits.bed INFO @ Mon, 12 Aug 2019 23:33:12: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8099 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:33:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:33:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:33:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.10_summits.bed INFO @ Mon, 12 Aug 2019 23:33:14: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5159 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:33:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011025/SRX5011025.20_summits.bed INFO @ Mon, 12 Aug 2019 23:33:52: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3002 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。