Job ID = 2590556 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,089,227 reads read : 26,178,454 reads written : 26,178,454 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: 00:30:59 13089227 reads; of these: 13089227 (100.00%) were paired; of these: 1947757 (14.88%) aligned concordantly 0 times 7878825 (60.19%) aligned concordantly exactly 1 time 3262645 (24.93%) aligned concordantly >1 times ---- 1947757 pairs aligned concordantly 0 times; of these: 328556 (16.87%) aligned discordantly 1 time ---- 1619201 pairs aligned 0 times concordantly or discordantly; of these: 3238402 mates make up the pairs; of these: 2349670 (72.56%) aligned 0 times 481573 (14.87%) aligned exactly 1 time 407159 (12.57%) aligned >1 times 91.02% overall alignment rate Time searching: 00:30:59 Overall time: 00:30:59 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 3126155 / 11451762 = 0.2730 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 23:10:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.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 23:10:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:10:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.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 23:10:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:10:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:10:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.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 23:10:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:10:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:10:31: 1000000 INFO @ Mon, 12 Aug 2019 23:10:33: 1000000 INFO @ Mon, 12 Aug 2019 23:10:34: 1000000 INFO @ Mon, 12 Aug 2019 23:10:41: 2000000 INFO @ Mon, 12 Aug 2019 23:10:43: 2000000 INFO @ Mon, 12 Aug 2019 23:10:46: 2000000 INFO @ Mon, 12 Aug 2019 23:10:50: 3000000 INFO @ Mon, 12 Aug 2019 23:10:53: 3000000 INFO @ Mon, 12 Aug 2019 23:10:57: 3000000 INFO @ Mon, 12 Aug 2019 23:11:00: 4000000 INFO @ Mon, 12 Aug 2019 23:11:02: 4000000 INFO @ Mon, 12 Aug 2019 23:11:08: 4000000 INFO @ Mon, 12 Aug 2019 23:11:09: 5000000 INFO @ Mon, 12 Aug 2019 23:11:12: 5000000 INFO @ Mon, 12 Aug 2019 23:11:19: 6000000 INFO @ Mon, 12 Aug 2019 23:11:20: 5000000 INFO @ Mon, 12 Aug 2019 23:11:21: 6000000 INFO @ Mon, 12 Aug 2019 23:11:28: 7000000 INFO @ Mon, 12 Aug 2019 23:11:30: 6000000 INFO @ Mon, 12 Aug 2019 23:11:31: 7000000 INFO @ Mon, 12 Aug 2019 23:11:38: 8000000 INFO @ Mon, 12 Aug 2019 23:11:40: 8000000 INFO @ Mon, 12 Aug 2019 23:11:41: 7000000 INFO @ Mon, 12 Aug 2019 23:11:47: 9000000 INFO @ Mon, 12 Aug 2019 23:11:50: 9000000 INFO @ Mon, 12 Aug 2019 23:11:51: 8000000 INFO @ Mon, 12 Aug 2019 23:11:57: 10000000 INFO @ Mon, 12 Aug 2019 23:11:59: 10000000 INFO @ Mon, 12 Aug 2019 23:12:01: 9000000 INFO @ Mon, 12 Aug 2019 23:12:06: 11000000 INFO @ Mon, 12 Aug 2019 23:12:08: 11000000 INFO @ Mon, 12 Aug 2019 23:12:11: 10000000 INFO @ Mon, 12 Aug 2019 23:12:15: 12000000 INFO @ Mon, 12 Aug 2019 23:12:18: 12000000 INFO @ Mon, 12 Aug 2019 23:12:21: 11000000 INFO @ Mon, 12 Aug 2019 23:12:25: 13000000 INFO @ Mon, 12 Aug 2019 23:12:27: 13000000 INFO @ Mon, 12 Aug 2019 23:12:31: 12000000 INFO @ Mon, 12 Aug 2019 23:12:34: 14000000 INFO @ Mon, 12 Aug 2019 23:12:36: 14000000 INFO @ Mon, 12 Aug 2019 23:12:41: 13000000 INFO @ Mon, 12 Aug 2019 23:12:43: 15000000 INFO @ Mon, 12 Aug 2019 23:12:46: 15000000 INFO @ Mon, 12 Aug 2019 23:12:51: 14000000 INFO @ Mon, 12 Aug 2019 23:12:52: 16000000 INFO @ Mon, 12 Aug 2019 23:12:55: 16000000 INFO @ Mon, 12 Aug 2019 23:13:01: 15000000 INFO @ Mon, 12 Aug 2019 23:13:02: 17000000 INFO @ Mon, 12 Aug 2019 23:13:04: 17000000 INFO @ Mon, 12 Aug 2019 23:13:07: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:13:07: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:13:07: #1 total tags in treatment: 8060567 INFO @ Mon, 12 Aug 2019 23:13:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:13:07: #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 23:13:07: #1 tags after filtering in treatment: 7633824 INFO @ Mon, 12 Aug 2019 23:13:07: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 12 Aug 2019 23:13:07: #1 finished! INFO @ Mon, 12 Aug 2019 23:13:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:13:08: #2 number of paired peaks: 1223 INFO @ Mon, 12 Aug 2019 23:13:08: start model_add_line... INFO @ Mon, 12 Aug 2019 23:13:08: start X-correlation... INFO @ Mon, 12 Aug 2019 23:13:08: end of X-cor INFO @ Mon, 12 Aug 2019 23:13:08: #2 finished! INFO @ Mon, 12 Aug 2019 23:13:08: #2 predicted fragment length is 154 bps INFO @ Mon, 12 Aug 2019 23:13:08: #2 alternative fragment length(s) may be 154 bps INFO @ Mon, 12 Aug 2019 23:13:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.05_model.r INFO @ Mon, 12 Aug 2019 23:13:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:13:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:13:09: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:13:09: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:13:09: #1 total tags in treatment: 8060567 INFO @ Mon, 12 Aug 2019 23:13:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:13:09: #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 23:13:09: #1 tags after filtering in treatment: 7633824 INFO @ Mon, 12 Aug 2019 23:13:09: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 12 Aug 2019 23:13:09: #1 finished! INFO @ Mon, 12 Aug 2019 23:13:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:13:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:13:10: #2 number of paired peaks: 1223 INFO @ Mon, 12 Aug 2019 23:13:10: start model_add_line... INFO @ Mon, 12 Aug 2019 23:13:10: start X-correlation... INFO @ Mon, 12 Aug 2019 23:13:10: end of X-cor INFO @ Mon, 12 Aug 2019 23:13:10: #2 finished! INFO @ Mon, 12 Aug 2019 23:13:10: #2 predicted fragment length is 154 bps INFO @ Mon, 12 Aug 2019 23:13:10: #2 alternative fragment length(s) may be 154 bps INFO @ Mon, 12 Aug 2019 23:13:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.20_model.r INFO @ Mon, 12 Aug 2019 23:13:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:13:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:13:10: 16000000 INFO @ Mon, 12 Aug 2019 23:13:20: 17000000 INFO @ Mon, 12 Aug 2019 23:13:25: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:13:25: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:13:25: #1 total tags in treatment: 8060567 INFO @ Mon, 12 Aug 2019 23:13:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:13:25: #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 23:13:25: #1 tags after filtering in treatment: 7633824 INFO @ Mon, 12 Aug 2019 23:13:25: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 12 Aug 2019 23:13:25: #1 finished! INFO @ Mon, 12 Aug 2019 23:13:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:13:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:13:26: #2 number of paired peaks: 1223 INFO @ Mon, 12 Aug 2019 23:13:26: start model_add_line... INFO @ Mon, 12 Aug 2019 23:13:26: start X-correlation... INFO @ Mon, 12 Aug 2019 23:13:26: end of X-cor INFO @ Mon, 12 Aug 2019 23:13:26: #2 finished! INFO @ Mon, 12 Aug 2019 23:13:26: #2 predicted fragment length is 154 bps INFO @ Mon, 12 Aug 2019 23:13:26: #2 alternative fragment length(s) may be 154 bps INFO @ Mon, 12 Aug 2019 23:13:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.10_model.r INFO @ Mon, 12 Aug 2019 23:13:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:13:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:13:31: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:13:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:13:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:13:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:13:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.05_summits.bed INFO @ Mon, 12 Aug 2019 23:13:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2118 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:13:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:13:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:13:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.20_summits.bed INFO @ Mon, 12 Aug 2019 23:13:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (612 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:13:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:14:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:14:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:14:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4501948/SRX4501948.10_summits.bed INFO @ Mon, 12 Aug 2019 23:14:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1211 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。