Job ID = 4303096 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 38,301,738 reads read : 76,603,476 reads written : 76,603,476 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1151107.sra.cache’: 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: 00:37:17 38301738 reads; of these: 38301738 (100.00%) were paired; of these: 6354912 (16.59%) aligned concordantly 0 times 27802586 (72.59%) aligned concordantly exactly 1 time 4144240 (10.82%) aligned concordantly >1 times ---- 6354912 pairs aligned concordantly 0 times; of these: 104894 (1.65%) aligned discordantly 1 time ---- 6250018 pairs aligned 0 times concordantly or discordantly; of these: 12500036 mates make up the pairs; of these: 11270591 (90.16%) aligned 0 times 1013913 (8.11%) aligned exactly 1 time 215532 (1.72%) aligned >1 times 85.29% overall alignment rate Time searching: 00:37:17 Overall time: 00:37:17 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 28 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] 24808876 / 32022776 = 0.7747 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 01:33:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.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 @ Thu, 12 Dec 2019 01:33:50: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:33:50: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:33:54: 1000000 INFO @ Thu, 12 Dec 2019 01:33:58: 2000000 INFO @ Thu, 12 Dec 2019 01:34:02: 3000000 INFO @ Thu, 12 Dec 2019 01:34:06: 4000000 INFO @ Thu, 12 Dec 2019 01:34:10: 5000000 INFO @ Thu, 12 Dec 2019 01:34:14: 6000000 INFO @ Thu, 12 Dec 2019 01:34:18: 7000000 INFO @ Thu, 12 Dec 2019 01:34:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.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 @ Thu, 12 Dec 2019 01:34:19: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:34:19: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:34:22: 8000000 INFO @ Thu, 12 Dec 2019 01:34:23: 1000000 INFO @ Thu, 12 Dec 2019 01:34:26: 9000000 INFO @ Thu, 12 Dec 2019 01:34:27: 2000000 INFO @ Thu, 12 Dec 2019 01:34:31: 10000000 INFO @ Thu, 12 Dec 2019 01:34:31: 3000000 INFO @ Thu, 12 Dec 2019 01:34:35: 11000000 INFO @ Thu, 12 Dec 2019 01:34:35: 4000000 INFO @ Thu, 12 Dec 2019 01:34:39: 5000000 INFO @ Thu, 12 Dec 2019 01:34:39: 12000000 INFO @ Thu, 12 Dec 2019 01:34:43: 6000000 INFO @ Thu, 12 Dec 2019 01:34:43: 13000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 01:34:47: 7000000 INFO @ Thu, 12 Dec 2019 01:34:47: 14000000 INFO @ Thu, 12 Dec 2019 01:34:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.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 @ Thu, 12 Dec 2019 01:34:49: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:34:49: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:34:51: 8000000 INFO @ Thu, 12 Dec 2019 01:34:52: 15000000 INFO @ Thu, 12 Dec 2019 01:34:53: 1000000 INFO @ Thu, 12 Dec 2019 01:34:55: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:34:55: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:34:55: #1 total tags in treatment: 7204186 INFO @ Thu, 12 Dec 2019 01:34:55: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:34:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:34:55: #1 tags after filtering in treatment: 4762462 INFO @ Thu, 12 Dec 2019 01:34:55: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 12 Dec 2019 01:34:55: #1 finished! INFO @ Thu, 12 Dec 2019 01:34:55: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:34:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:34:55: 9000000 INFO @ Thu, 12 Dec 2019 01:34:56: #2 number of paired peaks: 6039 INFO @ Thu, 12 Dec 2019 01:34:56: start model_add_line... INFO @ Thu, 12 Dec 2019 01:34:56: start X-correlation... INFO @ Thu, 12 Dec 2019 01:34:56: end of X-cor INFO @ Thu, 12 Dec 2019 01:34:56: #2 finished! INFO @ Thu, 12 Dec 2019 01:34:56: #2 predicted fragment length is 141 bps INFO @ Thu, 12 Dec 2019 01:34:56: #2 alternative fragment length(s) may be 141 bps INFO @ Thu, 12 Dec 2019 01:34:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.05_model.r INFO @ Thu, 12 Dec 2019 01:34:56: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:34:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:34:58: 2000000 INFO @ Thu, 12 Dec 2019 01:34:59: 10000000 INFO @ Thu, 12 Dec 2019 01:35:02: 3000000 INFO @ Thu, 12 Dec 2019 01:35:03: 11000000 INFO @ Thu, 12 Dec 2019 01:35:05: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:35:06: 4000000 INFO @ Thu, 12 Dec 2019 01:35:08: 12000000 INFO @ Thu, 12 Dec 2019 01:35:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.05_peaks.xls INFO @ Thu, 12 Dec 2019 01:35:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:35:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.05_summits.bed INFO @ Thu, 12 Dec 2019 01:35:10: Done! INFO @ Thu, 12 Dec 2019 01:35:10: 5000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12206 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:35:12: 13000000 INFO @ Thu, 12 Dec 2019 01:35:15: 6000000 INFO @ Thu, 12 Dec 2019 01:35:16: 14000000 INFO @ Thu, 12 Dec 2019 01:35:19: 7000000 INFO @ Thu, 12 Dec 2019 01:35:20: 15000000 INFO @ Thu, 12 Dec 2019 01:35:23: 8000000 INFO @ Thu, 12 Dec 2019 01:35:23: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:35:23: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:35:23: #1 total tags in treatment: 7204186 INFO @ Thu, 12 Dec 2019 01:35:23: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:35:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:35:23: #1 tags after filtering in treatment: 4762462 INFO @ Thu, 12 Dec 2019 01:35:23: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 12 Dec 2019 01:35:23: #1 finished! INFO @ Thu, 12 Dec 2019 01:35:23: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:35:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:35:24: #2 number of paired peaks: 6039 INFO @ Thu, 12 Dec 2019 01:35:24: start model_add_line... INFO @ Thu, 12 Dec 2019 01:35:24: start X-correlation... INFO @ Thu, 12 Dec 2019 01:35:24: end of X-cor INFO @ Thu, 12 Dec 2019 01:35:24: #2 finished! INFO @ Thu, 12 Dec 2019 01:35:24: #2 predicted fragment length is 141 bps INFO @ Thu, 12 Dec 2019 01:35:24: #2 alternative fragment length(s) may be 141 bps INFO @ Thu, 12 Dec 2019 01:35:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.10_model.r INFO @ Thu, 12 Dec 2019 01:35:25: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:35:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:35:27: 9000000 INFO @ Thu, 12 Dec 2019 01:35:31: 10000000 INFO @ Thu, 12 Dec 2019 01:35:33: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:35:35: 11000000 INFO @ Thu, 12 Dec 2019 01:35:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.10_peaks.xls INFO @ Thu, 12 Dec 2019 01:35:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:35:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.10_summits.bed INFO @ Thu, 12 Dec 2019 01:35:38: Done! INFO @ Thu, 12 Dec 2019 01:35:40: 12000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (9088 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:35:44: 13000000 INFO @ Thu, 12 Dec 2019 01:35:48: 14000000 INFO @ Thu, 12 Dec 2019 01:35:52: 15000000 INFO @ Thu, 12 Dec 2019 01:35:55: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:35:55: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:35:55: #1 total tags in treatment: 7204186 INFO @ Thu, 12 Dec 2019 01:35:55: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:35:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:35:55: #1 tags after filtering in treatment: 4762462 INFO @ Thu, 12 Dec 2019 01:35:55: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 12 Dec 2019 01:35:55: #1 finished! INFO @ Thu, 12 Dec 2019 01:35:55: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:35:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:35:56: #2 number of paired peaks: 6039 INFO @ Thu, 12 Dec 2019 01:35:56: start model_add_line... INFO @ Thu, 12 Dec 2019 01:35:56: start X-correlation... INFO @ Thu, 12 Dec 2019 01:35:56: end of X-cor INFO @ Thu, 12 Dec 2019 01:35:56: #2 finished! INFO @ Thu, 12 Dec 2019 01:35:56: #2 predicted fragment length is 141 bps INFO @ Thu, 12 Dec 2019 01:35:56: #2 alternative fragment length(s) may be 141 bps INFO @ Thu, 12 Dec 2019 01:35:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.20_model.r INFO @ Thu, 12 Dec 2019 01:35:56: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:35:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:36:05: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:36:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.20_peaks.xls INFO @ Thu, 12 Dec 2019 01:36:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:36:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456159/SRX456159.20_summits.bed INFO @ Thu, 12 Dec 2019 01:36:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6376 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。