Job ID = 2591009 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,181,487 reads read : 14,181,487 reads written : 14,181,487 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: 00:03:20 14181487 reads; of these: 14181487 (100.00%) were unpaired; of these: 3771023 (26.59%) aligned 0 times 9189403 (64.80%) aligned exactly 1 time 1221061 (8.61%) aligned >1 times 73.41% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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 8 files... [bam_rmdupse_core] 3594322 / 10410464 = 0.3453 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 @ Tue, 13 Aug 2019 00:39:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.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 @ Tue, 13 Aug 2019 00:39:04: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:39:04: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:39:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.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 @ Tue, 13 Aug 2019 00:39:05: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:39:05: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:39:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.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 @ Tue, 13 Aug 2019 00:39:06: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:39:06: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:39:17: 1000000 INFO @ Tue, 13 Aug 2019 00:39:17: 1000000 INFO @ Tue, 13 Aug 2019 00:39:18: 1000000 INFO @ Tue, 13 Aug 2019 00:39:24: 2000000 INFO @ Tue, 13 Aug 2019 00:39:27: 2000000 INFO @ Tue, 13 Aug 2019 00:39:29: 2000000 INFO @ Tue, 13 Aug 2019 00:39:32: 3000000 INFO @ Tue, 13 Aug 2019 00:39:37: 3000000 INFO @ Tue, 13 Aug 2019 00:39:39: 4000000 INFO @ Tue, 13 Aug 2019 00:39:40: 3000000 INFO @ Tue, 13 Aug 2019 00:39:46: 5000000 INFO @ Tue, 13 Aug 2019 00:39:47: 4000000 INFO @ Tue, 13 Aug 2019 00:39:51: 4000000 INFO @ Tue, 13 Aug 2019 00:39:53: 6000000 INFO @ Tue, 13 Aug 2019 00:39:56: 5000000 INFO @ Tue, 13 Aug 2019 00:39:59: #1 tag size is determined as 51 bps INFO @ Tue, 13 Aug 2019 00:39:59: #1 tag size = 51 INFO @ Tue, 13 Aug 2019 00:39:59: #1 total tags in treatment: 6816142 INFO @ Tue, 13 Aug 2019 00:39:59: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:39:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:39:59: #1 tags after filtering in treatment: 6816142 INFO @ Tue, 13 Aug 2019 00:39:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:39:59: #1 finished! INFO @ Tue, 13 Aug 2019 00:39:59: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:39:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:40:00: #2 number of paired peaks: 1753 INFO @ Tue, 13 Aug 2019 00:40:00: start model_add_line... INFO @ Tue, 13 Aug 2019 00:40:00: start X-correlation... INFO @ Tue, 13 Aug 2019 00:40:00: end of X-cor INFO @ Tue, 13 Aug 2019 00:40:00: #2 finished! INFO @ Tue, 13 Aug 2019 00:40:00: #2 predicted fragment length is 172 bps INFO @ Tue, 13 Aug 2019 00:40:00: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 13 Aug 2019 00:40:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.05_model.r INFO @ Tue, 13 Aug 2019 00:40:00: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:40:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:40:02: 5000000 INFO @ Tue, 13 Aug 2019 00:40:06: 6000000 INFO @ Tue, 13 Aug 2019 00:40:12: 6000000 INFO @ Tue, 13 Aug 2019 00:40:14: #1 tag size is determined as 51 bps INFO @ Tue, 13 Aug 2019 00:40:14: #1 tag size = 51 INFO @ Tue, 13 Aug 2019 00:40:14: #1 total tags in treatment: 6816142 INFO @ Tue, 13 Aug 2019 00:40:14: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:40:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:40:14: #1 tags after filtering in treatment: 6816142 INFO @ Tue, 13 Aug 2019 00:40:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:40:14: #1 finished! INFO @ Tue, 13 Aug 2019 00:40:14: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:40:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:40:15: #2 number of paired peaks: 1753 INFO @ Tue, 13 Aug 2019 00:40:15: start model_add_line... INFO @ Tue, 13 Aug 2019 00:40:15: start X-correlation... INFO @ Tue, 13 Aug 2019 00:40:15: end of X-cor INFO @ Tue, 13 Aug 2019 00:40:15: #2 finished! INFO @ Tue, 13 Aug 2019 00:40:15: #2 predicted fragment length is 172 bps INFO @ Tue, 13 Aug 2019 00:40:15: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 13 Aug 2019 00:40:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.20_model.r INFO @ Tue, 13 Aug 2019 00:40:15: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:40:20: #1 tag size is determined as 51 bps INFO @ Tue, 13 Aug 2019 00:40:20: #1 tag size = 51 INFO @ Tue, 13 Aug 2019 00:40:20: #1 total tags in treatment: 6816142 INFO @ Tue, 13 Aug 2019 00:40:20: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:40:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:40:20: #1 tags after filtering in treatment: 6816142 INFO @ Tue, 13 Aug 2019 00:40:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:40:20: #1 finished! INFO @ Tue, 13 Aug 2019 00:40:20: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:40:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:40:21: #2 number of paired peaks: 1753 INFO @ Tue, 13 Aug 2019 00:40:21: start model_add_line... INFO @ Tue, 13 Aug 2019 00:40:21: start X-correlation... INFO @ Tue, 13 Aug 2019 00:40:21: end of X-cor INFO @ Tue, 13 Aug 2019 00:40:21: #2 finished! INFO @ Tue, 13 Aug 2019 00:40:21: #2 predicted fragment length is 172 bps INFO @ Tue, 13 Aug 2019 00:40:21: #2 alternative fragment length(s) may be 172 bps INFO @ Tue, 13 Aug 2019 00:40:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.10_model.r INFO @ Tue, 13 Aug 2019 00:40:21: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:40:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:40:22: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.05_summits.bed INFO @ Tue, 13 Aug 2019 00:40:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6540 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:40:37: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:40:44: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:40:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:40:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:40:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.20_summits.bed INFO @ Tue, 13 Aug 2019 00:40:48: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1707 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645427/SRX645427.10_summits.bed INFO @ Tue, 13 Aug 2019 00:40:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3480 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。