Job ID = 2590836 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,674,613 reads read : 59,349,226 reads written : 29,674,613 reads 0-length : 29,674,613 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: 00:10:19 29674613 reads; of these: 29674613 (100.00%) were unpaired; of these: 8503472 (28.66%) aligned 0 times 15892452 (53.56%) aligned exactly 1 time 5278689 (17.79%) aligned >1 times 71.34% overall alignment rate Time searching: 00:10:19 Overall time: 00:10:19 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] 13735211 / 21171141 = 0.6488 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 23:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.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 23:50:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:50:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.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 23:50:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:50:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:50:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.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 23:50:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:50:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:50:13: 1000000 INFO @ Mon, 12 Aug 2019 23:50:14: 1000000 INFO @ Mon, 12 Aug 2019 23:50:15: 1000000 INFO @ Mon, 12 Aug 2019 23:50:21: 2000000 INFO @ Mon, 12 Aug 2019 23:50:22: 2000000 INFO @ Mon, 12 Aug 2019 23:50:25: 2000000 INFO @ Mon, 12 Aug 2019 23:50:28: 3000000 INFO @ Mon, 12 Aug 2019 23:50:30: 3000000 INFO @ Mon, 12 Aug 2019 23:50:35: 3000000 INFO @ Mon, 12 Aug 2019 23:50:36: 4000000 INFO @ Mon, 12 Aug 2019 23:50:37: 4000000 INFO @ Mon, 12 Aug 2019 23:50:44: 5000000 INFO @ Mon, 12 Aug 2019 23:50:45: 5000000 INFO @ Mon, 12 Aug 2019 23:50:45: 4000000 INFO @ Mon, 12 Aug 2019 23:50:52: 6000000 INFO @ Mon, 12 Aug 2019 23:50:53: 6000000 INFO @ Mon, 12 Aug 2019 23:50:55: 5000000 INFO @ Mon, 12 Aug 2019 23:51:00: 7000000 INFO @ Mon, 12 Aug 2019 23:51:01: 7000000 INFO @ Mon, 12 Aug 2019 23:51:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:51:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:51:03: #1 total tags in treatment: 7435930 INFO @ Mon, 12 Aug 2019 23:51:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:51:03: #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 23:51:03: #1 tags after filtering in treatment: 7435930 INFO @ Mon, 12 Aug 2019 23:51:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:51:03: #1 finished! INFO @ Mon, 12 Aug 2019 23:51:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:51:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:51:04: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:51:04: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:51:04: #1 total tags in treatment: 7435930 INFO @ Mon, 12 Aug 2019 23:51:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:51:04: #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 23:51:04: #1 tags after filtering in treatment: 7435930 INFO @ Mon, 12 Aug 2019 23:51:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:51:04: #1 finished! INFO @ Mon, 12 Aug 2019 23:51:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:51:04: #2 number of paired peaks: 3250 INFO @ Mon, 12 Aug 2019 23:51:04: start model_add_line... INFO @ Mon, 12 Aug 2019 23:51:04: start X-correlation... INFO @ Mon, 12 Aug 2019 23:51:04: end of X-cor INFO @ Mon, 12 Aug 2019 23:51:04: #2 finished! INFO @ Mon, 12 Aug 2019 23:51:04: #2 predicted fragment length is 110 bps INFO @ Mon, 12 Aug 2019 23:51:04: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 12 Aug 2019 23:51:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.05_model.r INFO @ Mon, 12 Aug 2019 23:51:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:51:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:51:05: #2 number of paired peaks: 3250 INFO @ Mon, 12 Aug 2019 23:51:05: start model_add_line... INFO @ Mon, 12 Aug 2019 23:51:05: start X-correlation... INFO @ Mon, 12 Aug 2019 23:51:05: end of X-cor INFO @ Mon, 12 Aug 2019 23:51:05: #2 finished! INFO @ Mon, 12 Aug 2019 23:51:05: #2 predicted fragment length is 110 bps INFO @ Mon, 12 Aug 2019 23:51:05: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 12 Aug 2019 23:51:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.20_model.r INFO @ Mon, 12 Aug 2019 23:51:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:51:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:51:06: 6000000 INFO @ Mon, 12 Aug 2019 23:51:15: 7000000 INFO @ Mon, 12 Aug 2019 23:51:19: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:51:19: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:51:19: #1 total tags in treatment: 7435930 INFO @ Mon, 12 Aug 2019 23:51:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:51:19: #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 23:51:19: #1 tags after filtering in treatment: 7435930 INFO @ Mon, 12 Aug 2019 23:51:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:51:19: #1 finished! INFO @ Mon, 12 Aug 2019 23:51:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:51:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:51:20: #2 number of paired peaks: 3250 INFO @ Mon, 12 Aug 2019 23:51:20: start model_add_line... INFO @ Mon, 12 Aug 2019 23:51:20: start X-correlation... INFO @ Mon, 12 Aug 2019 23:51:20: end of X-cor INFO @ Mon, 12 Aug 2019 23:51:20: #2 finished! INFO @ Mon, 12 Aug 2019 23:51:20: #2 predicted fragment length is 110 bps INFO @ Mon, 12 Aug 2019 23:51:20: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 12 Aug 2019 23:51:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.10_model.r INFO @ Mon, 12 Aug 2019 23:51:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:51:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:51:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.05_summits.bed INFO @ Mon, 12 Aug 2019 23:51:38: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7542 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.20_summits.bed INFO @ Mon, 12 Aug 2019 23:51:39: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2332 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011073/SRX5011073.10_summits.bed INFO @ Mon, 12 Aug 2019 23:51:54: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4425 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。