Job ID = 1293903 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,713,175 reads read : 30,713,175 reads written : 30,713,175 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:08:23 30713175 reads; of these: 30713175 (100.00%) were unpaired; of these: 1354629 (4.41%) aligned 0 times 22580228 (73.52%) aligned exactly 1 time 6778318 (22.07%) aligned >1 times 95.59% overall alignment rate Time searching: 00:08:23 Overall time: 00:08:23 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] 5971788 / 29358546 = 0.2034 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, 03 Jun 2019 03:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.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, 03 Jun 2019 03:20:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:20:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.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, 03 Jun 2019 03:20:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:20:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.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, 03 Jun 2019 03:20:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:20:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:20:21: 1000000 INFO @ Mon, 03 Jun 2019 03:20:22: 1000000 INFO @ Mon, 03 Jun 2019 03:20:22: 1000000 INFO @ Mon, 03 Jun 2019 03:20:28: 2000000 INFO @ Mon, 03 Jun 2019 03:20:30: 2000000 INFO @ Mon, 03 Jun 2019 03:20:30: 2000000 INFO @ Mon, 03 Jun 2019 03:20:35: 3000000 INFO @ Mon, 03 Jun 2019 03:20:38: 3000000 INFO @ Mon, 03 Jun 2019 03:20:38: 3000000 INFO @ Mon, 03 Jun 2019 03:20:42: 4000000 INFO @ Mon, 03 Jun 2019 03:20:46: 4000000 INFO @ Mon, 03 Jun 2019 03:20:46: 4000000 INFO @ Mon, 03 Jun 2019 03:20:49: 5000000 INFO @ Mon, 03 Jun 2019 03:20:54: 5000000 INFO @ Mon, 03 Jun 2019 03:20:54: 5000000 INFO @ Mon, 03 Jun 2019 03:20:56: 6000000 INFO @ Mon, 03 Jun 2019 03:21:01: 6000000 INFO @ Mon, 03 Jun 2019 03:21:01: 6000000 INFO @ Mon, 03 Jun 2019 03:21:03: 7000000 INFO @ Mon, 03 Jun 2019 03:21:09: 7000000 INFO @ Mon, 03 Jun 2019 03:21:09: 7000000 INFO @ Mon, 03 Jun 2019 03:21:10: 8000000 INFO @ Mon, 03 Jun 2019 03:21:16: 8000000 INFO @ Mon, 03 Jun 2019 03:21:16: 9000000 INFO @ Mon, 03 Jun 2019 03:21:17: 8000000 INFO @ Mon, 03 Jun 2019 03:21:23: 10000000 INFO @ Mon, 03 Jun 2019 03:21:23: 9000000 INFO @ Mon, 03 Jun 2019 03:21:24: 9000000 INFO @ Mon, 03 Jun 2019 03:21:30: 11000000 INFO @ Mon, 03 Jun 2019 03:21:30: 10000000 INFO @ Mon, 03 Jun 2019 03:21:31: 10000000 INFO @ Mon, 03 Jun 2019 03:21:36: 12000000 INFO @ Mon, 03 Jun 2019 03:21:37: 11000000 INFO @ Mon, 03 Jun 2019 03:21:38: 11000000 INFO @ Mon, 03 Jun 2019 03:21:43: 13000000 INFO @ Mon, 03 Jun 2019 03:21:45: 12000000 INFO @ Mon, 03 Jun 2019 03:21:45: 12000000 INFO @ Mon, 03 Jun 2019 03:21:50: 14000000 INFO @ Mon, 03 Jun 2019 03:21:52: 13000000 INFO @ Mon, 03 Jun 2019 03:21:53: 13000000 INFO @ Mon, 03 Jun 2019 03:21:56: 15000000 INFO @ Mon, 03 Jun 2019 03:21:59: 14000000 INFO @ Mon, 03 Jun 2019 03:22:00: 14000000 INFO @ Mon, 03 Jun 2019 03:22:03: 16000000 INFO @ Mon, 03 Jun 2019 03:22:06: 15000000 INFO @ Mon, 03 Jun 2019 03:22:07: 15000000 INFO @ Mon, 03 Jun 2019 03:22:09: 17000000 INFO @ Mon, 03 Jun 2019 03:22:13: 16000000 INFO @ Mon, 03 Jun 2019 03:22:14: 16000000 INFO @ Mon, 03 Jun 2019 03:22:16: 18000000 INFO @ Mon, 03 Jun 2019 03:22:20: 17000000 INFO @ Mon, 03 Jun 2019 03:22:21: 17000000 INFO @ Mon, 03 Jun 2019 03:22:23: 19000000 INFO @ Mon, 03 Jun 2019 03:22:27: 18000000 INFO @ Mon, 03 Jun 2019 03:22:29: 18000000 INFO @ Mon, 03 Jun 2019 03:22:30: 20000000 INFO @ Mon, 03 Jun 2019 03:22:35: 19000000 INFO @ Mon, 03 Jun 2019 03:22:36: 19000000 INFO @ Mon, 03 Jun 2019 03:22:37: 21000000 INFO @ Mon, 03 Jun 2019 03:22:42: 20000000 INFO @ Mon, 03 Jun 2019 03:22:43: 22000000 INFO @ Mon, 03 Jun 2019 03:22:44: 20000000 INFO @ Mon, 03 Jun 2019 03:22:50: 21000000 INFO @ Mon, 03 Jun 2019 03:22:50: 23000000 INFO @ Mon, 03 Jun 2019 03:22:52: 21000000 INFO @ Mon, 03 Jun 2019 03:22:53: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 03:22:53: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 03:22:53: #1 total tags in treatment: 23386758 INFO @ Mon, 03 Jun 2019 03:22:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:22:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:22:54: #1 tags after filtering in treatment: 23386758 INFO @ Mon, 03 Jun 2019 03:22:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:22:54: #1 finished! INFO @ Mon, 03 Jun 2019 03:22:54: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:22:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:22:56: #2 number of paired peaks: 570 WARNING @ Mon, 03 Jun 2019 03:22:56: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Mon, 03 Jun 2019 03:22:56: start model_add_line... INFO @ Mon, 03 Jun 2019 03:22:56: start X-correlation... INFO @ Mon, 03 Jun 2019 03:22:56: end of X-cor INFO @ Mon, 03 Jun 2019 03:22:56: #2 finished! INFO @ Mon, 03 Jun 2019 03:22:56: #2 predicted fragment length is 109 bps INFO @ Mon, 03 Jun 2019 03:22:56: #2 alternative fragment length(s) may be 4,109 bps INFO @ Mon, 03 Jun 2019 03:22:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.10_model.r INFO @ Mon, 03 Jun 2019 03:22:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:22:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:22:57: 22000000 INFO @ Mon, 03 Jun 2019 03:22:59: 22000000 INFO @ Mon, 03 Jun 2019 03:23:04: 23000000 INFO @ Mon, 03 Jun 2019 03:23:07: 23000000 INFO @ Mon, 03 Jun 2019 03:23:07: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 03:23:07: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 03:23:07: #1 total tags in treatment: 23386758 INFO @ Mon, 03 Jun 2019 03:23:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:23:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:23:08: #1 tags after filtering in treatment: 23386758 INFO @ Mon, 03 Jun 2019 03:23:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:23:08: #1 finished! INFO @ Mon, 03 Jun 2019 03:23:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:23:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:23:10: #2 number of paired peaks: 570 WARNING @ Mon, 03 Jun 2019 03:23:10: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Mon, 03 Jun 2019 03:23:10: start model_add_line... INFO @ Mon, 03 Jun 2019 03:23:10: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 03:23:10: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 03:23:10: #1 total tags in treatment: 23386758 INFO @ Mon, 03 Jun 2019 03:23:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:23:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:23:10: start X-correlation... INFO @ Mon, 03 Jun 2019 03:23:10: end of X-cor INFO @ Mon, 03 Jun 2019 03:23:10: #2 finished! INFO @ Mon, 03 Jun 2019 03:23:10: #2 predicted fragment length is 109 bps INFO @ Mon, 03 Jun 2019 03:23:10: #2 alternative fragment length(s) may be 4,109 bps INFO @ Mon, 03 Jun 2019 03:23:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.05_model.r INFO @ Mon, 03 Jun 2019 03:23:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:23:11: #1 tags after filtering in treatment: 23386758 INFO @ Mon, 03 Jun 2019 03:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:23:11: #1 finished! INFO @ Mon, 03 Jun 2019 03:23:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:23:13: #2 number of paired peaks: 570 WARNING @ Mon, 03 Jun 2019 03:23:13: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Mon, 03 Jun 2019 03:23:13: start model_add_line... INFO @ Mon, 03 Jun 2019 03:23:13: start X-correlation... INFO @ Mon, 03 Jun 2019 03:23:13: end of X-cor INFO @ Mon, 03 Jun 2019 03:23:13: #2 finished! INFO @ Mon, 03 Jun 2019 03:23:13: #2 predicted fragment length is 109 bps INFO @ Mon, 03 Jun 2019 03:23:13: #2 alternative fragment length(s) may be 4,109 bps INFO @ Mon, 03 Jun 2019 03:23:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.20_model.r INFO @ Mon, 03 Jun 2019 03:23:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:23:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:23:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:24:11: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:24:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:24:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:24:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:24:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.10_summits.bed INFO @ Mon, 03 Jun 2019 03:24:30: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8286 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:24:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.05_summits.bed INFO @ Mon, 03 Jun 2019 03:24:42: Done! pass1 - making usageList (15 chroms): 10 millis pass2 - checking and writing primary data (21152 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:24:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:24:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:24:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146998/SRX146998.20_summits.bed INFO @ Mon, 03 Jun 2019 03:24:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2682 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。