Job ID = 4178560 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,584,059 reads read : 43,168,118 reads written : 21,584,059 reads 0-length : 21,584,059 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: 00:00:01 Multiseed full-index search: 00:05:42 21584059 reads; of these: 21584059 (100.00%) were unpaired; of these: 5199702 (24.09%) aligned 0 times 13060465 (60.51%) aligned exactly 1 time 3323892 (15.40%) aligned >1 times 75.91% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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] 4065650 / 16384357 = 0.2481 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:20:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.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, 05 Dec 2019 13:20:02: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:20:02: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:20:08: 1000000 INFO @ Thu, 05 Dec 2019 13:20:13: 2000000 INFO @ Thu, 05 Dec 2019 13:20:18: 3000000 INFO @ Thu, 05 Dec 2019 13:20:23: 4000000 INFO @ Thu, 05 Dec 2019 13:20:28: 5000000 INFO @ Thu, 05 Dec 2019 13:20:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.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, 05 Dec 2019 13:20:32: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:20:32: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:20:34: 6000000 INFO @ Thu, 05 Dec 2019 13:20:38: 1000000 INFO @ Thu, 05 Dec 2019 13:20:40: 7000000 INFO @ Thu, 05 Dec 2019 13:20:44: 2000000 INFO @ Thu, 05 Dec 2019 13:20:46: 8000000 INFO @ Thu, 05 Dec 2019 13:20:50: 3000000 INFO @ Thu, 05 Dec 2019 13:20:52: 9000000 INFO @ Thu, 05 Dec 2019 13:20:56: 4000000 INFO @ Thu, 05 Dec 2019 13:20:58: 10000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:21:02: 5000000 INFO @ Thu, 05 Dec 2019 13:21:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.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, 05 Dec 2019 13:21:03: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:21:03: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:21:04: 11000000 INFO @ Thu, 05 Dec 2019 13:21:08: 6000000 INFO @ Thu, 05 Dec 2019 13:21:09: 1000000 INFO @ Thu, 05 Dec 2019 13:21:11: 12000000 INFO @ Thu, 05 Dec 2019 13:21:13: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:21:13: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:21:13: #1 total tags in treatment: 12318707 INFO @ Thu, 05 Dec 2019 13:21:13: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:21:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:21:13: #1 tags after filtering in treatment: 12318707 INFO @ Thu, 05 Dec 2019 13:21:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:21:13: #1 finished! INFO @ Thu, 05 Dec 2019 13:21:13: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:21:14: #2 number of paired peaks: 140 WARNING @ Thu, 05 Dec 2019 13:21:14: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Thu, 05 Dec 2019 13:21:14: start model_add_line... INFO @ Thu, 05 Dec 2019 13:21:14: start X-correlation... INFO @ Thu, 05 Dec 2019 13:21:14: end of X-cor INFO @ Thu, 05 Dec 2019 13:21:14: #2 finished! INFO @ Thu, 05 Dec 2019 13:21:14: #2 predicted fragment length is 120 bps INFO @ Thu, 05 Dec 2019 13:21:14: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 05 Dec 2019 13:21:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.05_model.r INFO @ Thu, 05 Dec 2019 13:21:14: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:21:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:21:14: 7000000 INFO @ Thu, 05 Dec 2019 13:21:15: 2000000 INFO @ Thu, 05 Dec 2019 13:21:20: 8000000 INFO @ Thu, 05 Dec 2019 13:21:21: 3000000 INFO @ Thu, 05 Dec 2019 13:21:26: 9000000 INFO @ Thu, 05 Dec 2019 13:21:27: 4000000 INFO @ Thu, 05 Dec 2019 13:21:32: 10000000 INFO @ Thu, 05 Dec 2019 13:21:33: 5000000 INFO @ Thu, 05 Dec 2019 13:21:38: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:21:38: 11000000 INFO @ Thu, 05 Dec 2019 13:21:39: 6000000 INFO @ Thu, 05 Dec 2019 13:21:44: 12000000 INFO @ Thu, 05 Dec 2019 13:21:45: 7000000 INFO @ Thu, 05 Dec 2019 13:21:46: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:21:46: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:21:46: #1 total tags in treatment: 12318707 INFO @ Thu, 05 Dec 2019 13:21:46: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:21:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:21:47: #1 tags after filtering in treatment: 12318707 INFO @ Thu, 05 Dec 2019 13:21:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:21:47: #1 finished! INFO @ Thu, 05 Dec 2019 13:21:47: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:21:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:21:47: #2 number of paired peaks: 140 WARNING @ Thu, 05 Dec 2019 13:21:47: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Thu, 05 Dec 2019 13:21:47: start model_add_line... INFO @ Thu, 05 Dec 2019 13:21:47: start X-correlation... INFO @ Thu, 05 Dec 2019 13:21:48: end of X-cor INFO @ Thu, 05 Dec 2019 13:21:48: #2 finished! INFO @ Thu, 05 Dec 2019 13:21:48: #2 predicted fragment length is 120 bps INFO @ Thu, 05 Dec 2019 13:21:48: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 05 Dec 2019 13:21:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.10_model.r INFO @ Thu, 05 Dec 2019 13:21:50: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:21:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:21:51: 8000000 INFO @ Thu, 05 Dec 2019 13:21:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:21:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:21:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.05_summits.bed INFO @ Thu, 05 Dec 2019 13:21:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2165 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:21:56: 9000000 INFO @ Thu, 05 Dec 2019 13:22:01: 10000000 INFO @ Thu, 05 Dec 2019 13:22:07: 11000000 INFO @ Thu, 05 Dec 2019 13:22:12: 12000000 INFO @ Thu, 05 Dec 2019 13:22:13: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:22:13: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:22:13: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:22:13: #1 total tags in treatment: 12318707 INFO @ Thu, 05 Dec 2019 13:22:13: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:22:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:22:14: #1 tags after filtering in treatment: 12318707 INFO @ Thu, 05 Dec 2019 13:22:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:22:14: #1 finished! INFO @ Thu, 05 Dec 2019 13:22:14: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:22:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:22:15: #2 number of paired peaks: 140 WARNING @ Thu, 05 Dec 2019 13:22:15: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Thu, 05 Dec 2019 13:22:15: start model_add_line... INFO @ Thu, 05 Dec 2019 13:22:15: start X-correlation... INFO @ Thu, 05 Dec 2019 13:22:15: end of X-cor INFO @ Thu, 05 Dec 2019 13:22:15: #2 finished! INFO @ Thu, 05 Dec 2019 13:22:15: #2 predicted fragment length is 120 bps INFO @ Thu, 05 Dec 2019 13:22:15: #2 alternative fragment length(s) may be 120 bps INFO @ Thu, 05 Dec 2019 13:22:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.20_model.r INFO @ Thu, 05 Dec 2019 13:22:15: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:22:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:22:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:22:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:22:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.10_summits.bed INFO @ Thu, 05 Dec 2019 13:22:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1310 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:22:38: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:22:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:22:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:22:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827832/SRX5827832.20_summits.bed INFO @ Thu, 05 Dec 2019 13:22:51: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (629 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。