Job ID = 4178539 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,850,487 reads read : 22,850,487 reads written : 22,850,487 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:20 22850487 reads; of these: 22850487 (100.00%) were unpaired; of these: 345774 (1.51%) aligned 0 times 18622393 (81.50%) aligned exactly 1 time 3882320 (16.99%) aligned >1 times 98.49% overall alignment rate Time searching: 00:10:21 Overall time: 00:10:21 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] 8507645 / 22504713 = 0.3780 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.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 13:09:35: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:09:35: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:09:50: 1000000 INFO @ Thu, 05 Dec 2019 13:10:02: 2000000 INFO @ Thu, 05 Dec 2019 13:10:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.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 13:10:03: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:10:03: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:10:12: 3000000 INFO @ Thu, 05 Dec 2019 13:10:14: 1000000 INFO @ Thu, 05 Dec 2019 13:10:23: 4000000 INFO @ Thu, 05 Dec 2019 13:10:23: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:10:32: 3000000 INFO @ Thu, 05 Dec 2019 13:10:33: 5000000 INFO @ Thu, 05 Dec 2019 13:10:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.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 13:10:33: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:10:33: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:10:41: 4000000 INFO @ Thu, 05 Dec 2019 13:10:45: 1000000 INFO @ Thu, 05 Dec 2019 13:10:47: 6000000 INFO @ Thu, 05 Dec 2019 13:10:50: 5000000 INFO @ Thu, 05 Dec 2019 13:10:56: 2000000 INFO @ Thu, 05 Dec 2019 13:11:00: 6000000 INFO @ Thu, 05 Dec 2019 13:11:02: 7000000 INFO @ Thu, 05 Dec 2019 13:11:08: 3000000 INFO @ Thu, 05 Dec 2019 13:11:10: 7000000 INFO @ Thu, 05 Dec 2019 13:11:14: 8000000 INFO @ Thu, 05 Dec 2019 13:11:18: 8000000 INFO @ Thu, 05 Dec 2019 13:11:19: 4000000 INFO @ Thu, 05 Dec 2019 13:11:27: 9000000 INFO @ Thu, 05 Dec 2019 13:11:27: 9000000 INFO @ Thu, 05 Dec 2019 13:11:30: 5000000 INFO @ Thu, 05 Dec 2019 13:11:35: 10000000 INFO @ Thu, 05 Dec 2019 13:11:39: 10000000 INFO @ Thu, 05 Dec 2019 13:11:43: 6000000 INFO @ Thu, 05 Dec 2019 13:11:46: 11000000 INFO @ Thu, 05 Dec 2019 13:11:52: 11000000 INFO @ Thu, 05 Dec 2019 13:11:56: 12000000 INFO @ Thu, 05 Dec 2019 13:11:56: 7000000 INFO @ Thu, 05 Dec 2019 13:12:05: 12000000 INFO @ Thu, 05 Dec 2019 13:12:05: 13000000 INFO @ Thu, 05 Dec 2019 13:12:09: 8000000 INFO @ Thu, 05 Dec 2019 13:12:17: 13000000 INFO @ Thu, 05 Dec 2019 13:12:18: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:12:18: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:12:18: #1 total tags in treatment: 13997068 INFO @ Thu, 05 Dec 2019 13:12:18: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:12:18: #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 13:12:19: #1 tags after filtering in treatment: 13997068 INFO @ Thu, 05 Dec 2019 13:12:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:12:19: #1 finished! INFO @ Thu, 05 Dec 2019 13:12:19: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:12:20: #2 number of paired peaks: 527 WARNING @ Thu, 05 Dec 2019 13:12:20: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Thu, 05 Dec 2019 13:12:20: start model_add_line... INFO @ Thu, 05 Dec 2019 13:12:20: start X-correlation... INFO @ Thu, 05 Dec 2019 13:12:20: end of X-cor INFO @ Thu, 05 Dec 2019 13:12:20: #2 finished! INFO @ Thu, 05 Dec 2019 13:12:20: #2 predicted fragment length is 101 bps INFO @ Thu, 05 Dec 2019 13:12:20: #2 alternative fragment length(s) may be 19,83,101,126,238,269,287,420,476,484 bps INFO @ Thu, 05 Dec 2019 13:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.10_model.r INFO @ Thu, 05 Dec 2019 13:12:20: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:12:21: 9000000 INFO @ Thu, 05 Dec 2019 13:12:29: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:12:29: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:12:29: #1 total tags in treatment: 13997068 INFO @ Thu, 05 Dec 2019 13:12:29: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:12:29: #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 13:12:29: #1 tags after filtering in treatment: 13997068 INFO @ Thu, 05 Dec 2019 13:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:12:29: #1 finished! INFO @ Thu, 05 Dec 2019 13:12:29: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:12:30: #2 number of paired peaks: 527 WARNING @ Thu, 05 Dec 2019 13:12:30: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Thu, 05 Dec 2019 13:12:30: start model_add_line... INFO @ Thu, 05 Dec 2019 13:12:31: start X-correlation... INFO @ Thu, 05 Dec 2019 13:12:31: end of X-cor INFO @ Thu, 05 Dec 2019 13:12:31: #2 finished! INFO @ Thu, 05 Dec 2019 13:12:31: #2 predicted fragment length is 101 bps INFO @ Thu, 05 Dec 2019 13:12:31: #2 alternative fragment length(s) may be 19,83,101,126,238,269,287,420,476,484 bps INFO @ Thu, 05 Dec 2019 13:12:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.05_model.r INFO @ Thu, 05 Dec 2019 13:12:31: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:12:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:12:32: 10000000 INFO @ Thu, 05 Dec 2019 13:12:47: 11000000 INFO @ Thu, 05 Dec 2019 13:13:00: 12000000 INFO @ Thu, 05 Dec 2019 13:13:11: 13000000 INFO @ Thu, 05 Dec 2019 13:13:16: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:13:21: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:13:21: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:13:21: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:13:21: #1 total tags in treatment: 13997068 INFO @ Thu, 05 Dec 2019 13:13:21: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:13:21: #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 13:13:21: #1 tags after filtering in treatment: 13997068 INFO @ Thu, 05 Dec 2019 13:13:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:13:21: #1 finished! INFO @ Thu, 05 Dec 2019 13:13:21: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:13:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:13:22: #2 number of paired peaks: 527 WARNING @ Thu, 05 Dec 2019 13:13:22: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Thu, 05 Dec 2019 13:13:22: start model_add_line... INFO @ Thu, 05 Dec 2019 13:13:23: start X-correlation... INFO @ Thu, 05 Dec 2019 13:13:23: end of X-cor INFO @ Thu, 05 Dec 2019 13:13:23: #2 finished! INFO @ Thu, 05 Dec 2019 13:13:23: #2 predicted fragment length is 101 bps INFO @ Thu, 05 Dec 2019 13:13:23: #2 alternative fragment length(s) may be 19,83,101,126,238,269,287,420,476,484 bps INFO @ Thu, 05 Dec 2019 13:13:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.20_model.r INFO @ Thu, 05 Dec 2019 13:13:23: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:13:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:13:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:13:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.10_summits.bed INFO @ Thu, 05 Dec 2019 13:13:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1068 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:13:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:13:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:13:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.05_summits.bed INFO @ Thu, 05 Dec 2019 13:13:43: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5012 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:14:12: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:14:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:14:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:14:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736590/SRX5736590.20_summits.bed INFO @ Thu, 05 Dec 2019 13:14:33: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。