Job ID = 2590871 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,390,495 reads read : 10,390,495 reads written : 10,390,495 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: 00:02:54 10390495 reads; of these: 10390495 (100.00%) were unpaired; of these: 441322 (4.25%) aligned 0 times 8500666 (81.81%) aligned exactly 1 time 1448507 (13.94%) aligned >1 times 95.75% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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_rmdupse_core] 2449558 / 9949173 = 0.2462 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 23:54:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.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 23:54:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:54:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:54:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.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 23:54:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:54:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:54:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.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 23:54:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:54:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:54:50: 1000000 INFO @ Mon, 12 Aug 2019 23:54:50: 1000000 INFO @ Mon, 12 Aug 2019 23:54:51: 1000000 INFO @ Mon, 12 Aug 2019 23:54:57: 2000000 INFO @ Mon, 12 Aug 2019 23:54:59: 2000000 INFO @ Mon, 12 Aug 2019 23:55:00: 2000000 INFO @ Mon, 12 Aug 2019 23:55:05: 3000000 INFO @ Mon, 12 Aug 2019 23:55:09: 3000000 INFO @ Mon, 12 Aug 2019 23:55:09: 3000000 INFO @ Mon, 12 Aug 2019 23:55:12: 4000000 INFO @ Mon, 12 Aug 2019 23:55:18: 4000000 INFO @ Mon, 12 Aug 2019 23:55:18: 4000000 INFO @ Mon, 12 Aug 2019 23:55:19: 5000000 INFO @ Mon, 12 Aug 2019 23:55:26: 6000000 INFO @ Mon, 12 Aug 2019 23:55:27: 5000000 INFO @ Mon, 12 Aug 2019 23:55:27: 5000000 INFO @ Mon, 12 Aug 2019 23:55:33: 7000000 INFO @ Mon, 12 Aug 2019 23:55:35: 6000000 INFO @ Mon, 12 Aug 2019 23:55:36: 6000000 INFO @ Mon, 12 Aug 2019 23:55:37: #1 tag size is determined as 44 bps INFO @ Mon, 12 Aug 2019 23:55:37: #1 tag size = 44 INFO @ Mon, 12 Aug 2019 23:55:37: #1 total tags in treatment: 7499615 INFO @ Mon, 12 Aug 2019 23:55:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:55:37: #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 23:55:37: #1 tags after filtering in treatment: 7499615 INFO @ Mon, 12 Aug 2019 23:55:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:55:37: #1 finished! INFO @ Mon, 12 Aug 2019 23:55:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:55:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:55:38: #2 number of paired peaks: 284 WARNING @ Mon, 12 Aug 2019 23:55:38: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Mon, 12 Aug 2019 23:55:38: start model_add_line... INFO @ Mon, 12 Aug 2019 23:55:38: start X-correlation... INFO @ Mon, 12 Aug 2019 23:55:38: end of X-cor INFO @ Mon, 12 Aug 2019 23:55:38: #2 finished! INFO @ Mon, 12 Aug 2019 23:55:38: #2 predicted fragment length is 124 bps INFO @ Mon, 12 Aug 2019 23:55:38: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 12 Aug 2019 23:55:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.20_model.r INFO @ Mon, 12 Aug 2019 23:55:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:55:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:55:44: 7000000 INFO @ Mon, 12 Aug 2019 23:55:45: 7000000 INFO @ Mon, 12 Aug 2019 23:55:49: #1 tag size is determined as 44 bps INFO @ Mon, 12 Aug 2019 23:55:49: #1 tag size = 44 INFO @ Mon, 12 Aug 2019 23:55:49: #1 total tags in treatment: 7499615 INFO @ Mon, 12 Aug 2019 23:55:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:55:49: #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 23:55:49: #1 tags after filtering in treatment: 7499615 INFO @ Mon, 12 Aug 2019 23:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:55:49: #1 finished! INFO @ Mon, 12 Aug 2019 23:55:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:55:49: #2 number of paired peaks: 284 WARNING @ Mon, 12 Aug 2019 23:55:49: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Mon, 12 Aug 2019 23:55:49: start model_add_line... INFO @ Mon, 12 Aug 2019 23:55:50: start X-correlation... INFO @ Mon, 12 Aug 2019 23:55:50: end of X-cor INFO @ Mon, 12 Aug 2019 23:55:50: #2 finished! INFO @ Mon, 12 Aug 2019 23:55:50: #2 predicted fragment length is 124 bps INFO @ Mon, 12 Aug 2019 23:55:50: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 12 Aug 2019 23:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.10_model.r INFO @ Mon, 12 Aug 2019 23:55:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:55:50: #1 tag size is determined as 44 bps INFO @ Mon, 12 Aug 2019 23:55:50: #1 tag size = 44 INFO @ Mon, 12 Aug 2019 23:55:50: #1 total tags in treatment: 7499615 INFO @ Mon, 12 Aug 2019 23:55:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:55:50: #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 23:55:50: #1 tags after filtering in treatment: 7499615 INFO @ Mon, 12 Aug 2019 23:55:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:55:50: #1 finished! INFO @ Mon, 12 Aug 2019 23:55:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:55:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:55:51: #2 number of paired peaks: 284 WARNING @ Mon, 12 Aug 2019 23:55:51: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Mon, 12 Aug 2019 23:55:51: start model_add_line... INFO @ Mon, 12 Aug 2019 23:55:51: start X-correlation... INFO @ Mon, 12 Aug 2019 23:55:51: end of X-cor INFO @ Mon, 12 Aug 2019 23:55:51: #2 finished! INFO @ Mon, 12 Aug 2019 23:55:51: #2 predicted fragment length is 124 bps INFO @ Mon, 12 Aug 2019 23:55:51: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 12 Aug 2019 23:55:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.05_model.r INFO @ Mon, 12 Aug 2019 23:55:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:56:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:56:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:56:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:56:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.20_summits.bed INFO @ Mon, 12 Aug 2019 23:56:10: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (90 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:56:11: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:56:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:56:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:56:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:56:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.10_summits.bed INFO @ Mon, 12 Aug 2019 23:56:22: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1446 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:56:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:56:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:56:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX507383/SRX507383.05_summits.bed INFO @ Mon, 12 Aug 2019 23:56:23: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5718 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。