Job ID = 4288978 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,812,687 reads read : 19,625,374 reads written : 9,812,687 reads 0-length : 9,812,687 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: 00:01:54 9812687 reads; of these: 9812687 (100.00%) were unpaired; of these: 1418103 (14.45%) aligned 0 times 4188640 (42.69%) aligned exactly 1 time 4205944 (42.86%) aligned >1 times 85.55% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 5695457 / 8394584 = 0.6785 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:06:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Tue, 10 Dec 2019 13:06:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:06:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:06:08: 1000000 INFO @ Tue, 10 Dec 2019 13:06:14: 2000000 INFO @ Tue, 10 Dec 2019 13:06:19: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 13:06:19: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 13:06:19: #1 total tags in treatment: 2699127 INFO @ Tue, 10 Dec 2019 13:06:19: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:06:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:06:19: #1 tags after filtering in treatment: 2699127 INFO @ Tue, 10 Dec 2019 13:06:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:06:19: #1 finished! INFO @ Tue, 10 Dec 2019 13:06:19: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:06:19: #2 number of paired peaks: 428 WARNING @ Tue, 10 Dec 2019 13:06:19: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 10 Dec 2019 13:06:19: start model_add_line... INFO @ Tue, 10 Dec 2019 13:06:19: start X-correlation... INFO @ Tue, 10 Dec 2019 13:06:19: end of X-cor INFO @ Tue, 10 Dec 2019 13:06:19: #2 finished! INFO @ Tue, 10 Dec 2019 13:06:19: #2 predicted fragment length is 245 bps INFO @ Tue, 10 Dec 2019 13:06:19: #2 alternative fragment length(s) may be 1,211,245,266 bps INFO @ Tue, 10 Dec 2019 13:06:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.05_model.r INFO @ Tue, 10 Dec 2019 13:06:19: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:06:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:06:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Tue, 10 Dec 2019 13:06:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:06:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:06:36: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:06:38: 1000000 INFO @ Tue, 10 Dec 2019 13:06:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:06:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:06:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.05_summits.bed INFO @ Tue, 10 Dec 2019 13:06:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (555 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:06:44: 2000000 INFO @ Tue, 10 Dec 2019 13:06:49: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 13:06:49: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 13:06:49: #1 total tags in treatment: 2699127 INFO @ Tue, 10 Dec 2019 13:06:49: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:06:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:06:49: #1 tags after filtering in treatment: 2699127 INFO @ Tue, 10 Dec 2019 13:06:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:06:49: #1 finished! INFO @ Tue, 10 Dec 2019 13:06:49: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:06:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:06:49: #2 number of paired peaks: 428 WARNING @ Tue, 10 Dec 2019 13:06:49: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 10 Dec 2019 13:06:49: start model_add_line... INFO @ Tue, 10 Dec 2019 13:06:50: start X-correlation... INFO @ Tue, 10 Dec 2019 13:06:50: end of X-cor INFO @ Tue, 10 Dec 2019 13:06:50: #2 finished! INFO @ Tue, 10 Dec 2019 13:06:50: #2 predicted fragment length is 245 bps INFO @ Tue, 10 Dec 2019 13:06:50: #2 alternative fragment length(s) may be 1,211,245,266 bps INFO @ Tue, 10 Dec 2019 13:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.10_model.r INFO @ Tue, 10 Dec 2019 13:06:50: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:06:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:07:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Tue, 10 Dec 2019 13:07:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:07:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:07:07: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:07:08: 1000000 INFO @ Tue, 10 Dec 2019 13:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:07:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:07:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.10_summits.bed INFO @ Tue, 10 Dec 2019 13:07:10: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (283 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:07:14: 2000000 INFO @ Tue, 10 Dec 2019 13:07:19: #1 tag size is determined as 50 bps INFO @ Tue, 10 Dec 2019 13:07:19: #1 tag size = 50 INFO @ Tue, 10 Dec 2019 13:07:19: #1 total tags in treatment: 2699127 INFO @ Tue, 10 Dec 2019 13:07:19: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:07:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:07:19: #1 tags after filtering in treatment: 2699127 INFO @ Tue, 10 Dec 2019 13:07:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:07:19: #1 finished! INFO @ Tue, 10 Dec 2019 13:07:19: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:07:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:07:19: #2 number of paired peaks: 428 WARNING @ Tue, 10 Dec 2019 13:07:19: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 10 Dec 2019 13:07:19: start model_add_line... INFO @ Tue, 10 Dec 2019 13:07:19: start X-correlation... INFO @ Tue, 10 Dec 2019 13:07:19: end of X-cor INFO @ Tue, 10 Dec 2019 13:07:19: #2 finished! INFO @ Tue, 10 Dec 2019 13:07:19: #2 predicted fragment length is 245 bps INFO @ Tue, 10 Dec 2019 13:07:19: #2 alternative fragment length(s) may be 1,211,245,266 bps INFO @ Tue, 10 Dec 2019 13:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.20_model.r INFO @ Tue, 10 Dec 2019 13:07:19: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:07:36: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 10 Dec 2019 13:07:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:07:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:07:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2354014/SRX2354014.20_summits.bed INFO @ Tue, 10 Dec 2019 13:07:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。