Job ID = 4289527 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,045,066 reads read : 7,045,066 reads written : 7,045,066 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: 00:00:49 7045066 reads; of these: 7045066 (100.00%) were unpaired; of these: 3029167 (43.00%) aligned 0 times 3666562 (52.04%) aligned exactly 1 time 349337 (4.96%) aligned >1 times 57.00% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 2716633 / 4015899 = 0.6765 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 14:41:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.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 14:41:42: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:41:42: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:41:50: 1000000 INFO @ Tue, 10 Dec 2019 14:41:53: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:41:53: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:41:53: #1 total tags in treatment: 1299266 INFO @ Tue, 10 Dec 2019 14:41:53: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:41:53: #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 14:41:53: #1 tags after filtering in treatment: 1299266 INFO @ Tue, 10 Dec 2019 14:41:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:41:53: #1 finished! INFO @ Tue, 10 Dec 2019 14:41:53: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:41:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:41:53: #2 number of paired peaks: 493 WARNING @ Tue, 10 Dec 2019 14:41:53: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Tue, 10 Dec 2019 14:41:53: start model_add_line... INFO @ Tue, 10 Dec 2019 14:41:53: start X-correlation... INFO @ Tue, 10 Dec 2019 14:41:53: end of X-cor INFO @ Tue, 10 Dec 2019 14:41:53: #2 finished! INFO @ Tue, 10 Dec 2019 14:41:53: #2 predicted fragment length is 99 bps INFO @ Tue, 10 Dec 2019 14:41:53: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 10 Dec 2019 14:41:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.05_model.r INFO @ Tue, 10 Dec 2019 14:41:53: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:41:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:41:57: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:41:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.05_peaks.xls INFO @ Tue, 10 Dec 2019 14:41:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:41:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.05_summits.bed INFO @ Tue, 10 Dec 2019 14:41:59: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (2396 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 14:42:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.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 14:42:12: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:42:12: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:42:19: 1000000 INFO @ Tue, 10 Dec 2019 14:42:21: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:42:21: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:42:21: #1 total tags in treatment: 1299266 INFO @ Tue, 10 Dec 2019 14:42:21: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:42:21: #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 14:42:21: #1 tags after filtering in treatment: 1299266 INFO @ Tue, 10 Dec 2019 14:42:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:42:21: #1 finished! INFO @ Tue, 10 Dec 2019 14:42:21: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:42:21: #2 number of paired peaks: 493 WARNING @ Tue, 10 Dec 2019 14:42:21: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Tue, 10 Dec 2019 14:42:21: start model_add_line... INFO @ Tue, 10 Dec 2019 14:42:21: start X-correlation... INFO @ Tue, 10 Dec 2019 14:42:21: end of X-cor INFO @ Tue, 10 Dec 2019 14:42:21: #2 finished! INFO @ Tue, 10 Dec 2019 14:42:21: #2 predicted fragment length is 99 bps INFO @ Tue, 10 Dec 2019 14:42:21: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 10 Dec 2019 14:42:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.10_model.r INFO @ Tue, 10 Dec 2019 14:42:21: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:42:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:42:26: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:42:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.10_peaks.xls INFO @ Tue, 10 Dec 2019 14:42:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:42:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.10_summits.bed INFO @ Tue, 10 Dec 2019 14:42:28: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1779 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Tue, 10 Dec 2019 14:42:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.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 14:42:42: #1 read tag files... INFO @ Tue, 10 Dec 2019 14:42:42: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 14:42:49: 1000000 INFO @ Tue, 10 Dec 2019 14:42:51: #1 tag size is determined as 41 bps INFO @ Tue, 10 Dec 2019 14:42:51: #1 tag size = 41 INFO @ Tue, 10 Dec 2019 14:42:51: #1 total tags in treatment: 1299266 INFO @ Tue, 10 Dec 2019 14:42:51: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 14:42:51: #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 14:42:51: #1 tags after filtering in treatment: 1299266 INFO @ Tue, 10 Dec 2019 14:42:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 14:42:51: #1 finished! INFO @ Tue, 10 Dec 2019 14:42:51: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 14:42:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 14:42:51: #2 number of paired peaks: 493 WARNING @ Tue, 10 Dec 2019 14:42:51: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Tue, 10 Dec 2019 14:42:51: start model_add_line... INFO @ Tue, 10 Dec 2019 14:42:51: start X-correlation... INFO @ Tue, 10 Dec 2019 14:42:51: end of X-cor INFO @ Tue, 10 Dec 2019 14:42:51: #2 finished! INFO @ Tue, 10 Dec 2019 14:42:51: #2 predicted fragment length is 99 bps INFO @ Tue, 10 Dec 2019 14:42:51: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 10 Dec 2019 14:42:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.20_model.r INFO @ Tue, 10 Dec 2019 14:42:51: #3 Call peaks... INFO @ Tue, 10 Dec 2019 14:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 14:42:56: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 14:42:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.20_peaks.xls INFO @ Tue, 10 Dec 2019 14:42:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 14:42:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6932530/SRX6932530.20_summits.bed INFO @ Tue, 10 Dec 2019 14:42:57: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (1077 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。