Job ID = 2010773 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,387,772 reads read : 3,387,772 reads written : 3,387,772 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: 00:00:40 3387772 reads; of these: 3387772 (100.00%) were unpaired; of these: 392535 (11.59%) aligned 0 times 2504474 (73.93%) aligned exactly 1 time 490763 (14.49%) aligned >1 times 88.41% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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] 726909 / 2995237 = 0.2427 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 @ Sat, 06 Jul 2019 00:34:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.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 @ Sat, 06 Jul 2019 00:34:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:34:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:34:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.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 @ Sat, 06 Jul 2019 00:34:43: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:34:43: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:34:50: 1000000 INFO @ Sat, 06 Jul 2019 00:34:50: 1000000 INFO @ Sat, 06 Jul 2019 00:34:58: 2000000 INFO @ Sat, 06 Jul 2019 00:34:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.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 @ Sat, 06 Jul 2019 00:34:58: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:34:58: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:34:58: 2000000 INFO @ Sat, 06 Jul 2019 00:35:00: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:35:00: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:35:00: #1 total tags in treatment: 2268328 INFO @ Sat, 06 Jul 2019 00:35:00: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:35:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:35:00: #1 tags after filtering in treatment: 2268328 INFO @ Sat, 06 Jul 2019 00:35:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:35:00: #1 finished! INFO @ Sat, 06 Jul 2019 00:35:00: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:35:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:35:00: #2 number of paired peaks: 176 WARNING @ Sat, 06 Jul 2019 00:35:00: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 06 Jul 2019 00:35:00: start model_add_line... INFO @ Sat, 06 Jul 2019 00:35:00: start X-correlation... INFO @ Sat, 06 Jul 2019 00:35:00: end of X-cor INFO @ Sat, 06 Jul 2019 00:35:00: #2 finished! INFO @ Sat, 06 Jul 2019 00:35:00: #2 predicted fragment length is 302 bps INFO @ Sat, 06 Jul 2019 00:35:00: #2 alternative fragment length(s) may be 18,92,157,186,221,272,302,375,488 bps INFO @ Sat, 06 Jul 2019 00:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.10_model.r INFO @ Sat, 06 Jul 2019 00:35:00: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 00:35:00: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:35:00: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:35:00: #1 total tags in treatment: 2268328 INFO @ Sat, 06 Jul 2019 00:35:00: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:35:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:35:01: #1 tags after filtering in treatment: 2268328 INFO @ Sat, 06 Jul 2019 00:35:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:35:01: #1 finished! INFO @ Sat, 06 Jul 2019 00:35:01: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:35:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:35:01: #2 number of paired peaks: 176 WARNING @ Sat, 06 Jul 2019 00:35:01: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 06 Jul 2019 00:35:01: start model_add_line... INFO @ Sat, 06 Jul 2019 00:35:01: start X-correlation... INFO @ Sat, 06 Jul 2019 00:35:01: end of X-cor INFO @ Sat, 06 Jul 2019 00:35:01: #2 finished! INFO @ Sat, 06 Jul 2019 00:35:01: #2 predicted fragment length is 302 bps INFO @ Sat, 06 Jul 2019 00:35:01: #2 alternative fragment length(s) may be 18,92,157,186,221,272,302,375,488 bps INFO @ Sat, 06 Jul 2019 00:35:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.05_model.r INFO @ Sat, 06 Jul 2019 00:35:01: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:35:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 00:35:07: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 00:35:08: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 00:35:08: 1000000 INFO @ Sat, 06 Jul 2019 00:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.10_peaks.xls INFO @ Sat, 06 Jul 2019 00:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.10_summits.bed INFO @ Sat, 06 Jul 2019 00:35:09: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:35:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.05_peaks.xls INFO @ Sat, 06 Jul 2019 00:35:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:35:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.05_summits.bed INFO @ Sat, 06 Jul 2019 00:35:10: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:35:19: 2000000 INFO @ Sat, 06 Jul 2019 00:35:21: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:35:21: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:35:21: #1 total tags in treatment: 2268328 INFO @ Sat, 06 Jul 2019 00:35:21: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:35:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:35:21: #1 tags after filtering in treatment: 2268328 INFO @ Sat, 06 Jul 2019 00:35:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:35:21: #1 finished! INFO @ Sat, 06 Jul 2019 00:35:21: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:35:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:35:21: #2 number of paired peaks: 176 WARNING @ Sat, 06 Jul 2019 00:35:21: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 06 Jul 2019 00:35:21: start model_add_line... INFO @ Sat, 06 Jul 2019 00:35:21: start X-correlation... INFO @ Sat, 06 Jul 2019 00:35:21: end of X-cor INFO @ Sat, 06 Jul 2019 00:35:21: #2 finished! INFO @ Sat, 06 Jul 2019 00:35:21: #2 predicted fragment length is 302 bps INFO @ Sat, 06 Jul 2019 00:35:21: #2 alternative fragment length(s) may be 18,92,157,186,221,272,302,375,488 bps INFO @ Sat, 06 Jul 2019 00:35:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.20_model.r INFO @ Sat, 06 Jul 2019 00:35:21: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:35:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 00:35:28: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 00:35:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.20_peaks.xls BedGraph に変換しました。 INFO @ Sat, 06 Jul 2019 00:36:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.20_peaks.narrowPeak BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:36:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX390619/SRX390619.20_summits.bed INFO @ Sat, 06 Jul 2019 00:36:08: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。