Job ID = 2010698 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,533,366 reads read : 5,066,732 reads written : 5,066,732 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: 00:01:28 2533366 reads; of these: 2533366 (100.00%) were paired; of these: 1412728 (55.76%) aligned concordantly 0 times 848971 (33.51%) aligned concordantly exactly 1 time 271667 (10.72%) aligned concordantly >1 times ---- 1412728 pairs aligned concordantly 0 times; of these: 6218 (0.44%) aligned discordantly 1 time ---- 1406510 pairs aligned 0 times concordantly or discordantly; of these: 2813020 mates make up the pairs; of these: 1988945 (70.70%) aligned 0 times 620858 (22.07%) aligned exactly 1 time 203217 (7.22%) aligned >1 times 60.75% overall alignment rate Time searching: 00:01:28 Overall time: 00:01:28 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 101640 / 1126603 = 0.0902 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 @ Fri, 05 Jul 2019 23:59:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.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 @ Fri, 05 Jul 2019 23:59:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:59:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.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 @ Fri, 05 Jul 2019 23:59:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:59:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:59:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.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 @ Fri, 05 Jul 2019 23:59:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:59:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:59:42: 1000000 INFO @ Fri, 05 Jul 2019 23:59:43: 1000000 INFO @ Fri, 05 Jul 2019 23:59:45: 1000000 INFO @ Fri, 05 Jul 2019 23:59:48: 2000000 INFO @ Fri, 05 Jul 2019 23:59:51: 2000000 INFO @ Fri, 05 Jul 2019 23:59:53: 2000000 INFO @ Fri, 05 Jul 2019 23:59:53: #1 tag size is determined as 37 bps INFO @ Fri, 05 Jul 2019 23:59:53: #1 tag size = 37 INFO @ Fri, 05 Jul 2019 23:59:53: #1 total tags in treatment: 1019099 INFO @ Fri, 05 Jul 2019 23:59:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:59:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:59:53: #1 tags after filtering in treatment: 822903 INFO @ Fri, 05 Jul 2019 23:59:53: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 23:59:53: #1 finished! INFO @ Fri, 05 Jul 2019 23:59:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:59:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:59:54: #2 number of paired peaks: 237 WARNING @ Fri, 05 Jul 2019 23:59:54: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Fri, 05 Jul 2019 23:59:54: start model_add_line... INFO @ Fri, 05 Jul 2019 23:59:54: start X-correlation... INFO @ Fri, 05 Jul 2019 23:59:54: end of X-cor INFO @ Fri, 05 Jul 2019 23:59:54: #2 finished! INFO @ Fri, 05 Jul 2019 23:59:54: #2 predicted fragment length is 204 bps INFO @ Fri, 05 Jul 2019 23:59:54: #2 alternative fragment length(s) may be 3,171,189,204,234 bps INFO @ Fri, 05 Jul 2019 23:59:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.05_model.r INFO @ Fri, 05 Jul 2019 23:59:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:59:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:59:57: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:59:58: #1 tag size is determined as 37 bps INFO @ Fri, 05 Jul 2019 23:59:58: #1 tag size = 37 INFO @ Fri, 05 Jul 2019 23:59:58: #1 total tags in treatment: 1019099 INFO @ Fri, 05 Jul 2019 23:59:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:59:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:59:58: #1 tags after filtering in treatment: 822903 INFO @ Fri, 05 Jul 2019 23:59:58: #1 Redundant rate of treatment: 0.19 INFO @ Fri, 05 Jul 2019 23:59:58: #1 finished! INFO @ Fri, 05 Jul 2019 23:59:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:59:58: #2 number of paired peaks: 237 WARNING @ Fri, 05 Jul 2019 23:59:58: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Fri, 05 Jul 2019 23:59:58: start model_add_line... INFO @ Fri, 05 Jul 2019 23:59:58: start X-correlation... INFO @ Fri, 05 Jul 2019 23:59:58: end of X-cor INFO @ Fri, 05 Jul 2019 23:59:58: #2 finished! INFO @ Fri, 05 Jul 2019 23:59:58: #2 predicted fragment length is 204 bps INFO @ Fri, 05 Jul 2019 23:59:58: #2 alternative fragment length(s) may be 3,171,189,204,234 bps INFO @ Fri, 05 Jul 2019 23:59:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.10_model.r INFO @ Fri, 05 Jul 2019 23:59:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:59:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:59:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:59:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:59:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.05_summits.bed INFO @ Fri, 05 Jul 2019 23:59:58: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (290 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:00:00: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:00:00: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:00:00: #1 total tags in treatment: 1019099 INFO @ Sat, 06 Jul 2019 00:00:00: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:00:00: #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 00:00:00: #1 tags after filtering in treatment: 822903 INFO @ Sat, 06 Jul 2019 00:00:00: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 06 Jul 2019 00:00:00: #1 finished! INFO @ Sat, 06 Jul 2019 00:00:00: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:00:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:00:00: #2 number of paired peaks: 237 WARNING @ Sat, 06 Jul 2019 00:00:00: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Sat, 06 Jul 2019 00:00:00: start model_add_line... INFO @ Sat, 06 Jul 2019 00:00:00: start X-correlation... INFO @ Sat, 06 Jul 2019 00:00:00: end of X-cor INFO @ Sat, 06 Jul 2019 00:00:00: #2 finished! INFO @ Sat, 06 Jul 2019 00:00:00: #2 predicted fragment length is 204 bps INFO @ Sat, 06 Jul 2019 00:00:00: #2 alternative fragment length(s) may be 3,171,189,204,234 bps INFO @ Sat, 06 Jul 2019 00:00:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.20_model.r INFO @ Sat, 06 Jul 2019 00:00:00: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:00:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 00:00:01: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 00:00:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.10_peaks.xls INFO @ Sat, 06 Jul 2019 00:00:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:00:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.10_summits.bed INFO @ Sat, 06 Jul 2019 00:00:02: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (100 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:00:04: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 00:00:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.20_peaks.xls INFO @ Sat, 06 Jul 2019 00:00:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:00:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX3865938/SRX3865938.20_summits.bed INFO @ Sat, 06 Jul 2019 00:00:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (23 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。