Job ID = 2010554 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,864,875 reads read : 19,729,750 reads written : 19,729,750 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: 00:03:29 9864875 reads; of these: 9864875 (100.00%) were paired; of these: 7791968 (78.99%) aligned concordantly 0 times 1563579 (15.85%) aligned concordantly exactly 1 time 509328 (5.16%) aligned concordantly >1 times ---- 7791968 pairs aligned concordantly 0 times; of these: 42003 (0.54%) aligned discordantly 1 time ---- 7749965 pairs aligned 0 times concordantly or discordantly; of these: 15499930 mates make up the pairs; of these: 15307604 (98.76%) aligned 0 times 96079 (0.62%) aligned exactly 1 time 96247 (0.62%) aligned >1 times 22.41% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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] 333100 / 2111259 = 0.1578 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 23:13:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.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 23:13:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:13:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:13:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.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 23:13:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:13:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:13:16: 1000000 INFO @ Fri, 05 Jul 2019 23:13:17: 1000000 INFO @ Fri, 05 Jul 2019 23:13:23: 2000000 INFO @ Fri, 05 Jul 2019 23:13:28: 2000000 INFO @ Fri, 05 Jul 2019 23:13:30: 3000000 INFO @ Fri, 05 Jul 2019 23:13:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.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 23:13:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:13:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:13:35: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:13:35: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:13:35: #1 total tags in treatment: 1743763 INFO @ Fri, 05 Jul 2019 23:13:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:13:35: #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 23:13:35: #1 tags after filtering in treatment: 1166143 INFO @ Fri, 05 Jul 2019 23:13:35: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 23:13:35: #1 finished! INFO @ Fri, 05 Jul 2019 23:13:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:13:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:13:36: #2 number of paired peaks: 1016 INFO @ Fri, 05 Jul 2019 23:13:36: start model_add_line... INFO @ Fri, 05 Jul 2019 23:13:36: start X-correlation... INFO @ Fri, 05 Jul 2019 23:13:36: end of X-cor INFO @ Fri, 05 Jul 2019 23:13:36: #2 finished! INFO @ Fri, 05 Jul 2019 23:13:36: #2 predicted fragment length is 198 bps INFO @ Fri, 05 Jul 2019 23:13:36: #2 alternative fragment length(s) may be 2,198,227 bps INFO @ Fri, 05 Jul 2019 23:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.10_model.r INFO @ Fri, 05 Jul 2019 23:13:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:13:38: 3000000 INFO @ Fri, 05 Jul 2019 23:13:39: 1000000 INFO @ Fri, 05 Jul 2019 23:13:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:13:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:13:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:13:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.10_summits.bed INFO @ Fri, 05 Jul 2019 23:13:45: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (302 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:13:45: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:13:45: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:13:45: #1 total tags in treatment: 1743763 INFO @ Fri, 05 Jul 2019 23:13:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:13:45: #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 23:13:45: #1 tags after filtering in treatment: 1166143 INFO @ Fri, 05 Jul 2019 23:13:45: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 23:13:45: #1 finished! INFO @ Fri, 05 Jul 2019 23:13:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:13:45: #2 number of paired peaks: 1016 INFO @ Fri, 05 Jul 2019 23:13:45: start model_add_line... INFO @ Fri, 05 Jul 2019 23:13:46: start X-correlation... INFO @ Fri, 05 Jul 2019 23:13:46: end of X-cor INFO @ Fri, 05 Jul 2019 23:13:46: #2 finished! INFO @ Fri, 05 Jul 2019 23:13:46: #2 predicted fragment length is 198 bps INFO @ Fri, 05 Jul 2019 23:13:46: #2 alternative fragment length(s) may be 2,198,227 bps INFO @ Fri, 05 Jul 2019 23:13:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.05_model.r INFO @ Fri, 05 Jul 2019 23:13:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:13:48: 2000000 INFO @ Fri, 05 Jul 2019 23:13:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:13:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:13:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:13:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.05_summits.bed INFO @ Fri, 05 Jul 2019 23:13:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (392 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 23:13:57: 3000000 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:14:03: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:14:03: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:14:03: #1 total tags in treatment: 1743763 INFO @ Fri, 05 Jul 2019 23:14:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:14:03: #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 23:14:03: #1 tags after filtering in treatment: 1166143 INFO @ Fri, 05 Jul 2019 23:14:03: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 05 Jul 2019 23:14:03: #1 finished! INFO @ Fri, 05 Jul 2019 23:14:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:14:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:14:04: #2 number of paired peaks: 1016 INFO @ Fri, 05 Jul 2019 23:14:04: start model_add_line... INFO @ Fri, 05 Jul 2019 23:14:04: start X-correlation... INFO @ Fri, 05 Jul 2019 23:14:04: end of X-cor INFO @ Fri, 05 Jul 2019 23:14:04: #2 finished! INFO @ Fri, 05 Jul 2019 23:14:04: #2 predicted fragment length is 198 bps INFO @ Fri, 05 Jul 2019 23:14:04: #2 alternative fragment length(s) may be 2,198,227 bps INFO @ Fri, 05 Jul 2019 23:14:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.20_model.r INFO @ Fri, 05 Jul 2019 23:14:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:14:04: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:14:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:14:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:14:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:14:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381255/SRX381255.20_summits.bed INFO @ Fri, 05 Jul 2019 23:14:18: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (207 records, 4 fields): 4 millis CompletedMACS2peakCalling