Job ID = 2011916 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,308,962 reads read : 6,617,924 reads written : 6,617,924 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: 00:01:56 3308962 reads; of these: 3308962 (100.00%) were paired; of these: 369130 (11.16%) aligned concordantly 0 times 2673974 (80.81%) aligned concordantly exactly 1 time 265858 (8.03%) aligned concordantly >1 times ---- 369130 pairs aligned concordantly 0 times; of these: 244754 (66.31%) aligned discordantly 1 time ---- 124376 pairs aligned 0 times concordantly or discordantly; of these: 248752 mates make up the pairs; of these: 129408 (52.02%) aligned 0 times 57712 (23.20%) aligned exactly 1 time 61632 (24.78%) aligned >1 times 98.04% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 561961 / 3183524 = 0.1765 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 03:20:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.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 03:20:59: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:20:59: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:21:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.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 03:21:00: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:21:00: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:21:06: 1000000 INFO @ Sat, 06 Jul 2019 03:21:07: 1000000 INFO @ Sat, 06 Jul 2019 03:21:12: 2000000 INFO @ Sat, 06 Jul 2019 03:21:13: 2000000 INFO @ Sat, 06 Jul 2019 03:21:18: 3000000 INFO @ Sat, 06 Jul 2019 03:21:19: 3000000 INFO @ Sat, 06 Jul 2019 03:21:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.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 03:21:21: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:21:21: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:21:24: 4000000 INFO @ Sat, 06 Jul 2019 03:21:25: 4000000 INFO @ Sat, 06 Jul 2019 03:21:28: 1000000 INFO @ Sat, 06 Jul 2019 03:21:30: 5000000 INFO @ Sat, 06 Jul 2019 03:21:31: 5000000 INFO @ Sat, 06 Jul 2019 03:21:33: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:21:33: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:21:33: #1 total tags in treatment: 2387846 INFO @ Sat, 06 Jul 2019 03:21:33: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:21:33: #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 03:21:33: #1 tags after filtering in treatment: 1235216 INFO @ Sat, 06 Jul 2019 03:21:33: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 06 Jul 2019 03:21:33: #1 finished! INFO @ Sat, 06 Jul 2019 03:21:33: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:21:33: #2 number of paired peaks: 282 WARNING @ Sat, 06 Jul 2019 03:21:33: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Sat, 06 Jul 2019 03:21:33: start model_add_line... INFO @ Sat, 06 Jul 2019 03:21:33: start X-correlation... INFO @ Sat, 06 Jul 2019 03:21:33: end of X-cor INFO @ Sat, 06 Jul 2019 03:21:33: #2 finished! INFO @ Sat, 06 Jul 2019 03:21:33: #2 predicted fragment length is 285 bps INFO @ Sat, 06 Jul 2019 03:21:33: #2 alternative fragment length(s) may be 285 bps INFO @ Sat, 06 Jul 2019 03:21:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.05_model.r INFO @ Sat, 06 Jul 2019 03:21:33: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:21:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:21:33: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:21:33: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:21:33: #1 total tags in treatment: 2387846 INFO @ Sat, 06 Jul 2019 03:21:33: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:21:33: #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 03:21:34: #1 tags after filtering in treatment: 1235216 INFO @ Sat, 06 Jul 2019 03:21:34: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 06 Jul 2019 03:21:34: #1 finished! INFO @ Sat, 06 Jul 2019 03:21:34: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:21:34: #2 number of paired peaks: 282 WARNING @ Sat, 06 Jul 2019 03:21:34: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Sat, 06 Jul 2019 03:21:34: start model_add_line... INFO @ Sat, 06 Jul 2019 03:21:34: start X-correlation... INFO @ Sat, 06 Jul 2019 03:21:34: end of X-cor INFO @ Sat, 06 Jul 2019 03:21:34: #2 finished! INFO @ Sat, 06 Jul 2019 03:21:34: #2 predicted fragment length is 285 bps INFO @ Sat, 06 Jul 2019 03:21:34: #2 alternative fragment length(s) may be 285 bps INFO @ Sat, 06 Jul 2019 03:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.10_model.r INFO @ Sat, 06 Jul 2019 03:21:34: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:21:35: 2000000 INFO @ Sat, 06 Jul 2019 03:21:39: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:21:40: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:21:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:21:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:21:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.05_summits.bed INFO @ Sat, 06 Jul 2019 03:21:41: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (671 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:21:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:21:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:21:41: 3000000 INFO @ Sat, 06 Jul 2019 03:21:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.10_summits.bed INFO @ Sat, 06 Jul 2019 03:21:42: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (482 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:21:48: 4000000 INFO @ Sat, 06 Jul 2019 03:21:55: 5000000 INFO @ Sat, 06 Jul 2019 03:21:57: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:21:57: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:21:57: #1 total tags in treatment: 2387846 INFO @ Sat, 06 Jul 2019 03:21:57: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:21:57: #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 03:21:57: #1 tags after filtering in treatment: 1235216 INFO @ Sat, 06 Jul 2019 03:21:57: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 06 Jul 2019 03:21:57: #1 finished! INFO @ Sat, 06 Jul 2019 03:21:57: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:21:57: #2 number of paired peaks: 282 WARNING @ Sat, 06 Jul 2019 03:21:57: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Sat, 06 Jul 2019 03:21:57: start model_add_line... INFO @ Sat, 06 Jul 2019 03:21:57: start X-correlation... INFO @ Sat, 06 Jul 2019 03:21:57: end of X-cor INFO @ Sat, 06 Jul 2019 03:21:57: #2 finished! INFO @ Sat, 06 Jul 2019 03:21:57: #2 predicted fragment length is 285 bps INFO @ Sat, 06 Jul 2019 03:21:57: #2 alternative fragment length(s) may be 285 bps INFO @ Sat, 06 Jul 2019 03:21:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.20_model.r INFO @ Sat, 06 Jul 2019 03:21:57: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:22:03: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383689/SRX5383689.20_summits.bed INFO @ Sat, 06 Jul 2019 03:22:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (296 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。