Job ID = 2011732 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,130,866 reads read : 12,261,732 reads written : 12,261,732 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1171741.sra.cache’: 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: 00:02:46 6130866 reads; of these: 6130866 (100.00%) were paired; of these: 5346675 (87.21%) aligned concordantly 0 times 193823 (3.16%) aligned concordantly exactly 1 time 590368 (9.63%) aligned concordantly >1 times ---- 5346675 pairs aligned concordantly 0 times; of these: 216188 (4.04%) aligned discordantly 1 time ---- 5130487 pairs aligned 0 times concordantly or discordantly; of these: 10260974 mates make up the pairs; of these: 8448995 (82.34%) aligned 0 times 855731 (8.34%) aligned exactly 1 time 956248 (9.32%) aligned >1 times 31.09% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 362514 / 807932 = 0.4487 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 02:18:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.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 02:18:53: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:18:53: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:18:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.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 02:18:54: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:18:54: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:18:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.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 02:18:55: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:18:55: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:19:00: 1000000 INFO @ Sat, 06 Jul 2019 02:19:03: 1000000 INFO @ Sat, 06 Jul 2019 02:19:04: 1000000 INFO @ Sat, 06 Jul 2019 02:19:08: 2000000 INFO @ Sat, 06 Jul 2019 02:19:13: 2000000 INFO @ Sat, 06 Jul 2019 02:19:13: 2000000 INFO @ Sat, 06 Jul 2019 02:19:15: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:19:16: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:19:16: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:19:16: #1 total tags in treatment: 430077 INFO @ Sat, 06 Jul 2019 02:19:16: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:19:16: #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 02:19:16: #1 tags after filtering in treatment: 124684 INFO @ Sat, 06 Jul 2019 02:19:16: #1 Redundant rate of treatment: 0.71 INFO @ Sat, 06 Jul 2019 02:19:16: #1 finished! INFO @ Sat, 06 Jul 2019 02:19:16: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:19:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:19:16: #2 number of paired peaks: 475 WARNING @ Sat, 06 Jul 2019 02:19:16: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Sat, 06 Jul 2019 02:19:16: start model_add_line... INFO @ Sat, 06 Jul 2019 02:19:16: start X-correlation... INFO @ Sat, 06 Jul 2019 02:19:16: end of X-cor INFO @ Sat, 06 Jul 2019 02:19:16: #2 finished! INFO @ Sat, 06 Jul 2019 02:19:16: #2 predicted fragment length is 259 bps INFO @ Sat, 06 Jul 2019 02:19:16: #2 alternative fragment length(s) may be 31,241,259,585 bps INFO @ Sat, 06 Jul 2019 02:19:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.05_model.r INFO @ Sat, 06 Jul 2019 02:19:23: 3000000 INFO @ Sat, 06 Jul 2019 02:19:23: 3000000 INFO @ Sat, 06 Jul 2019 02:19:23: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:19:23: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:19:23: #1 total tags in treatment: 430077 INFO @ Sat, 06 Jul 2019 02:19:23: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:19:23: #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 02:19:23: #1 tags after filtering in treatment: 124684 INFO @ Sat, 06 Jul 2019 02:19:23: #1 Redundant rate of treatment: 0.71 INFO @ Sat, 06 Jul 2019 02:19:23: #1 finished! INFO @ Sat, 06 Jul 2019 02:19:23: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:19:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:19:23: #2 number of paired peaks: 475 WARNING @ Sat, 06 Jul 2019 02:19:23: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Sat, 06 Jul 2019 02:19:23: start model_add_line... INFO @ Sat, 06 Jul 2019 02:19:23: start X-correlation... INFO @ Sat, 06 Jul 2019 02:19:23: end of X-cor INFO @ Sat, 06 Jul 2019 02:19:23: #2 finished! INFO @ Sat, 06 Jul 2019 02:19:23: #2 predicted fragment length is 259 bps INFO @ Sat, 06 Jul 2019 02:19:23: #2 alternative fragment length(s) may be 31,241,259,585 bps INFO @ Sat, 06 Jul 2019 02:19:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.20_model.r INFO @ Sat, 06 Jul 2019 02:19:23: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:19:23: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:19:23: #1 total tags in treatment: 430077 INFO @ Sat, 06 Jul 2019 02:19:23: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:19:23: #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 02:19:23: #1 tags after filtering in treatment: 124684 INFO @ Sat, 06 Jul 2019 02:19:23: #1 Redundant rate of treatment: 0.71 INFO @ Sat, 06 Jul 2019 02:19:23: #1 finished! INFO @ Sat, 06 Jul 2019 02:19:23: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:19:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:19:23: #2 number of paired peaks: 475 WARNING @ Sat, 06 Jul 2019 02:19:23: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Sat, 06 Jul 2019 02:19:23: start model_add_line... INFO @ Sat, 06 Jul 2019 02:19:23: start X-correlation... INFO @ Sat, 06 Jul 2019 02:19:23: end of X-cor INFO @ Sat, 06 Jul 2019 02:19:23: #2 finished! INFO @ Sat, 06 Jul 2019 02:19:23: #2 predicted fragment length is 259 bps INFO @ Sat, 06 Jul 2019 02:19:23: #2 alternative fragment length(s) may be 31,241,259,585 bps INFO @ Sat, 06 Jul 2019 02:19:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.10_model.r INFO @ Sat, 06 Jul 2019 02:19:29: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:19:29: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:19:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:19:29: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:19:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:19:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:19:30: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:19:30: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:19:30: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:19:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.10_peaks.xls INFO @ Sat, 06 Jul 2019 02:19:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.20_peaks.xls INFO @ Sat, 06 Jul 2019 02:19:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:19:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:19:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.10_summits.bed INFO @ Sat, 06 Jul 2019 02:19:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.20_summits.bed INFO @ Sat, 06 Jul 2019 02:19:30: Done! INFO @ Sat, 06 Jul 2019 02:19:30: Done! INFO @ Sat, 06 Jul 2019 02:19:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.05_peaks.xls INFO @ Sat, 06 Jul 2019 02:19:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:19:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX472783/SRX472783.05_summits.bed INFO @ Sat, 06 Jul 2019 02:19:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (40 records, 4 fields): 3 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (129 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。