Job ID = 2011675 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 48,503,065 reads read : 97,006,130 reads written : 97,006,130 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1146742.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: 00:05:43 48503065 reads; of these: 48503065 (100.00%) were paired; of these: 46318263 (95.50%) aligned concordantly 0 times 1858939 (3.83%) aligned concordantly exactly 1 time 325863 (0.67%) aligned concordantly >1 times ---- 46318263 pairs aligned concordantly 0 times; of these: 57835 (0.12%) aligned discordantly 1 time ---- 46260428 pairs aligned 0 times concordantly or discordantly; of these: 92520856 mates make up the pairs; of these: 92415907 (99.89%) aligned 0 times 69284 (0.07%) aligned exactly 1 time 35665 (0.04%) aligned >1 times 4.73% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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] 1813157 / 2231484 = 0.8125 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 02:07:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.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 02:07:48: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:07:48: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:07:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.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 02:07:49: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:07:49: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:07:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.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 02:07:50: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:07:50: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:07:58: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:07:58: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:07:58: #1 total tags in treatment: 418853 INFO @ Sat, 06 Jul 2019 02:07:58: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:07:58: #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 02:07:58: #1 tags after filtering in treatment: 384063 INFO @ Sat, 06 Jul 2019 02:07:58: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 06 Jul 2019 02:07:58: #1 finished! INFO @ Sat, 06 Jul 2019 02:07:58: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:07:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:07:58: #2 number of paired peaks: 242 WARNING @ Sat, 06 Jul 2019 02:07:58: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sat, 06 Jul 2019 02:07:58: start model_add_line... INFO @ Sat, 06 Jul 2019 02:07:58: start X-correlation... INFO @ Sat, 06 Jul 2019 02:07:58: end of X-cor INFO @ Sat, 06 Jul 2019 02:07:58: #2 finished! INFO @ Sat, 06 Jul 2019 02:07:58: #2 predicted fragment length is 153 bps INFO @ Sat, 06 Jul 2019 02:07:58: #2 alternative fragment length(s) may be 2,54,72,109,138,153,191,272,367,528,555,581,586 bps INFO @ Sat, 06 Jul 2019 02:07:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.05_model.r INFO @ Sat, 06 Jul 2019 02:07:58: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:07:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:07:59: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:08:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.05_peaks.xls INFO @ Sat, 06 Jul 2019 02:08:00: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:08:00: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:08:00: #1 total tags in treatment: 418853 INFO @ Sat, 06 Jul 2019 02:08:00: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:08:00: #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 02:08:00: #1 tags after filtering in treatment: 384063 INFO @ Sat, 06 Jul 2019 02:08:00: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 06 Jul 2019 02:08:00: #1 finished! INFO @ Sat, 06 Jul 2019 02:08:00: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:08:00: #2 number of paired peaks: 242 WARNING @ Sat, 06 Jul 2019 02:08:00: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sat, 06 Jul 2019 02:08:00: start model_add_line... INFO @ Sat, 06 Jul 2019 02:08:00: start X-correlation... INFO @ Sat, 06 Jul 2019 02:08:00: end of X-cor INFO @ Sat, 06 Jul 2019 02:08:00: #2 finished! INFO @ Sat, 06 Jul 2019 02:08:00: #2 predicted fragment length is 153 bps INFO @ Sat, 06 Jul 2019 02:08:00: #2 alternative fragment length(s) may be 2,54,72,109,138,153,191,272,367,528,555,581,586 bps INFO @ Sat, 06 Jul 2019 02:08:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.10_model.r INFO @ Sat, 06 Jul 2019 02:08:01: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:08:01: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:08:01: #1 total tags in treatment: 418853 INFO @ Sat, 06 Jul 2019 02:08:01: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:08:01: #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 02:08:01: #1 tags after filtering in treatment: 384063 INFO @ Sat, 06 Jul 2019 02:08:01: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 06 Jul 2019 02:08:01: #1 finished! INFO @ Sat, 06 Jul 2019 02:08:01: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:08:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:08:01: #2 number of paired peaks: 242 WARNING @ Sat, 06 Jul 2019 02:08:01: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sat, 06 Jul 2019 02:08:01: start model_add_line... INFO @ Sat, 06 Jul 2019 02:08:01: start X-correlation... INFO @ Sat, 06 Jul 2019 02:08:01: end of X-cor INFO @ Sat, 06 Jul 2019 02:08:01: #2 finished! INFO @ Sat, 06 Jul 2019 02:08:01: #2 predicted fragment length is 153 bps INFO @ Sat, 06 Jul 2019 02:08:01: #2 alternative fragment length(s) may be 2,54,72,109,138,153,191,272,367,528,555,581,586 bps INFO @ Sat, 06 Jul 2019 02:08:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.20_model.r BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:08:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:08:22: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:08:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.05_summits.bed INFO @ Sat, 06 Jul 2019 02:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:08:22: Done! INFO @ Sat, 06 Jul 2019 02:08:22: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:08:22: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (196 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:08:23: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:08:23: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.20_peaks.xls INFO @ Sat, 06 Jul 2019 02:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.20_summits.bed INFO @ Sat, 06 Jul 2019 02:08:24: Done! INFO @ Sat, 06 Jul 2019 02:08:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.10_peaks.xls INFO @ Sat, 06 Jul 2019 02:08:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:08:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX455452/SRX455452.10_summits.bed INFO @ Sat, 06 Jul 2019 02:08:24: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 2 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (70 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling