Job ID = 2007876 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 203,710 reads read : 407,420 reads written : 407,420 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: 00:00:06 203710 reads; of these: 203710 (100.00%) were paired; of these: 45179 (22.18%) aligned concordantly 0 times 142287 (69.85%) aligned concordantly exactly 1 time 16244 (7.97%) aligned concordantly >1 times ---- 45179 pairs aligned concordantly 0 times; of these: 5269 (11.66%) aligned discordantly 1 time ---- 39910 pairs aligned 0 times concordantly or discordantly; of these: 79820 mates make up the pairs; of these: 76765 (96.17%) aligned 0 times 1644 (2.06%) aligned exactly 1 time 1411 (1.77%) aligned >1 times 81.16% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 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] 3715 / 163383 = 0.0227 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 16:37:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.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 16:37:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:37:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.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 16:37:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:37:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:37:02: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:37:02: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:37:02: #1 total tags in treatment: 154890 INFO @ Fri, 05 Jul 2019 16:37:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:37:02: #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 16:37:02: #1 tags after filtering in treatment: 153677 INFO @ Fri, 05 Jul 2019 16:37:02: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:37:02: #1 finished! INFO @ Fri, 05 Jul 2019 16:37:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:37:02: #2 number of paired peaks: 149 WARNING @ Fri, 05 Jul 2019 16:37:02: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 05 Jul 2019 16:37:02: start model_add_line... INFO @ Fri, 05 Jul 2019 16:37:02: start X-correlation... INFO @ Fri, 05 Jul 2019 16:37:02: end of X-cor INFO @ Fri, 05 Jul 2019 16:37:02: #2 finished! INFO @ Fri, 05 Jul 2019 16:37:02: #2 predicted fragment length is 271 bps INFO @ Fri, 05 Jul 2019 16:37:02: #2 alternative fragment length(s) may be 16,56,71,107,138,154,185,212,230,255,271,310,349,438,468,519,563 bps INFO @ Fri, 05 Jul 2019 16:37:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.05_model.r INFO @ Fri, 05 Jul 2019 16:37:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:37:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.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 16:37:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:37:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:37:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:37:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:37:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:37:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.05_summits.bed INFO @ Fri, 05 Jul 2019 16:37:03: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:37:03: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:37:03: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:37:03: #1 total tags in treatment: 154890 INFO @ Fri, 05 Jul 2019 16:37:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:37:03: #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 16:37:03: #1 tags after filtering in treatment: 153677 INFO @ Fri, 05 Jul 2019 16:37:03: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:37:03: #1 finished! INFO @ Fri, 05 Jul 2019 16:37:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:37:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:37:03: #2 number of paired peaks: 149 WARNING @ Fri, 05 Jul 2019 16:37:03: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 05 Jul 2019 16:37:03: start model_add_line... INFO @ Fri, 05 Jul 2019 16:37:03: start X-correlation... INFO @ Fri, 05 Jul 2019 16:37:03: end of X-cor INFO @ Fri, 05 Jul 2019 16:37:03: #2 finished! INFO @ Fri, 05 Jul 2019 16:37:03: #2 predicted fragment length is 271 bps INFO @ Fri, 05 Jul 2019 16:37:03: #2 alternative fragment length(s) may be 16,56,71,107,138,154,185,212,230,255,271,310,349,438,468,519,563 bps INFO @ Fri, 05 Jul 2019 16:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.10_model.r INFO @ Fri, 05 Jul 2019 16:37:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:37:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:37:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:37:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:37:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.10_summits.bed INFO @ Fri, 05 Jul 2019 16:37:04: Done! INFO @ Fri, 05 Jul 2019 16:37:04: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:37:04: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:37:04: #1 total tags in treatment: 154890 INFO @ Fri, 05 Jul 2019 16:37:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:37:04: #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 16:37:04: #1 tags after filtering in treatment: 153677 INFO @ Fri, 05 Jul 2019 16:37:04: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:37:04: #1 finished! INFO @ Fri, 05 Jul 2019 16:37:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:37:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:37:04: #2 number of paired peaks: 149 WARNING @ Fri, 05 Jul 2019 16:37:04: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 05 Jul 2019 16:37:04: start model_add_line... INFO @ Fri, 05 Jul 2019 16:37:04: start X-correlation... pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:37:04: end of X-cor INFO @ Fri, 05 Jul 2019 16:37:04: #2 finished! INFO @ Fri, 05 Jul 2019 16:37:04: #2 predicted fragment length is 271 bps INFO @ Fri, 05 Jul 2019 16:37:04: #2 alternative fragment length(s) may be 16,56,71,107,138,154,185,212,230,255,271,310,349,438,468,519,563 bps INFO @ Fri, 05 Jul 2019 16:37:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.20_model.r INFO @ Fri, 05 Jul 2019 16:37:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:37:04: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:37:05: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:37:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462415/ERX462415.20_summits.bed INFO @ Fri, 05 Jul 2019 16:37:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。