Job ID = 2007978 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,779,920 reads read : 3,559,840 reads written : 3,559,840 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: 00:02:03 1779920 reads; of these: 1779920 (100.00%) were paired; of these: 188162 (10.57%) aligned concordantly 0 times 1454969 (81.74%) aligned concordantly exactly 1 time 136789 (7.69%) aligned concordantly >1 times ---- 188162 pairs aligned concordantly 0 times; of these: 44860 (23.84%) aligned discordantly 1 time ---- 143302 pairs aligned 0 times concordantly or discordantly; of these: 286604 mates make up the pairs; of these: 252014 (87.93%) aligned 0 times 21513 (7.51%) aligned exactly 1 time 13077 (4.56%) aligned >1 times 92.92% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 155974 / 1626207 = 0.0959 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 17:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.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 17:04:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:04:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.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 17:04:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:04:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:04:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.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 17:04:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:04:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:04:57: 1000000 INFO @ Fri, 05 Jul 2019 17:05:00: 1000000 INFO @ Fri, 05 Jul 2019 17:05:01: 1000000 INFO @ Fri, 05 Jul 2019 17:05:06: 2000000 INFO @ Fri, 05 Jul 2019 17:05:12: 2000000 INFO @ Fri, 05 Jul 2019 17:05:15: 2000000 INFO @ Fri, 05 Jul 2019 17:05:15: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:05:15: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:05:15: #1 total tags in treatment: 1437777 INFO @ Fri, 05 Jul 2019 17:05:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:05:15: #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 17:05:15: #1 tags after filtering in treatment: 1354413 INFO @ Fri, 05 Jul 2019 17:05:15: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:05:15: #1 finished! INFO @ Fri, 05 Jul 2019 17:05:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:05:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:05:15: #2 number of paired peaks: 175 WARNING @ Fri, 05 Jul 2019 17:05:15: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Fri, 05 Jul 2019 17:05:15: start model_add_line... INFO @ Fri, 05 Jul 2019 17:05:15: start X-correlation... INFO @ Fri, 05 Jul 2019 17:05:15: end of X-cor INFO @ Fri, 05 Jul 2019 17:05:15: #2 finished! INFO @ Fri, 05 Jul 2019 17:05:15: #2 predicted fragment length is 215 bps INFO @ Fri, 05 Jul 2019 17:05:15: #2 alternative fragment length(s) may be 1,23,43,70,109,128,148,181,184,187,215,252,273,287,357,387,488,530,533,574,589 bps INFO @ Fri, 05 Jul 2019 17:05:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.10_model.r INFO @ Fri, 05 Jul 2019 17:05:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:05:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:05:20: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:05:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:05:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:05:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.10_summits.bed INFO @ Fri, 05 Jul 2019 17:05:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:05:22: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:05:22: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:05:22: #1 total tags in treatment: 1437777 INFO @ Fri, 05 Jul 2019 17:05:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:05:22: #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 17:05:22: #1 tags after filtering in treatment: 1354413 INFO @ Fri, 05 Jul 2019 17:05:22: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:05:22: #1 finished! INFO @ Fri, 05 Jul 2019 17:05:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:05:22: #2 number of paired peaks: 175 WARNING @ Fri, 05 Jul 2019 17:05:22: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Fri, 05 Jul 2019 17:05:22: start model_add_line... INFO @ Fri, 05 Jul 2019 17:05:22: start X-correlation... INFO @ Fri, 05 Jul 2019 17:05:22: end of X-cor INFO @ Fri, 05 Jul 2019 17:05:22: #2 finished! INFO @ Fri, 05 Jul 2019 17:05:22: #2 predicted fragment length is 215 bps INFO @ Fri, 05 Jul 2019 17:05:22: #2 alternative fragment length(s) may be 1,23,43,70,109,128,148,181,184,187,215,252,273,287,357,387,488,530,533,574,589 bps INFO @ Fri, 05 Jul 2019 17:05:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.20_model.r INFO @ Fri, 05 Jul 2019 17:05:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:05:22: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:05:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:05:28: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:05:28: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:05:28: #1 total tags in treatment: 1437777 INFO @ Fri, 05 Jul 2019 17:05:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:05:28: #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 17:05:28: #1 tags after filtering in treatment: 1354413 INFO @ Fri, 05 Jul 2019 17:05:28: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:05:28: #1 finished! INFO @ Fri, 05 Jul 2019 17:05:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:05:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:05:28: #2 number of paired peaks: 175 WARNING @ Fri, 05 Jul 2019 17:05:28: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Fri, 05 Jul 2019 17:05:28: start model_add_line... INFO @ Fri, 05 Jul 2019 17:05:28: start X-correlation... INFO @ Fri, 05 Jul 2019 17:05:28: end of X-cor INFO @ Fri, 05 Jul 2019 17:05:28: #2 finished! INFO @ Fri, 05 Jul 2019 17:05:28: #2 predicted fragment length is 215 bps INFO @ Fri, 05 Jul 2019 17:05:28: #2 alternative fragment length(s) may be 1,23,43,70,109,128,148,181,184,187,215,252,273,287,357,387,488,530,533,574,589 bps INFO @ Fri, 05 Jul 2019 17:05:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.05_model.r INFO @ Fri, 05 Jul 2019 17:05:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:05:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:05:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:05:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:05:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.20_summits.bed INFO @ Fri, 05 Jul 2019 17:05:29: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:05:33: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:05:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.05_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 17:05:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:05:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471768/ERX471768.05_summits.bed INFO @ Fri, 05 Jul 2019 17:05:48: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 3 millis BigWig に変換しました。 CompletedMACS2peakCalling