Job ID = 2008351 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,394,432 reads read : 12,788,864 reads written : 12,788,864 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628983.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: 00:04:08 6394432 reads; of these: 6394432 (100.00%) were paired; of these: 361023 (5.65%) aligned concordantly 0 times 5655565 (88.45%) aligned concordantly exactly 1 time 377844 (5.91%) aligned concordantly >1 times ---- 361023 pairs aligned concordantly 0 times; of these: 26273 (7.28%) aligned discordantly 1 time ---- 334750 pairs aligned 0 times concordantly or discordantly; of these: 669500 mates make up the pairs; of these: 636709 (95.10%) aligned 0 times 20112 (3.00%) aligned exactly 1 time 12679 (1.89%) aligned >1 times 95.02% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:12 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] 5643532 / 6053242 = 0.9323 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 18:54:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.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 18:54:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:54:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:54:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.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 18:54:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:54:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:54:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.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 18:54:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:54:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:54:22: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:54:22: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:54:22: #1 total tags in treatment: 410114 INFO @ Fri, 05 Jul 2019 18:54:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:54:22: #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 18:54:22: #1 tags after filtering in treatment: 346171 INFO @ Fri, 05 Jul 2019 18:54:22: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 05 Jul 2019 18:54:22: #1 finished! INFO @ Fri, 05 Jul 2019 18:54:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:54:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:54:22: #2 number of paired peaks: 139 WARNING @ Fri, 05 Jul 2019 18:54:22: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Fri, 05 Jul 2019 18:54:22: start model_add_line... INFO @ Fri, 05 Jul 2019 18:54:22: start X-correlation... INFO @ Fri, 05 Jul 2019 18:54:22: end of X-cor INFO @ Fri, 05 Jul 2019 18:54:22: #2 finished! INFO @ Fri, 05 Jul 2019 18:54:22: #2 predicted fragment length is 162 bps INFO @ Fri, 05 Jul 2019 18:54:22: #2 alternative fragment length(s) may be 18,79,104,122,162,201,239,300,318,395,449,475,527,564,579 bps INFO @ Fri, 05 Jul 2019 18:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.05_model.r INFO @ Fri, 05 Jul 2019 18:54:23: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:54:23: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:54:23: #1 total tags in treatment: 410114 INFO @ Fri, 05 Jul 2019 18:54:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:54:23: #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 18:54:23: #1 tags after filtering in treatment: 346171 INFO @ Fri, 05 Jul 2019 18:54:23: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 05 Jul 2019 18:54:23: #1 finished! INFO @ Fri, 05 Jul 2019 18:54:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:54:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:54:23: #2 number of paired peaks: 139 WARNING @ Fri, 05 Jul 2019 18:54:23: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Fri, 05 Jul 2019 18:54:23: start model_add_line... INFO @ Fri, 05 Jul 2019 18:54:23: start X-correlation... INFO @ Fri, 05 Jul 2019 18:54:23: end of X-cor INFO @ Fri, 05 Jul 2019 18:54:23: #2 finished! INFO @ Fri, 05 Jul 2019 18:54:23: #2 predicted fragment length is 162 bps INFO @ Fri, 05 Jul 2019 18:54:23: #2 alternative fragment length(s) may be 18,79,104,122,162,201,239,300,318,395,449,475,527,564,579 bps INFO @ Fri, 05 Jul 2019 18:54:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.10_model.r INFO @ Fri, 05 Jul 2019 18:54:29: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:54:29: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:54:29: #1 total tags in treatment: 410114 INFO @ Fri, 05 Jul 2019 18:54:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:54:29: #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 18:54:29: #1 tags after filtering in treatment: 346171 INFO @ Fri, 05 Jul 2019 18:54:29: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 05 Jul 2019 18:54:29: #1 finished! INFO @ Fri, 05 Jul 2019 18:54:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:54:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:54:29: #2 number of paired peaks: 139 WARNING @ Fri, 05 Jul 2019 18:54:29: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Fri, 05 Jul 2019 18:54:29: start model_add_line... INFO @ Fri, 05 Jul 2019 18:54:29: start X-correlation... INFO @ Fri, 05 Jul 2019 18:54:29: end of X-cor INFO @ Fri, 05 Jul 2019 18:54:29: #2 finished! INFO @ Fri, 05 Jul 2019 18:54:29: #2 predicted fragment length is 162 bps INFO @ Fri, 05 Jul 2019 18:54:29: #2 alternative fragment length(s) may be 18,79,104,122,162,201,239,300,318,395,449,475,527,564,579 bps INFO @ Fri, 05 Jul 2019 18:54:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.20_model.r INFO @ Fri, 05 Jul 2019 18:54:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:54:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:54:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:54:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:54:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:54:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:54:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:54:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:54:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.20_summits.bed INFO @ Fri, 05 Jul 2019 18:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.10_summits.bed INFO @ Fri, 05 Jul 2019 18:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:54:46: Done! INFO @ Fri, 05 Jul 2019 18:54:46: Done! INFO @ Fri, 05 Jul 2019 18:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585853/ERX585853.05_summits.bed INFO @ Fri, 05 Jul 2019 18:54:46: Done! pass1 - making usageList (9 chroms): 1 millis pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (17 records, 4 fields): 2 millis pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 2 millis pass2 - checking and writing primary data (138 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。