Job ID = 2008263 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,518,832 reads read : 3,037,664 reads written : 3,037,664 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629080.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: 00:01:02 1518832 reads; of these: 1518832 (100.00%) were paired; of these: 89463 (5.89%) aligned concordantly 0 times 1286816 (84.72%) aligned concordantly exactly 1 time 142553 (9.39%) aligned concordantly >1 times ---- 89463 pairs aligned concordantly 0 times; of these: 11899 (13.30%) aligned discordantly 1 time ---- 77564 pairs aligned 0 times concordantly or discordantly; of these: 155128 mates make up the pairs; of these: 145420 (93.74%) aligned 0 times 5252 (3.39%) aligned exactly 1 time 4456 (2.87%) aligned >1 times 95.21% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 1352826 / 1438430 = 0.9405 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 18:11:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.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 18:11:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:11:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.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 18:11:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:11:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:11:20: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:11:20: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:11:20: #1 total tags in treatment: 86614 INFO @ Fri, 05 Jul 2019 18:11:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:11:20: #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 18:11:20: #1 tags after filtering in treatment: 80233 INFO @ Fri, 05 Jul 2019 18:11:20: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 18:11:20: #1 finished! INFO @ Fri, 05 Jul 2019 18:11:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:11:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:11:20: #2 number of paired peaks: 287 WARNING @ Fri, 05 Jul 2019 18:11:20: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Fri, 05 Jul 2019 18:11:20: start model_add_line... INFO @ Fri, 05 Jul 2019 18:11:20: start X-correlation... INFO @ Fri, 05 Jul 2019 18:11:20: end of X-cor INFO @ Fri, 05 Jul 2019 18:11:20: #2 finished! INFO @ Fri, 05 Jul 2019 18:11:20: #2 predicted fragment length is 249 bps INFO @ Fri, 05 Jul 2019 18:11:20: #2 alternative fragment length(s) may be 16,57,86,129,155,192,249,332,438,551,589 bps INFO @ Fri, 05 Jul 2019 18:11:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.05_model.r INFO @ Fri, 05 Jul 2019 18:11:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:11:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:11:21: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:11:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:11:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:11:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.05_summits.bed INFO @ Fri, 05 Jul 2019 18:11:21: Done! INFO @ Fri, 05 Jul 2019 18:11:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.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 18:11:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:11:21: #1 read treatment tags... pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 18:11:21: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:11:21: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:11:21: #1 total tags in treatment: 86614 INFO @ Fri, 05 Jul 2019 18:11:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:11:21: #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 18:11:21: #1 tags after filtering in treatment: 80233 INFO @ Fri, 05 Jul 2019 18:11:21: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 18:11:21: #1 finished! INFO @ Fri, 05 Jul 2019 18:11:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:11:21: #2 number of paired peaks: 287 WARNING @ Fri, 05 Jul 2019 18:11:21: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Fri, 05 Jul 2019 18:11:21: start model_add_line... INFO @ Fri, 05 Jul 2019 18:11:21: start X-correlation... INFO @ Fri, 05 Jul 2019 18:11:21: end of X-cor INFO @ Fri, 05 Jul 2019 18:11:21: #2 finished! INFO @ Fri, 05 Jul 2019 18:11:21: #2 predicted fragment length is 249 bps INFO @ Fri, 05 Jul 2019 18:11:21: #2 alternative fragment length(s) may be 16,57,86,129,155,192,249,332,438,551,589 bps INFO @ Fri, 05 Jul 2019 18:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.10_model.r INFO @ Fri, 05 Jul 2019 18:11:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:11:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:11:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:11:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:11:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.10_summits.bed INFO @ Fri, 05 Jul 2019 18:11:22: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:11:22: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:11:22: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:11:22: #1 total tags in treatment: 86614 INFO @ Fri, 05 Jul 2019 18:11:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:11:22: #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 18:11:22: #1 tags after filtering in treatment: 80233 INFO @ Fri, 05 Jul 2019 18:11:22: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 18:11:22: #1 finished! INFO @ Fri, 05 Jul 2019 18:11:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:11:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:11:22: #2 number of paired peaks: 287 WARNING @ Fri, 05 Jul 2019 18:11:22: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Fri, 05 Jul 2019 18:11:22: start model_add_line... INFO @ Fri, 05 Jul 2019 18:11:22: start X-correlation... INFO @ Fri, 05 Jul 2019 18:11:22: end of X-cor INFO @ Fri, 05 Jul 2019 18:11:22: #2 finished! INFO @ Fri, 05 Jul 2019 18:11:22: #2 predicted fragment length is 249 bps INFO @ Fri, 05 Jul 2019 18:11:22: #2 alternative fragment length(s) may be 16,57,86,129,155,192,249,332,438,551,589 bps INFO @ Fri, 05 Jul 2019 18:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.20_model.r INFO @ Fri, 05 Jul 2019 18:11:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:11:22: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:11:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:11:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:11:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:11:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585785/ERX585785.20_summits.bed INFO @ Fri, 05 Jul 2019 18:11:23: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling