Job ID = 2008257 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 324,501 reads read : 649,002 reads written : 649,002 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629061.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: 00:00:25 324501 reads; of these: 324501 (100.00%) were paired; of these: 33329 (10.27%) aligned concordantly 0 times 262512 (80.90%) aligned concordantly exactly 1 time 28660 (8.83%) aligned concordantly >1 times ---- 33329 pairs aligned concordantly 0 times; of these: 2431 (7.29%) aligned discordantly 1 time ---- 30898 pairs aligned 0 times concordantly or discordantly; of these: 61796 mates make up the pairs; of these: 59941 (97.00%) aligned 0 times 834 (1.35%) aligned exactly 1 time 1021 (1.65%) aligned >1 times 90.76% overall alignment rate Time searching: 00:00:25 Overall time: 00:00:25 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] 270835 / 293178 = 0.9238 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 18:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.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 18:07:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:07:32: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:07:32: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:07:32: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:07:32: #1 total tags in treatment: 22204 INFO @ Fri, 05 Jul 2019 18:07:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:07:32: #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 18:07:32: #1 tags after filtering in treatment: 21493 INFO @ Fri, 05 Jul 2019 18:07:32: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 18:07:32: #1 finished! INFO @ Fri, 05 Jul 2019 18:07:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:07:32: #2 number of paired peaks: 282 WARNING @ Fri, 05 Jul 2019 18:07:32: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Fri, 05 Jul 2019 18:07:32: start model_add_line... INFO @ Fri, 05 Jul 2019 18:07:32: start X-correlation... INFO @ Fri, 05 Jul 2019 18:07:32: end of X-cor INFO @ Fri, 05 Jul 2019 18:07:32: #2 finished! INFO @ Fri, 05 Jul 2019 18:07:32: #2 predicted fragment length is 242 bps INFO @ Fri, 05 Jul 2019 18:07:32: #2 alternative fragment length(s) may be 30,89,118,157,174,216,242,271,292,342,467,520,553,573 bps INFO @ Fri, 05 Jul 2019 18:07:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.05_model.r INFO @ Fri, 05 Jul 2019 18:07:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:07:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:07:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:07:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:07:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:07:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.05_summits.bed INFO @ Fri, 05 Jul 2019 18:07:32: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 18:07:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.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 18:07:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:07:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:07:33: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:07:33: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:07:33: #1 total tags in treatment: 22204 INFO @ Fri, 05 Jul 2019 18:07:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:07:33: #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 18:07:33: #1 tags after filtering in treatment: 21493 INFO @ Fri, 05 Jul 2019 18:07:33: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 18:07:33: #1 finished! INFO @ Fri, 05 Jul 2019 18:07:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:07:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:07:33: #2 number of paired peaks: 282 WARNING @ Fri, 05 Jul 2019 18:07:33: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Fri, 05 Jul 2019 18:07:33: start model_add_line... INFO @ Fri, 05 Jul 2019 18:07:33: start X-correlation... INFO @ Fri, 05 Jul 2019 18:07:33: end of X-cor INFO @ Fri, 05 Jul 2019 18:07:33: #2 finished! INFO @ Fri, 05 Jul 2019 18:07:33: #2 predicted fragment length is 242 bps INFO @ Fri, 05 Jul 2019 18:07:33: #2 alternative fragment length(s) may be 30,89,118,157,174,216,242,271,292,342,467,520,553,573 bps INFO @ Fri, 05 Jul 2019 18:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.10_model.r INFO @ Fri, 05 Jul 2019 18:07:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:07:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:07:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:07:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:07:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.10_summits.bed INFO @ Fri, 05 Jul 2019 18:07:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:07:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.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 18:07:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:07:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:07:34: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:07:34: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:07:34: #1 total tags in treatment: 22204 INFO @ Fri, 05 Jul 2019 18:07:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:07:34: #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 18:07:34: #1 tags after filtering in treatment: 21493 INFO @ Fri, 05 Jul 2019 18:07:34: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 18:07:34: #1 finished! INFO @ Fri, 05 Jul 2019 18:07:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:07:34: #2 number of paired peaks: 282 WARNING @ Fri, 05 Jul 2019 18:07:34: Fewer paired peaks (282) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 282 pairs to build model! INFO @ Fri, 05 Jul 2019 18:07:34: start model_add_line... INFO @ Fri, 05 Jul 2019 18:07:34: start X-correlation... INFO @ Fri, 05 Jul 2019 18:07:34: end of X-cor INFO @ Fri, 05 Jul 2019 18:07:34: #2 finished! INFO @ Fri, 05 Jul 2019 18:07:34: #2 predicted fragment length is 242 bps INFO @ Fri, 05 Jul 2019 18:07:34: #2 alternative fragment length(s) may be 30,89,118,157,174,216,242,271,292,342,467,520,553,573 bps INFO @ Fri, 05 Jul 2019 18:07:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.20_model.r INFO @ Fri, 05 Jul 2019 18:07:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:07:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:07:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:07:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:07:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:07:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585780/ERX585780.20_summits.bed INFO @ Fri, 05 Jul 2019 18:07:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling