Job ID = 2007654 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,049,829 reads read : 2,049,829 reads written : 2,049,829 spots read : 1,957,130 reads read : 1,957,130 reads written : 1,957,130 spots read : 2,135,826 reads read : 2,135,826 reads written : 2,135,826 spots read : 1,945,085 reads read : 1,945,085 reads written : 1,945,085 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529810.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529811.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529812.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: 00:01:56 8087870 reads; of these: 8087870 (100.00%) were unpaired; of these: 289338 (3.58%) aligned 0 times 6289160 (77.76%) aligned exactly 1 time 1509372 (18.66%) aligned >1 times 96.42% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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_rmdupse_core] 7642290 / 7798532 = 0.9800 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 16:19:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.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 16:19:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:19:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:19:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.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 16:19:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:19:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:19:43: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:19:43: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:19:43: #1 total tags in treatment: 156242 INFO @ Fri, 05 Jul 2019 16:19:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:19:43: #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 16:19:43: #1 tags after filtering in treatment: 156242 INFO @ Fri, 05 Jul 2019 16:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:19:43: #1 finished! INFO @ Fri, 05 Jul 2019 16:19:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:19:43: #2 number of paired peaks: 404 WARNING @ Fri, 05 Jul 2019 16:19:43: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Fri, 05 Jul 2019 16:19:43: start model_add_line... INFO @ Fri, 05 Jul 2019 16:19:43: start X-correlation... INFO @ Fri, 05 Jul 2019 16:19:43: end of X-cor INFO @ Fri, 05 Jul 2019 16:19:43: #2 finished! INFO @ Fri, 05 Jul 2019 16:19:43: #2 predicted fragment length is 167 bps INFO @ Fri, 05 Jul 2019 16:19:43: #2 alternative fragment length(s) may be 36,83,112,167,186,204,224,298,353,383,432,436,457,492,516,567,575 bps INFO @ Fri, 05 Jul 2019 16:19:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.05_model.r INFO @ Fri, 05 Jul 2019 16:19:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:19:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.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 16:19:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:19:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:19:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:19:43: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:19:43: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:19:43: #1 total tags in treatment: 156242 INFO @ Fri, 05 Jul 2019 16:19:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:19:43: #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 16:19:43: #1 tags after filtering in treatment: 156242 INFO @ Fri, 05 Jul 2019 16:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:19:43: #1 finished! INFO @ Fri, 05 Jul 2019 16:19:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:19:44: #2 number of paired peaks: 404 WARNING @ Fri, 05 Jul 2019 16:19:44: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Fri, 05 Jul 2019 16:19:44: start model_add_line... INFO @ Fri, 05 Jul 2019 16:19:44: start X-correlation... INFO @ Fri, 05 Jul 2019 16:19:44: end of X-cor INFO @ Fri, 05 Jul 2019 16:19:44: #2 finished! INFO @ Fri, 05 Jul 2019 16:19:44: #2 predicted fragment length is 167 bps INFO @ Fri, 05 Jul 2019 16:19:44: #2 alternative fragment length(s) may be 36,83,112,167,186,204,224,298,353,383,432,436,457,492,516,567,575 bps INFO @ Fri, 05 Jul 2019 16:19:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.10_model.r INFO @ Fri, 05 Jul 2019 16:19:44: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:19:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:19:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:19:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:19:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.05_summits.bed INFO @ Fri, 05 Jul 2019 16:19:44: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (37 records, 4 fields): 2 millis BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:19:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:19:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:19:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:19:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.10_summits.bed INFO @ Fri, 05 Jul 2019 16:19:44: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:19:45: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:19:45: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:19:45: #1 total tags in treatment: 156242 INFO @ Fri, 05 Jul 2019 16:19:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:19:45: #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 16:19:45: #1 tags after filtering in treatment: 156242 INFO @ Fri, 05 Jul 2019 16:19:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:19:45: #1 finished! INFO @ Fri, 05 Jul 2019 16:19:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:19:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:19:45: #2 number of paired peaks: 404 WARNING @ Fri, 05 Jul 2019 16:19:45: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Fri, 05 Jul 2019 16:19:45: start model_add_line... INFO @ Fri, 05 Jul 2019 16:19:45: start X-correlation... INFO @ Fri, 05 Jul 2019 16:19:45: end of X-cor INFO @ Fri, 05 Jul 2019 16:19:45: #2 finished! INFO @ Fri, 05 Jul 2019 16:19:45: #2 predicted fragment length is 167 bps INFO @ Fri, 05 Jul 2019 16:19:45: #2 alternative fragment length(s) may be 36,83,112,167,186,204,224,298,353,383,432,436,457,492,516,567,575 bps INFO @ Fri, 05 Jul 2019 16:19:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.20_model.r INFO @ Fri, 05 Jul 2019 16:19:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:19:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:19:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:19:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:19:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:19:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548248/ERX2548248.20_summits.bed INFO @ Fri, 05 Jul 2019 16:19:46: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling