Job ID = 2010339 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,598,341 reads read : 17,598,341 reads written : 17,598,341 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1022916.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: 00:02:05 17598341 reads; of these: 17598341 (100.00%) were unpaired; of these: 10782484 (61.27%) aligned 0 times 6036309 (34.30%) aligned exactly 1 time 779548 (4.43%) aligned >1 times 38.73% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 4979445 / 6815857 = 0.7306 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 22:10:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.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 22:10:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:10:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:11:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.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 22:11:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:11:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:11:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.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 22:11:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 22:11:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 22:11:09: 1000000 INFO @ Fri, 05 Jul 2019 22:11:09: 1000000 INFO @ Fri, 05 Jul 2019 22:11:12: 1000000 INFO @ Fri, 05 Jul 2019 22:11:17: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:11:17: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:11:17: #1 total tags in treatment: 1836412 INFO @ Fri, 05 Jul 2019 22:11:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:11:17: #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 22:11:17: #1 tags after filtering in treatment: 1836412 INFO @ Fri, 05 Jul 2019 22:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:11:17: #1 finished! INFO @ Fri, 05 Jul 2019 22:11:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:11:17: #2 number of paired peaks: 120 WARNING @ Fri, 05 Jul 2019 22:11:17: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Fri, 05 Jul 2019 22:11:17: start model_add_line... INFO @ Fri, 05 Jul 2019 22:11:17: start X-correlation... INFO @ Fri, 05 Jul 2019 22:11:17: end of X-cor INFO @ Fri, 05 Jul 2019 22:11:17: #2 finished! INFO @ Fri, 05 Jul 2019 22:11:17: #2 predicted fragment length is 172 bps INFO @ Fri, 05 Jul 2019 22:11:17: #2 alternative fragment length(s) may be 172,598 bps INFO @ Fri, 05 Jul 2019 22:11:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.10_model.r INFO @ Fri, 05 Jul 2019 22:11:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:11:18: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:11:18: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:11:18: #1 total tags in treatment: 1836412 INFO @ Fri, 05 Jul 2019 22:11:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:11:18: #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 22:11:18: #1 tags after filtering in treatment: 1836412 INFO @ Fri, 05 Jul 2019 22:11:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:11:18: #1 finished! INFO @ Fri, 05 Jul 2019 22:11:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:11:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:11:18: #2 number of paired peaks: 120 WARNING @ Fri, 05 Jul 2019 22:11:18: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Fri, 05 Jul 2019 22:11:18: start model_add_line... INFO @ Fri, 05 Jul 2019 22:11:18: start X-correlation... INFO @ Fri, 05 Jul 2019 22:11:18: end of X-cor INFO @ Fri, 05 Jul 2019 22:11:18: #2 finished! INFO @ Fri, 05 Jul 2019 22:11:18: #2 predicted fragment length is 172 bps INFO @ Fri, 05 Jul 2019 22:11:18: #2 alternative fragment length(s) may be 172,598 bps INFO @ Fri, 05 Jul 2019 22:11:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.05_model.r INFO @ Fri, 05 Jul 2019 22:11:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:11:21: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 22:11:21: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 22:11:21: #1 total tags in treatment: 1836412 INFO @ Fri, 05 Jul 2019 22:11:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 22:11:21: #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 22:11:21: #1 tags after filtering in treatment: 1836412 INFO @ Fri, 05 Jul 2019 22:11:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 22:11:21: #1 finished! INFO @ Fri, 05 Jul 2019 22:11:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 22:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 22:11:21: #2 number of paired peaks: 120 WARNING @ Fri, 05 Jul 2019 22:11:21: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Fri, 05 Jul 2019 22:11:21: start model_add_line... INFO @ Fri, 05 Jul 2019 22:11:21: start X-correlation... INFO @ Fri, 05 Jul 2019 22:11:22: end of X-cor INFO @ Fri, 05 Jul 2019 22:11:22: #2 finished! INFO @ Fri, 05 Jul 2019 22:11:22: #2 predicted fragment length is 172 bps INFO @ Fri, 05 Jul 2019 22:11:22: #2 alternative fragment length(s) may be 172,598 bps INFO @ Fri, 05 Jul 2019 22:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.20_model.r INFO @ Fri, 05 Jul 2019 22:11:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 22:11:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 22:11:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:11:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 22:11:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.10_peaks.xls INFO @ Fri, 05 Jul 2019 22:11:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:11:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.10_summits.bed INFO @ Fri, 05 Jul 2019 22:11:26: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (915 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:11:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.05_peaks.xls INFO @ Fri, 05 Jul 2019 22:11:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:11:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.05_summits.bed INFO @ Fri, 05 Jul 2019 22:11:27: Done! INFO @ Fri, 05 Jul 2019 22:11:28: #3 Call peaks for each chromosome... pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1324 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 22:11:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.20_peaks.xls INFO @ Fri, 05 Jul 2019 22:11:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 22:11:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX372024/SRX372024.20_summits.bed INFO @ Fri, 05 Jul 2019 22:11:30: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (476 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。