Job ID = 2005997 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T05:40:49 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 456,946 reads read : 456,946 reads written : 456,946 spots read : 434,863 reads read : 434,863 reads written : 434,863 spots read : 445,835 reads read : 445,835 reads written : 445,835 spots read : 439,477 reads read : 439,477 reads written : 439,477 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529262.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529263.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529264.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529265.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:41 1777121 reads; of these: 1777121 (100.00%) were unpaired; of these: 84879 (4.78%) aligned 0 times 1296377 (72.95%) aligned exactly 1 time 395865 (22.28%) aligned >1 times 95.22% overall alignment rate Time searching: 00:00:42 Overall time: 00:00:42 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] 1516437 / 1692242 = 0.8961 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 14:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.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 14:46:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:46:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.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 14:46:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:46:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.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 14:46:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:46:20: #1 read treatment tags... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 14:46:22: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:46:22: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:46:22: #1 total tags in treatment: 175805 INFO @ Fri, 05 Jul 2019 14:46:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:46:22: #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 14:46:22: #1 tags after filtering in treatment: 175805 INFO @ Fri, 05 Jul 2019 14:46:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:46:22: #1 finished! INFO @ Fri, 05 Jul 2019 14:46:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:46:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:46:22: #2 number of paired peaks: 196 WARNING @ Fri, 05 Jul 2019 14:46:22: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Fri, 05 Jul 2019 14:46:22: start model_add_line... INFO @ Fri, 05 Jul 2019 14:46:22: start X-correlation... INFO @ Fri, 05 Jul 2019 14:46:22: end of X-cor INFO @ Fri, 05 Jul 2019 14:46:22: #2 finished! INFO @ Fri, 05 Jul 2019 14:46:22: #2 predicted fragment length is 172 bps INFO @ Fri, 05 Jul 2019 14:46:22: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 05 Jul 2019 14:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.20_model.r INFO @ Fri, 05 Jul 2019 14:46:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:46:22: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:46:22: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:46:22: #1 total tags in treatment: 175805 INFO @ Fri, 05 Jul 2019 14:46:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:46:22: #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 14:46:22: #1 tags after filtering in treatment: 175805 INFO @ Fri, 05 Jul 2019 14:46:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:46:22: #1 finished! INFO @ Fri, 05 Jul 2019 14:46:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:46:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:46:22: #2 number of paired peaks: 196 WARNING @ Fri, 05 Jul 2019 14:46:22: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Fri, 05 Jul 2019 14:46:22: start model_add_line... INFO @ Fri, 05 Jul 2019 14:46:22: start X-correlation... INFO @ Fri, 05 Jul 2019 14:46:22: end of X-cor INFO @ Fri, 05 Jul 2019 14:46:22: #2 finished! INFO @ Fri, 05 Jul 2019 14:46:22: #2 predicted fragment length is 172 bps INFO @ Fri, 05 Jul 2019 14:46:22: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 05 Jul 2019 14:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.05_model.r INFO @ Fri, 05 Jul 2019 14:46:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:46:22: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 14:46:22: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 14:46:22: #1 total tags in treatment: 175805 INFO @ Fri, 05 Jul 2019 14:46:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:46:22: #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 14:46:22: #1 tags after filtering in treatment: 175805 INFO @ Fri, 05 Jul 2019 14:46:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:46:22: #1 finished! INFO @ Fri, 05 Jul 2019 14:46:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:46:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:46:22: #2 number of paired peaks: 196 WARNING @ Fri, 05 Jul 2019 14:46:22: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Fri, 05 Jul 2019 14:46:22: start model_add_line... INFO @ Fri, 05 Jul 2019 14:46:22: start X-correlation... INFO @ Fri, 05 Jul 2019 14:46:22: end of X-cor INFO @ Fri, 05 Jul 2019 14:46:22: #2 finished! INFO @ Fri, 05 Jul 2019 14:46:22: #2 predicted fragment length is 172 bps INFO @ Fri, 05 Jul 2019 14:46:22: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 05 Jul 2019 14:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.10_model.r INFO @ Fri, 05 Jul 2019 14:46:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:46:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:46:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:46:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.20_summits.bed INFO @ Fri, 05 Jul 2019 14:46:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 14:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:46:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.05_summits.bed INFO @ Fri, 05 Jul 2019 14:46:23: Done! INFO @ Fri, 05 Jul 2019 14:46:23: #3 Call peaks for each chromosome... pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (204 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 14:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:46:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548087/ERX2548087.10_summits.bed INFO @ Fri, 05 Jul 2019 14:46:23: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling