Job ID = 2007722 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:22:26 fasterq-dump.2.9.6 err: index.c get_nearest_offset() -> too many rounds pos = 24 of 40 spots read : 12,670 reads read : 25,340 reads written : 25,340 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:00 12670 reads; of these: 12670 (100.00%) were paired; of these: 1738 (13.72%) aligned concordantly 0 times 10169 (80.26%) aligned concordantly exactly 1 time 763 (6.02%) aligned concordantly >1 times ---- 1738 pairs aligned concordantly 0 times; of these: 696 (40.05%) aligned discordantly 1 time ---- 1042 pairs aligned 0 times concordantly or discordantly; of these: 2084 mates make up the pairs; of these: 1754 (84.17%) aligned 0 times 220 (10.56%) aligned exactly 1 time 110 (5.28%) aligned >1 times 93.08% overall alignment rate Time searching: 00:00:00 Overall time: 00:00:00 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] 11 / 11528 = 0.0010 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 05 Jul 2019 16:22:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.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 BedGraph に変換中... INFO @ Fri, 05 Jul 2019 16:22:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:41: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:22:41: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:22:41: #1 total tags in treatment: 10922 INFO @ Fri, 05 Jul 2019 16:22:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:41: #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 16:22:41: #1 tags after filtering in treatment: 10916 INFO @ Fri, 05 Jul 2019 16:22:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:41: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:41: #2 number of paired peaks: 624 WARNING @ Fri, 05 Jul 2019 16:22:41: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:41: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:41: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:41: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:41: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:41: #2 predicted fragment length is 298 bps INFO @ Fri, 05 Jul 2019 16:22:41: #2 alternative fragment length(s) may be 235,268,298 bps INFO @ Fri, 05 Jul 2019 16:22:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.05_model.r INFO @ Fri, 05 Jul 2019 16:22:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:22:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.05_summits.bed INFO @ Fri, 05 Jul 2019 16:22:41: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:22:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.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 16:22:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:42: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:22:42: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:22:42: #1 total tags in treatment: 10922 INFO @ Fri, 05 Jul 2019 16:22:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:42: #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 16:22:42: #1 tags after filtering in treatment: 10916 INFO @ Fri, 05 Jul 2019 16:22:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:42: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:42: #2 number of paired peaks: 624 WARNING @ Fri, 05 Jul 2019 16:22:42: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:42: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:42: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:42: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:42: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:42: #2 predicted fragment length is 298 bps INFO @ Fri, 05 Jul 2019 16:22:42: #2 alternative fragment length(s) may be 235,268,298 bps INFO @ Fri, 05 Jul 2019 16:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.10_model.r INFO @ Fri, 05 Jul 2019 16:22:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:22:42: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.10_summits.bed INFO @ Fri, 05 Jul 2019 16:22:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:22:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.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 16:22:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:43: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:22:43: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:22:43: #1 total tags in treatment: 10922 INFO @ Fri, 05 Jul 2019 16:22:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:43: #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 16:22:43: #1 tags after filtering in treatment: 10916 INFO @ Fri, 05 Jul 2019 16:22:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:43: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:43: #2 number of paired peaks: 624 WARNING @ Fri, 05 Jul 2019 16:22:43: Fewer paired peaks (624) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 624 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:43: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:43: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:43: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:43: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:43: #2 predicted fragment length is 298 bps INFO @ Fri, 05 Jul 2019 16:22:43: #2 alternative fragment length(s) may be 235,268,298 bps INFO @ Fri, 05 Jul 2019 16:22:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.20_model.r INFO @ Fri, 05 Jul 2019 16:22:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:22:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433673/ERX433673.20_summits.bed INFO @ Fri, 05 Jul 2019 16:22:43: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling