Job ID = 2007720 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:21:52 fasterq-dump.2.9.6 err: index.c get_nearest_offset() -> too many rounds pos = 40 of 56 spots read : 23,997 reads read : 47,994 reads written : 47,994 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: 00:00:01 23997 reads; of these: 23997 (100.00%) were paired; of these: 1512 (6.30%) aligned concordantly 0 times 20053 (83.56%) aligned concordantly exactly 1 time 2432 (10.13%) aligned concordantly >1 times ---- 1512 pairs aligned concordantly 0 times; of these: 404 (26.72%) aligned discordantly 1 time ---- 1108 pairs aligned 0 times concordantly or discordantly; of these: 2216 mates make up the pairs; of these: 1852 (83.57%) aligned 0 times 222 (10.02%) aligned exactly 1 time 142 (6.41%) aligned >1 times 96.14% overall alignment rate Time searching: 00:00:01 Overall time: 00:00:01 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] 24 / 22748 = 0.0011 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 16:22:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.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 16:22:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:08: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:22:08: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:22:08: #1 total tags in treatment: 22461 INFO @ Fri, 05 Jul 2019 16:22:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:08: #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 16:22:08: #1 tags after filtering in treatment: 22430 INFO @ Fri, 05 Jul 2019 16:22:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:08: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:08: #2 number of paired peaks: 143 WARNING @ Fri, 05 Jul 2019 16:22:08: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:08: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:08: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:08: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:08: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:08: #2 predicted fragment length is 306 bps INFO @ Fri, 05 Jul 2019 16:22:08: #2 alternative fragment length(s) may be 38,78,103,120,140,156,180,197,228,245,266,289,306,352,385,423,460,494,534,558 bps INFO @ Fri, 05 Jul 2019 16:22:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.05_model.r INFO @ Fri, 05 Jul 2019 16:22:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:22:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.05_summits.bed INFO @ Fri, 05 Jul 2019 16:22:08: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BigWig に変換しました。 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:22:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.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 16:22:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:09: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:22:09: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:22:09: #1 total tags in treatment: 22461 INFO @ Fri, 05 Jul 2019 16:22:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:09: #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 16:22:09: #1 tags after filtering in treatment: 22430 INFO @ Fri, 05 Jul 2019 16:22:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:09: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:09: #2 number of paired peaks: 143 WARNING @ Fri, 05 Jul 2019 16:22:09: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:09: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:09: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:09: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:09: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:09: #2 predicted fragment length is 306 bps INFO @ Fri, 05 Jul 2019 16:22:09: #2 alternative fragment length(s) may be 38,78,103,120,140,156,180,197,228,245,266,289,306,352,385,423,460,494,534,558 bps INFO @ Fri, 05 Jul 2019 16:22:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.10_model.r INFO @ Fri, 05 Jul 2019 16:22:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:22:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.10_summits.bed INFO @ Fri, 05 Jul 2019 16:22:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 16:22:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.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 16:22:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:10: #1 read treatment tags... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:22:10: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:22:10: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:22:10: #1 total tags in treatment: 22461 INFO @ Fri, 05 Jul 2019 16:22:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:10: #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 16:22:10: #1 tags after filtering in treatment: 22430 INFO @ Fri, 05 Jul 2019 16:22:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:10: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:10: #2 number of paired peaks: 143 WARNING @ Fri, 05 Jul 2019 16:22:10: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:10: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:10: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:10: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:10: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:10: #2 predicted fragment length is 306 bps INFO @ Fri, 05 Jul 2019 16:22:10: #2 alternative fragment length(s) may be 38,78,103,120,140,156,180,197,228,245,266,289,306,352,385,423,460,494,534,558 bps INFO @ Fri, 05 Jul 2019 16:22:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.20_model.r INFO @ Fri, 05 Jul 2019 16:22:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:22:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433671/ERX433671.20_summits.bed INFO @ Fri, 05 Jul 2019 16:22:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling