Job ID = 2008311 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,489,885 reads read : 14,979,770 reads written : 14,979,770 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628950.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: 00:03:54 7489885 reads; of these: 7489885 (100.00%) were paired; of these: 665428 (8.88%) aligned concordantly 0 times 6177862 (82.48%) aligned concordantly exactly 1 time 646595 (8.63%) aligned concordantly >1 times ---- 665428 pairs aligned concordantly 0 times; of these: 43380 (6.52%) aligned discordantly 1 time ---- 622048 pairs aligned 0 times concordantly or discordantly; of these: 1244096 mates make up the pairs; of these: 1198491 (96.33%) aligned 0 times 25504 (2.05%) aligned exactly 1 time 20101 (1.62%) aligned >1 times 92.00% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 6487608 / 6858104 = 0.9460 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 18:32:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.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 18:32:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:32:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:32:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.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 18:32:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:32:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:32:43: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:32:43: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:32:44: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:32:44: #1 total tags in treatment: 375193 INFO @ Fri, 05 Jul 2019 18:32:44: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:32:44: #1 total tags in treatment: 375193 INFO @ Fri, 05 Jul 2019 18:32:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:32:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:32:44: #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 18:32:44: #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 18:32:44: #1 tags after filtering in treatment: 319539 INFO @ Fri, 05 Jul 2019 18:32:44: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 05 Jul 2019 18:32:44: #1 finished! INFO @ Fri, 05 Jul 2019 18:32:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:32:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:32:44: #1 tags after filtering in treatment: 319539 INFO @ Fri, 05 Jul 2019 18:32:44: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 05 Jul 2019 18:32:44: #1 finished! INFO @ Fri, 05 Jul 2019 18:32:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:32:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:32:44: #2 number of paired peaks: 343 WARNING @ Fri, 05 Jul 2019 18:32:44: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Fri, 05 Jul 2019 18:32:44: start model_add_line... INFO @ Fri, 05 Jul 2019 18:32:44: #2 number of paired peaks: 343 WARNING @ Fri, 05 Jul 2019 18:32:44: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Fri, 05 Jul 2019 18:32:44: start model_add_line... INFO @ Fri, 05 Jul 2019 18:32:44: start X-correlation... INFO @ Fri, 05 Jul 2019 18:32:44: start X-correlation... INFO @ Fri, 05 Jul 2019 18:32:44: end of X-cor INFO @ Fri, 05 Jul 2019 18:32:44: #2 finished! INFO @ Fri, 05 Jul 2019 18:32:44: #2 predicted fragment length is 158 bps INFO @ Fri, 05 Jul 2019 18:32:44: #2 alternative fragment length(s) may be 21,54,78,109,158,212,240,294,314,379,396,458,478,492,535,560 bps INFO @ Fri, 05 Jul 2019 18:32:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.05_model.r INFO @ Fri, 05 Jul 2019 18:32:44: end of X-cor INFO @ Fri, 05 Jul 2019 18:32:44: #2 finished! INFO @ Fri, 05 Jul 2019 18:32:44: #2 predicted fragment length is 158 bps INFO @ Fri, 05 Jul 2019 18:32:44: #2 alternative fragment length(s) may be 21,54,78,109,158,212,240,294,314,379,396,458,478,492,535,560 bps INFO @ Fri, 05 Jul 2019 18:32:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.10_model.r INFO @ Fri, 05 Jul 2019 18:32:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.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 18:32:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:32:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:32:48: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:32:48: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:32:48: #1 total tags in treatment: 375193 INFO @ Fri, 05 Jul 2019 18:32:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:32:48: #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 18:32:48: #1 tags after filtering in treatment: 319539 INFO @ Fri, 05 Jul 2019 18:32:48: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 05 Jul 2019 18:32:48: #1 finished! INFO @ Fri, 05 Jul 2019 18:32:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:32:48: #2 number of paired peaks: 343 WARNING @ Fri, 05 Jul 2019 18:32:48: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Fri, 05 Jul 2019 18:32:48: start model_add_line... INFO @ Fri, 05 Jul 2019 18:32:48: start X-correlation... INFO @ Fri, 05 Jul 2019 18:32:48: end of X-cor INFO @ Fri, 05 Jul 2019 18:32:48: #2 finished! INFO @ Fri, 05 Jul 2019 18:32:48: #2 predicted fragment length is 158 bps INFO @ Fri, 05 Jul 2019 18:32:48: #2 alternative fragment length(s) may be 21,54,78,109,158,212,240,294,314,379,396,458,478,492,535,560 bps INFO @ Fri, 05 Jul 2019 18:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.20_model.r INFO @ Fri, 05 Jul 2019 18:33:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:33:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:33:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:33:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:33:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:33:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:33:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:33:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:33:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:33:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:33:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:33:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:33:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.10_summits.bed INFO @ Fri, 05 Jul 2019 18:33:03: Done! INFO @ Fri, 05 Jul 2019 18:33:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:33:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.20_summits.bed INFO @ Fri, 05 Jul 2019 18:33:03: Done! INFO @ Fri, 05 Jul 2019 18:33:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:33:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:33:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585821/ERX585821.05_summits.bed INFO @ Fri, 05 Jul 2019 18:33:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 4 millis pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 1 millis pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 0 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。