Job ID = 2007815 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 219,735 reads read : 439,470 reads written : 439,470 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: 00:00:07 219735 reads; of these: 219735 (100.00%) were paired; of these: 25856 (11.77%) aligned concordantly 0 times 173988 (79.18%) aligned concordantly exactly 1 time 19891 (9.05%) aligned concordantly >1 times ---- 25856 pairs aligned concordantly 0 times; of these: 3894 (15.06%) aligned discordantly 1 time ---- 21962 pairs aligned 0 times concordantly or discordantly; of these: 43924 mates make up the pairs; of these: 40674 (92.60%) aligned 0 times 1980 (4.51%) aligned exactly 1 time 1270 (2.89%) aligned >1 times 90.74% overall alignment rate Time searching: 00:00:07 Overall time: 00:00:07 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] 1966 / 196734 = 0.0100 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 16:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.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 16:31:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:31:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:31:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.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 16:31:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:31:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:31:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.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 16:31:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:31:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:31:12: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:31:12: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:31:12: #1 total tags in treatment: 191929 INFO @ Fri, 05 Jul 2019 16:31:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:31:12: #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 16:31:12: #1 tags after filtering in treatment: 190205 INFO @ Fri, 05 Jul 2019 16:31:12: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:31:12: #1 finished! INFO @ Fri, 05 Jul 2019 16:31:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:31:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:31:12: #2 number of paired peaks: 148 WARNING @ Fri, 05 Jul 2019 16:31:12: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Fri, 05 Jul 2019 16:31:12: start model_add_line... INFO @ Fri, 05 Jul 2019 16:31:12: start X-correlation... INFO @ Fri, 05 Jul 2019 16:31:12: end of X-cor INFO @ Fri, 05 Jul 2019 16:31:12: #2 finished! INFO @ Fri, 05 Jul 2019 16:31:12: #2 predicted fragment length is 226 bps INFO @ Fri, 05 Jul 2019 16:31:12: #2 alternative fragment length(s) may be 3,23,32,63,78,110,143,159,196,226,247,297,335,357,391,431,475,508,528,545,562,594 bps INFO @ Fri, 05 Jul 2019 16:31:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.05_model.r INFO @ Fri, 05 Jul 2019 16:31:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:31:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:31:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:31:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:31:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:31:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.05_summits.bed INFO @ Fri, 05 Jul 2019 16:31:13: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 9 millis INFO @ Fri, 05 Jul 2019 16:31:13: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:31:13: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:31:13: #1 total tags in treatment: 191929 INFO @ Fri, 05 Jul 2019 16:31:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:31:13: #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 16:31:13: #1 tags after filtering in treatment: 190205 INFO @ Fri, 05 Jul 2019 16:31:13: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:31:13: #1 finished! INFO @ Fri, 05 Jul 2019 16:31:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:31:13: #2 number of paired peaks: 148 WARNING @ Fri, 05 Jul 2019 16:31:13: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Fri, 05 Jul 2019 16:31:13: start model_add_line... INFO @ Fri, 05 Jul 2019 16:31:13: start X-correlation... INFO @ Fri, 05 Jul 2019 16:31:13: end of X-cor INFO @ Fri, 05 Jul 2019 16:31:13: #2 finished! INFO @ Fri, 05 Jul 2019 16:31:13: #2 predicted fragment length is 226 bps INFO @ Fri, 05 Jul 2019 16:31:13: #2 alternative fragment length(s) may be 3,23,32,63,78,110,143,159,196,226,247,297,335,357,391,431,475,508,528,545,562,594 bps INFO @ Fri, 05 Jul 2019 16:31:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.10_model.r INFO @ Fri, 05 Jul 2019 16:31:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:31:14: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:31:14: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:31:14: #1 total tags in treatment: 191929 INFO @ Fri, 05 Jul 2019 16:31:14: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:31:14: #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 16:31:14: #1 tags after filtering in treatment: 190205 INFO @ Fri, 05 Jul 2019 16:31:14: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:31:14: #1 finished! INFO @ Fri, 05 Jul 2019 16:31:14: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:31:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:31:14: #2 number of paired peaks: 148 WARNING @ Fri, 05 Jul 2019 16:31:14: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Fri, 05 Jul 2019 16:31:14: start model_add_line... INFO @ Fri, 05 Jul 2019 16:31:14: start X-correlation... INFO @ Fri, 05 Jul 2019 16:31:14: end of X-cor INFO @ Fri, 05 Jul 2019 16:31:14: #2 finished! INFO @ Fri, 05 Jul 2019 16:31:14: #2 predicted fragment length is 226 bps INFO @ Fri, 05 Jul 2019 16:31:14: #2 alternative fragment length(s) may be 3,23,32,63,78,110,143,159,196,226,247,297,335,357,391,431,475,508,528,545,562,594 bps INFO @ Fri, 05 Jul 2019 16:31:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.20_model.r INFO @ Fri, 05 Jul 2019 16:31:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:31:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:31:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:31:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:31:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:31:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.10_summits.bed INFO @ Fri, 05 Jul 2019 16:31:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 16:31:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:31:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:31:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462370/ERX462370.20_summits.bed INFO @ Fri, 05 Jul 2019 16:31:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。