Job ID = 2010561 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,626,900 reads read : 11,253,800 reads written : 11,253,800 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: 00:05:37 5626900 reads; of these: 5626900 (100.00%) were paired; of these: 898080 (15.96%) aligned concordantly 0 times 3311938 (58.86%) aligned concordantly exactly 1 time 1416882 (25.18%) aligned concordantly >1 times ---- 898080 pairs aligned concordantly 0 times; of these: 83877 (9.34%) aligned discordantly 1 time ---- 814203 pairs aligned 0 times concordantly or discordantly; of these: 1628406 mates make up the pairs; of these: 1407570 (86.44%) aligned 0 times 97829 (6.01%) aligned exactly 1 time 123007 (7.55%) aligned >1 times 87.49% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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_sort_core] merging from 8 files... [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] 481820 / 4803650 = 0.1003 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 23:16:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.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 23:16:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:16:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:16:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.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 23:16:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:16:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:16:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.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 23:16:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:16:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:16:08: 1000000 INFO @ Fri, 05 Jul 2019 23:16:09: 1000000 INFO @ Fri, 05 Jul 2019 23:16:11: 1000000 INFO @ Fri, 05 Jul 2019 23:16:15: 2000000 INFO @ Fri, 05 Jul 2019 23:16:16: 2000000 INFO @ Fri, 05 Jul 2019 23:16:19: 2000000 INFO @ Fri, 05 Jul 2019 23:16:22: 3000000 INFO @ Fri, 05 Jul 2019 23:16:23: 3000000 INFO @ Fri, 05 Jul 2019 23:16:28: 3000000 INFO @ Fri, 05 Jul 2019 23:16:29: 4000000 INFO @ Fri, 05 Jul 2019 23:16:30: 4000000 INFO @ Fri, 05 Jul 2019 23:16:36: 5000000 INFO @ Fri, 05 Jul 2019 23:16:36: 4000000 INFO @ Fri, 05 Jul 2019 23:16:37: 5000000 INFO @ Fri, 05 Jul 2019 23:16:43: 6000000 INFO @ Fri, 05 Jul 2019 23:16:44: 6000000 INFO @ Fri, 05 Jul 2019 23:16:44: 5000000 INFO @ Fri, 05 Jul 2019 23:16:50: 7000000 INFO @ Fri, 05 Jul 2019 23:16:51: 7000000 INFO @ Fri, 05 Jul 2019 23:16:53: 6000000 INFO @ Fri, 05 Jul 2019 23:16:57: 8000000 INFO @ Fri, 05 Jul 2019 23:16:58: 8000000 INFO @ Fri, 05 Jul 2019 23:17:01: 7000000 INFO @ Fri, 05 Jul 2019 23:17:03: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:17:03: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:17:03: #1 total tags in treatment: 4249274 INFO @ Fri, 05 Jul 2019 23:17:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:17:03: #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 23:17:03: #1 tags after filtering in treatment: 2672281 INFO @ Fri, 05 Jul 2019 23:17:03: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 23:17:03: #1 finished! INFO @ Fri, 05 Jul 2019 23:17:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:17:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:17:04: #2 number of paired peaks: 309 WARNING @ Fri, 05 Jul 2019 23:17:04: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 05 Jul 2019 23:17:04: start model_add_line... INFO @ Fri, 05 Jul 2019 23:17:04: start X-correlation... INFO @ Fri, 05 Jul 2019 23:17:04: end of X-cor INFO @ Fri, 05 Jul 2019 23:17:04: #2 finished! INFO @ Fri, 05 Jul 2019 23:17:04: #2 predicted fragment length is 190 bps INFO @ Fri, 05 Jul 2019 23:17:04: #2 alternative fragment length(s) may be 0,149,190,202,233 bps INFO @ Fri, 05 Jul 2019 23:17:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.05_model.r INFO @ Fri, 05 Jul 2019 23:17:04: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:17:04: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:17:04: #1 total tags in treatment: 4249274 INFO @ Fri, 05 Jul 2019 23:17:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:17:04: #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 23:17:04: #1 tags after filtering in treatment: 2672281 INFO @ Fri, 05 Jul 2019 23:17:04: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 23:17:04: #1 finished! INFO @ Fri, 05 Jul 2019 23:17:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:17:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:17:04: #2 number of paired peaks: 309 WARNING @ Fri, 05 Jul 2019 23:17:04: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 05 Jul 2019 23:17:04: start model_add_line... INFO @ Fri, 05 Jul 2019 23:17:04: start X-correlation... INFO @ Fri, 05 Jul 2019 23:17:04: end of X-cor INFO @ Fri, 05 Jul 2019 23:17:04: #2 finished! INFO @ Fri, 05 Jul 2019 23:17:04: #2 predicted fragment length is 190 bps INFO @ Fri, 05 Jul 2019 23:17:04: #2 alternative fragment length(s) may be 0,149,190,202,233 bps INFO @ Fri, 05 Jul 2019 23:17:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.10_model.r INFO @ Fri, 05 Jul 2019 23:17:10: 8000000 INFO @ Fri, 05 Jul 2019 23:17:17: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:17:17: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:17:17: #1 total tags in treatment: 4249274 INFO @ Fri, 05 Jul 2019 23:17:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:17:17: #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 23:17:17: #1 tags after filtering in treatment: 2672281 INFO @ Fri, 05 Jul 2019 23:17:17: #1 Redundant rate of treatment: 0.37 INFO @ Fri, 05 Jul 2019 23:17:17: #1 finished! INFO @ Fri, 05 Jul 2019 23:17:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:17:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:17:17: #2 number of paired peaks: 309 WARNING @ Fri, 05 Jul 2019 23:17:17: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 05 Jul 2019 23:17:17: start model_add_line... INFO @ Fri, 05 Jul 2019 23:17:17: start X-correlation... INFO @ Fri, 05 Jul 2019 23:17:17: end of X-cor INFO @ Fri, 05 Jul 2019 23:17:17: #2 finished! INFO @ Fri, 05 Jul 2019 23:17:17: #2 predicted fragment length is 190 bps INFO @ Fri, 05 Jul 2019 23:17:17: #2 alternative fragment length(s) may be 0,149,190,202,233 bps INFO @ Fri, 05 Jul 2019 23:17:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.20_model.r INFO @ Fri, 05 Jul 2019 23:17:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:17:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:17:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:17:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:17:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:17:17: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:17:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:17:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:17:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:17:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:17:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:17:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.20_summits.bed INFO @ Fri, 05 Jul 2019 23:17:33: Done! INFO @ Fri, 05 Jul 2019 23:17:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:17:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:17:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.10_summits.bed INFO @ Fri, 05 Jul 2019 23:17:33: Done! pass1 - making usageList (17 chroms): 1 millis pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (420 records, 4 fields): 5 millis pass2 - checking and writing primary data (122 records, 4 fields): 25 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:17:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:17:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:17:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381262/SRX381262.05_summits.bed INFO @ Fri, 05 Jul 2019 23:17:33: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (670 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。