Job ID = 2011901 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,422,366 reads read : 6,844,732 reads written : 6,844,732 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: 00:02:23 3422366 reads; of these: 3422366 (100.00%) were paired; of these: 413788 (12.09%) aligned concordantly 0 times 2594151 (75.80%) aligned concordantly exactly 1 time 414427 (12.11%) aligned concordantly >1 times ---- 413788 pairs aligned concordantly 0 times; of these: 252622 (61.05%) aligned discordantly 1 time ---- 161166 pairs aligned 0 times concordantly or discordantly; of these: 322332 mates make up the pairs; of these: 169950 (52.73%) aligned 0 times 64238 (19.93%) aligned exactly 1 time 88144 (27.35%) aligned >1 times 97.52% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 94340 / 3259910 = 0.0289 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 @ Sat, 06 Jul 2019 03:11:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.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 @ Sat, 06 Jul 2019 03:11:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:11:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.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 @ Sat, 06 Jul 2019 03:11:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:11:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:11:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.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 @ Sat, 06 Jul 2019 03:11:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:11:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:11:12: 1000000 INFO @ Sat, 06 Jul 2019 03:11:13: 1000000 INFO @ Sat, 06 Jul 2019 03:11:15: 1000000 INFO @ Sat, 06 Jul 2019 03:11:21: 2000000 INFO @ Sat, 06 Jul 2019 03:11:22: 2000000 INFO @ Sat, 06 Jul 2019 03:11:24: 2000000 INFO @ Sat, 06 Jul 2019 03:11:29: 3000000 INFO @ Sat, 06 Jul 2019 03:11:33: 3000000 INFO @ Sat, 06 Jul 2019 03:11:35: 3000000 INFO @ Sat, 06 Jul 2019 03:11:35: 4000000 INFO @ Sat, 06 Jul 2019 03:11:42: 5000000 INFO @ Sat, 06 Jul 2019 03:11:43: 4000000 INFO @ Sat, 06 Jul 2019 03:11:45: 4000000 INFO @ Sat, 06 Jul 2019 03:11:49: 6000000 INFO @ Sat, 06 Jul 2019 03:11:52: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:11:52: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:11:52: #1 total tags in treatment: 2919146 INFO @ Sat, 06 Jul 2019 03:11:52: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:11:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:11:52: #1 tags after filtering in treatment: 2423942 INFO @ Sat, 06 Jul 2019 03:11:52: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 06 Jul 2019 03:11:52: #1 finished! INFO @ Sat, 06 Jul 2019 03:11:52: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:11:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:11:52: 5000000 INFO @ Sat, 06 Jul 2019 03:11:52: #2 number of paired peaks: 174 WARNING @ Sat, 06 Jul 2019 03:11:52: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 06 Jul 2019 03:11:52: start model_add_line... INFO @ Sat, 06 Jul 2019 03:11:52: start X-correlation... INFO @ Sat, 06 Jul 2019 03:11:53: end of X-cor INFO @ Sat, 06 Jul 2019 03:11:53: #2 finished! INFO @ Sat, 06 Jul 2019 03:11:53: #2 predicted fragment length is 306 bps INFO @ Sat, 06 Jul 2019 03:11:53: #2 alternative fragment length(s) may be 190,236,260,306,348,450,561,592,596 bps INFO @ Sat, 06 Jul 2019 03:11:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.10_model.r INFO @ Sat, 06 Jul 2019 03:11:53: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:11:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:11:54: 5000000 INFO @ Sat, 06 Jul 2019 03:12:00: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:12:00: 6000000 INFO @ Sat, 06 Jul 2019 03:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.10_summits.bed INFO @ Sat, 06 Jul 2019 03:12:03: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:12:03: 6000000 INFO @ Sat, 06 Jul 2019 03:12:04: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:12:04: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:12:04: #1 total tags in treatment: 2919146 INFO @ Sat, 06 Jul 2019 03:12:04: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:12:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:12:04: #1 tags after filtering in treatment: 2423942 INFO @ Sat, 06 Jul 2019 03:12:04: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 06 Jul 2019 03:12:04: #1 finished! INFO @ Sat, 06 Jul 2019 03:12:04: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:12:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:12:04: #2 number of paired peaks: 174 WARNING @ Sat, 06 Jul 2019 03:12:04: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 06 Jul 2019 03:12:04: start model_add_line... INFO @ Sat, 06 Jul 2019 03:12:04: start X-correlation... INFO @ Sat, 06 Jul 2019 03:12:04: end of X-cor INFO @ Sat, 06 Jul 2019 03:12:04: #2 finished! INFO @ Sat, 06 Jul 2019 03:12:04: #2 predicted fragment length is 306 bps INFO @ Sat, 06 Jul 2019 03:12:04: #2 alternative fragment length(s) may be 190,236,260,306,348,450,561,592,596 bps INFO @ Sat, 06 Jul 2019 03:12:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.05_model.r INFO @ Sat, 06 Jul 2019 03:12:04: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:12:07: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:12:07: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:12:07: #1 total tags in treatment: 2919146 INFO @ Sat, 06 Jul 2019 03:12:07: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:12:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:12:07: #1 tags after filtering in treatment: 2423942 INFO @ Sat, 06 Jul 2019 03:12:07: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 06 Jul 2019 03:12:07: #1 finished! INFO @ Sat, 06 Jul 2019 03:12:07: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:12:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:12:08: #2 number of paired peaks: 174 WARNING @ Sat, 06 Jul 2019 03:12:08: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 06 Jul 2019 03:12:08: start model_add_line... INFO @ Sat, 06 Jul 2019 03:12:08: start X-correlation... INFO @ Sat, 06 Jul 2019 03:12:08: end of X-cor INFO @ Sat, 06 Jul 2019 03:12:08: #2 finished! INFO @ Sat, 06 Jul 2019 03:12:08: #2 predicted fragment length is 306 bps INFO @ Sat, 06 Jul 2019 03:12:08: #2 alternative fragment length(s) may be 190,236,260,306,348,450,561,592,596 bps INFO @ Sat, 06 Jul 2019 03:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.20_model.r INFO @ Sat, 06 Jul 2019 03:12:08: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:12:11: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:12:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:12:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.05_summits.bed INFO @ Sat, 06 Jul 2019 03:12:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:12:15: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:12:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:12:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:12:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383674/SRX5383674.20_summits.bed INFO @ Sat, 06 Jul 2019 03:12:18: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。