Job ID = 2008027 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,678,935 reads read : 3,357,870 reads written : 3,357,870 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: 00:02:34 1678935 reads; of these: 1678935 (100.00%) were paired; of these: 169059 (10.07%) aligned concordantly 0 times 1397781 (83.25%) aligned concordantly exactly 1 time 112095 (6.68%) aligned concordantly >1 times ---- 169059 pairs aligned concordantly 0 times; of these: 88623 (52.42%) aligned discordantly 1 time ---- 80436 pairs aligned 0 times concordantly or discordantly; of these: 160872 mates make up the pairs; of these: 114932 (71.44%) aligned 0 times 28358 (17.63%) aligned exactly 1 time 17582 (10.93%) aligned >1 times 96.58% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 56354 / 1580173 = 0.0357 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 17:20:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.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 17:20:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:20:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:20:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.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 17:20:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:20:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:20:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.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 17:20:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:20:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:20:40: 1000000 INFO @ Fri, 05 Jul 2019 17:20:41: 1000000 INFO @ Fri, 05 Jul 2019 17:20:43: 1000000 INFO @ Fri, 05 Jul 2019 17:20:51: 2000000 INFO @ Fri, 05 Jul 2019 17:20:52: 2000000 INFO @ Fri, 05 Jul 2019 17:20:54: 2000000 INFO @ Fri, 05 Jul 2019 17:21:01: 3000000 INFO @ Fri, 05 Jul 2019 17:21:02: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:21:02: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:21:02: #1 total tags in treatment: 1455015 INFO @ Fri, 05 Jul 2019 17:21:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:21:02: #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 17:21:02: #1 tags after filtering in treatment: 1325953 INFO @ Fri, 05 Jul 2019 17:21:02: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 05 Jul 2019 17:21:02: #1 finished! INFO @ Fri, 05 Jul 2019 17:21:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:21:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:21:03: #2 number of paired peaks: 275 WARNING @ Fri, 05 Jul 2019 17:21:03: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Fri, 05 Jul 2019 17:21:03: start model_add_line... INFO @ Fri, 05 Jul 2019 17:21:03: start X-correlation... INFO @ Fri, 05 Jul 2019 17:21:03: end of X-cor INFO @ Fri, 05 Jul 2019 17:21:03: #2 finished! INFO @ Fri, 05 Jul 2019 17:21:03: #2 predicted fragment length is 207 bps INFO @ Fri, 05 Jul 2019 17:21:03: #2 alternative fragment length(s) may be 189,207 bps INFO @ Fri, 05 Jul 2019 17:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.10_model.r INFO @ Fri, 05 Jul 2019 17:21:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:21:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:21:03: 3000000 INFO @ Fri, 05 Jul 2019 17:21:04: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:21:04: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:21:04: #1 total tags in treatment: 1455015 INFO @ Fri, 05 Jul 2019 17:21:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:21:04: #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 17:21:04: #1 tags after filtering in treatment: 1325953 INFO @ Fri, 05 Jul 2019 17:21:04: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 05 Jul 2019 17:21:04: #1 finished! INFO @ Fri, 05 Jul 2019 17:21:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:21:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:21:04: #2 number of paired peaks: 275 WARNING @ Fri, 05 Jul 2019 17:21:04: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Fri, 05 Jul 2019 17:21:04: start model_add_line... INFO @ Fri, 05 Jul 2019 17:21:04: start X-correlation... INFO @ Fri, 05 Jul 2019 17:21:04: end of X-cor INFO @ Fri, 05 Jul 2019 17:21:04: #2 finished! INFO @ Fri, 05 Jul 2019 17:21:04: #2 predicted fragment length is 207 bps INFO @ Fri, 05 Jul 2019 17:21:04: #2 alternative fragment length(s) may be 189,207 bps INFO @ Fri, 05 Jul 2019 17:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.05_model.r INFO @ Fri, 05 Jul 2019 17:21:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:21:05: 3000000 INFO @ Fri, 05 Jul 2019 17:21:06: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:21:06: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:21:06: #1 total tags in treatment: 1455015 INFO @ Fri, 05 Jul 2019 17:21:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:21:06: #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 17:21:06: #1 tags after filtering in treatment: 1325953 INFO @ Fri, 05 Jul 2019 17:21:06: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 05 Jul 2019 17:21:06: #1 finished! INFO @ Fri, 05 Jul 2019 17:21:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:21:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:21:06: #2 number of paired peaks: 275 WARNING @ Fri, 05 Jul 2019 17:21:06: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Fri, 05 Jul 2019 17:21:06: start model_add_line... INFO @ Fri, 05 Jul 2019 17:21:06: start X-correlation... INFO @ Fri, 05 Jul 2019 17:21:06: end of X-cor INFO @ Fri, 05 Jul 2019 17:21:06: #2 finished! INFO @ Fri, 05 Jul 2019 17:21:06: #2 predicted fragment length is 207 bps INFO @ Fri, 05 Jul 2019 17:21:06: #2 alternative fragment length(s) may be 189,207 bps INFO @ Fri, 05 Jul 2019 17:21:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.20_model.r INFO @ Fri, 05 Jul 2019 17:21:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:21:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:21:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:21:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:21:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:21:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:21:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.10_summits.bed INFO @ Fri, 05 Jul 2019 17:21:10: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (403 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:21:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:21:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:21:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:21:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.05_summits.bed INFO @ Fri, 05 Jul 2019 17:21:11: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (722 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 17:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471813/ERX471813.20_summits.bed INFO @ Fri, 05 Jul 2019 17:21:13: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (215 records, 4 fields): 83 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。