Job ID = 11192839 sra ファイルのダウンロード中... Completed: 616999K bytes transferred in 8 seconds (626825K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 9026624 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2252363/SRR4432854.sra Written 9026624 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2252363/SRR4432854.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:08:31 9026624 reads; of these: 9026624 (100.00%) were paired; of these: 905062 (10.03%) aligned concordantly 0 times 6781293 (75.13%) aligned concordantly exactly 1 time 1340269 (14.85%) aligned concordantly >1 times ---- 905062 pairs aligned concordantly 0 times; of these: 113188 (12.51%) aligned discordantly 1 time ---- 791874 pairs aligned 0 times concordantly or discordantly; of these: 1583748 mates make up the pairs; of these: 1193916 (75.39%) aligned 0 times 279614 (17.66%) aligned exactly 1 time 110218 (6.96%) aligned >1 times 93.39% overall alignment rate Time searching: 00:08:31 Overall time: 00:08:31 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] 7924288 / 8230955 = 0.9627 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, 15 Sep 2018 10:10:52: # Command line: callpeak -t SRX2252363.bam -f BAM -g 12100000 -n SRX2252363.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2252363.20 # format = BAM # ChIP-seq file = ['SRX2252363.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, 15 Sep 2018 10:10:52: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:10:52: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:10:52: # Command line: callpeak -t SRX2252363.bam -f BAM -g 12100000 -n SRX2252363.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2252363.05 # format = BAM # ChIP-seq file = ['SRX2252363.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, 15 Sep 2018 10:10:52: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:10:52: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:10:52: # Command line: callpeak -t SRX2252363.bam -f BAM -g 12100000 -n SRX2252363.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2252363.10 # format = BAM # ChIP-seq file = ['SRX2252363.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, 15 Sep 2018 10:10:52: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:10:52: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:10:57: 1000000 INFO @ Sat, 15 Sep 2018 10:10:57: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:10:57: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:10:57: #1 total tags in treatment: 292886 INFO @ Sat, 15 Sep 2018 10:10:57: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:10:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:10:57: #1 tags after filtering in treatment: 257665 INFO @ Sat, 15 Sep 2018 10:10:57: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 15 Sep 2018 10:10:57: #1 finished! INFO @ Sat, 15 Sep 2018 10:10:57: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:10:57: 1000000 INFO @ Sat, 15 Sep 2018 10:10:57: #2 number of paired peaks: 358 WARNING @ Sat, 15 Sep 2018 10:10:57: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Sat, 15 Sep 2018 10:10:57: start model_add_line... INFO @ Sat, 15 Sep 2018 10:10:57: start X-correlation... INFO @ Sat, 15 Sep 2018 10:10:57: end of X-cor INFO @ Sat, 15 Sep 2018 10:10:57: #2 finished! INFO @ Sat, 15 Sep 2018 10:10:57: #2 predicted fragment length is 191 bps INFO @ Sat, 15 Sep 2018 10:10:57: #2 alternative fragment length(s) may be 4,61,108,144,191,214,237,253,286,303,360,442,515,551,569,591 bps INFO @ Sat, 15 Sep 2018 10:10:57: #2.2 Generate R script for model : SRX2252363.10_model.r INFO @ Sat, 15 Sep 2018 10:10:57: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:10:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:10:57: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:10:57: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:10:57: #1 total tags in treatment: 292886 INFO @ Sat, 15 Sep 2018 10:10:57: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:10:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:10:57: #1 tags after filtering in treatment: 257665 INFO @ Sat, 15 Sep 2018 10:10:57: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 15 Sep 2018 10:10:57: #1 finished! INFO @ Sat, 15 Sep 2018 10:10:57: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:10:57: #2 number of paired peaks: 358 WARNING @ Sat, 15 Sep 2018 10:10:57: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Sat, 15 Sep 2018 10:10:57: start model_add_line... INFO @ Sat, 15 Sep 2018 10:10:57: start X-correlation... INFO @ Sat, 15 Sep 2018 10:10:57: end of X-cor INFO @ Sat, 15 Sep 2018 10:10:57: #2 finished! INFO @ Sat, 15 Sep 2018 10:10:57: #2 predicted fragment length is 191 bps INFO @ Sat, 15 Sep 2018 10:10:57: #2 alternative fragment length(s) may be 4,61,108,144,191,214,237,253,286,303,360,442,515,551,569,591 bps INFO @ Sat, 15 Sep 2018 10:10:57: #2.2 Generate R script for model : SRX2252363.20_model.r INFO @ Sat, 15 Sep 2018 10:10:57: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:10:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:10:57: 1000000 INFO @ Sat, 15 Sep 2018 10:10:57: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:10:57: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:10:57: #1 total tags in treatment: 292886 INFO @ Sat, 15 Sep 2018 10:10:57: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:10:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:10:57: #1 tags after filtering in treatment: 257665 INFO @ Sat, 15 Sep 2018 10:10:57: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 15 Sep 2018 10:10:57: #1 finished! INFO @ Sat, 15 Sep 2018 10:10:57: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:10:57: #2 number of paired peaks: 358 WARNING @ Sat, 15 Sep 2018 10:10:57: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Sat, 15 Sep 2018 10:10:57: start model_add_line... INFO @ Sat, 15 Sep 2018 10:10:57: start X-correlation... INFO @ Sat, 15 Sep 2018 10:10:57: end of X-cor INFO @ Sat, 15 Sep 2018 10:10:57: #2 finished! INFO @ Sat, 15 Sep 2018 10:10:57: #2 predicted fragment length is 191 bps INFO @ Sat, 15 Sep 2018 10:10:57: #2 alternative fragment length(s) may be 4,61,108,144,191,214,237,253,286,303,360,442,515,551,569,591 bps INFO @ Sat, 15 Sep 2018 10:10:57: #2.2 Generate R script for model : SRX2252363.05_model.r INFO @ Sat, 15 Sep 2018 10:10:57: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:10:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:10:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:10:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:10:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:10:59: #4 Write output xls file... SRX2252363.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:10:59: #4 Write peak in narrowPeak format file... SRX2252363.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:10:59: #4 Write summits bed file... SRX2252363.10_summits.bed INFO @ Sat, 15 Sep 2018 10:10:59: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (54 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:10:59: #4 Write output xls file... SRX2252363.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:10:59: #4 Write peak in narrowPeak format file... SRX2252363.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:10:59: #4 Write summits bed file... SRX2252363.20_summits.bed INFO @ Sat, 15 Sep 2018 10:10:59: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:10:59: #4 Write output xls file... SRX2252363.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:10:59: #4 Write peak in narrowPeak format file... SRX2252363.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:10:59: #4 Write summits bed file... SRX2252363.05_summits.bed INFO @ Sat, 15 Sep 2018 10:10:59: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (125 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。