Job ID = 9162007 sra ファイルのダウンロード中... Completed: 1243644K bytes transferred in 13 seconds (739873K bits/sec), in 1 file, 2 directories. 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... Written 20092762 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423739/SRR2931028.sra Written 20092762 spots total 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: 00:12:11 20092762 reads; of these: 20092762 (100.00%) were paired; of these: 6082881 (30.27%) aligned concordantly 0 times 12387005 (61.65%) aligned concordantly exactly 1 time 1622876 (8.08%) aligned concordantly >1 times ---- 6082881 pairs aligned concordantly 0 times; of these: 29420 (0.48%) aligned discordantly 1 time ---- 6053461 pairs aligned 0 times concordantly or discordantly; of these: 12106922 mates make up the pairs; of these: 11750378 (97.06%) aligned 0 times 300613 (2.48%) aligned exactly 1 time 55931 (0.46%) aligned >1 times 70.76% overall alignment rate Time searching: 00:12:11 Overall time: 00:12:11 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 12 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] 11363380 / 14019343 = 0.8106 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 @ Wed, 28 Jun 2017 05:34:10: # Command line: callpeak -t SRX1423739.bam -f BAM -g 12100000 -n SRX1423739.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423739.05 # format = BAM # ChIP-seq file = ['SRX1423739.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 @ Wed, 28 Jun 2017 05:34:10: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:34:10: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:34:10: # Command line: callpeak -t SRX1423739.bam -f BAM -g 12100000 -n SRX1423739.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423739.20 # format = BAM # ChIP-seq file = ['SRX1423739.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 @ Wed, 28 Jun 2017 05:34:10: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:34:10: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:34:10: # Command line: callpeak -t SRX1423739.bam -f BAM -g 12100000 -n SRX1423739.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423739.10 # format = BAM # ChIP-seq file = ['SRX1423739.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 @ Wed, 28 Jun 2017 05:34:10: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:34:10: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:34:17: 1000000 INFO @ Wed, 28 Jun 2017 05:34:17: 1000000 INFO @ Wed, 28 Jun 2017 05:34:17: 1000000 INFO @ Wed, 28 Jun 2017 05:34:24: 2000000 INFO @ Wed, 28 Jun 2017 05:34:24: 2000000 INFO @ Wed, 28 Jun 2017 05:34:24: 2000000 INFO @ Wed, 28 Jun 2017 05:34:31: 3000000 INFO @ Wed, 28 Jun 2017 05:34:31: 3000000 INFO @ Wed, 28 Jun 2017 05:34:31: 3000000 INFO @ Wed, 28 Jun 2017 05:34:37: 4000000 INFO @ Wed, 28 Jun 2017 05:34:37: 4000000 INFO @ Wed, 28 Jun 2017 05:34:38: 4000000 INFO @ Wed, 28 Jun 2017 05:34:44: 5000000 INFO @ Wed, 28 Jun 2017 05:34:44: 5000000 INFO @ Wed, 28 Jun 2017 05:34:45: 5000000 INFO @ Wed, 28 Jun 2017 05:34:49: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:34:49: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:34:49: #1 total tags in treatment: 2655792 INFO @ Wed, 28 Jun 2017 05:34:49: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:34:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:34:49: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:34:49: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:34:49: #1 total tags in treatment: 2655792 INFO @ Wed, 28 Jun 2017 05:34:49: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:34:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:34:49: #1 tags after filtering in treatment: 2283861 INFO @ Wed, 28 Jun 2017 05:34:49: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 05:34:49: #1 finished! INFO @ Wed, 28 Jun 2017 05:34:49: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:34:49: #1 tags after filtering in treatment: 2283861 INFO @ Wed, 28 Jun 2017 05:34:49: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 05:34:49: #1 finished! INFO @ Wed, 28 Jun 2017 05:34:49: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:34:49: #2 number of paired peaks: 108 WARNING @ Wed, 28 Jun 2017 05:34:49: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Wed, 28 Jun 2017 05:34:49: start model_add_line... INFO @ Wed, 28 Jun 2017 05:34:49: #2 number of paired peaks: 108 WARNING @ Wed, 28 Jun 2017 05:34:49: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Wed, 28 Jun 2017 05:34:49: start model_add_line... INFO @ Wed, 28 Jun 2017 05:34:49: start X-correlation... INFO @ Wed, 28 Jun 2017 05:34:49: end of X-cor INFO @ Wed, 28 Jun 2017 05:34:49: #2 finished! INFO @ Wed, 28 Jun 2017 05:34:49: #2 predicted fragment length is 114 bps INFO @ Wed, 28 Jun 2017 05:34:49: #2 alternative fragment length(s) may be 2,57,89,114,146,160,208,221,226 bps INFO @ Wed, 28 Jun 2017 05:34:49: #2.2 Generate R script for model : SRX1423739.20_model.r INFO @ Wed, 28 Jun 2017 05:34:49: start X-correlation... INFO @ Wed, 28 Jun 2017 05:34:49: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:34:49: end of X-cor INFO @ Wed, 28 Jun 2017 05:34:49: #2 finished! INFO @ Wed, 28 Jun 2017 05:34:49: #2 predicted fragment length is 114 bps INFO @ Wed, 28 Jun 2017 05:34:49: #2 alternative fragment length(s) may be 2,57,89,114,146,160,208,221,226 bps INFO @ Wed, 28 Jun 2017 05:34:49: #2.2 Generate R script for model : SRX1423739.05_model.r INFO @ Wed, 28 Jun 2017 05:34:49: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:34:50: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:34:50: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:34:50: #1 total tags in treatment: 2655792 INFO @ Wed, 28 Jun 2017 05:34:50: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:34:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:34:50: #1 tags after filtering in treatment: 2283861 INFO @ Wed, 28 Jun 2017 05:34:50: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 05:34:50: #1 finished! INFO @ Wed, 28 Jun 2017 05:34:50: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:34:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:34:50: #2 number of paired peaks: 108 WARNING @ Wed, 28 Jun 2017 05:34:50: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Wed, 28 Jun 2017 05:34:50: start model_add_line... INFO @ Wed, 28 Jun 2017 05:34:50: start X-correlation... INFO @ Wed, 28 Jun 2017 05:34:50: end of X-cor INFO @ Wed, 28 Jun 2017 05:34:50: #2 finished! INFO @ Wed, 28 Jun 2017 05:34:50: #2 predicted fragment length is 114 bps INFO @ Wed, 28 Jun 2017 05:34:50: #2 alternative fragment length(s) may be 2,57,89,114,146,160,208,221,226 bps INFO @ Wed, 28 Jun 2017 05:34:50: #2.2 Generate R script for model : SRX1423739.10_model.r INFO @ Wed, 28 Jun 2017 05:34:50: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:34:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:34:55: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:34:55: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:34:56: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:34:57: #4 Write output xls file... SRX1423739.20_peaks.xls INFO @ Wed, 28 Jun 2017 05:34:57: #4 Write peak in narrowPeak format file... SRX1423739.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:34:57: #4 Write summits bed file... SRX1423739.20_summits.bed INFO @ Wed, 28 Jun 2017 05:34:57: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (127 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 05:34:57: #4 Write output xls file... SRX1423739.05_peaks.xls INFO @ Wed, 28 Jun 2017 05:34:57: #4 Write peak in narrowPeak format file... SRX1423739.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:34:57: #4 Write summits bed file... SRX1423739.05_summits.bed INFO @ Wed, 28 Jun 2017 05:34:57: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (585 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 05:34:59: #4 Write output xls file... SRX1423739.10_peaks.xls INFO @ Wed, 28 Jun 2017 05:34:59: #4 Write peak in narrowPeak format file... SRX1423739.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:34:59: #4 Write summits bed file... SRX1423739.10_summits.bed INFO @ Wed, 28 Jun 2017 05:34:59: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (272 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。