Job ID = 9160027 sra ファイルのダウンロード中... Completed: 31559K bytes transferred in 3 seconds (76202K 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 1067063 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2574966/SRR5270915.sra Written 1067063 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: 00:00:53 1067063 reads; of these: 1067063 (100.00%) were paired; of these: 146612 (13.74%) aligned concordantly 0 times 450163 (42.19%) aligned concordantly exactly 1 time 470288 (44.07%) aligned concordantly >1 times ---- 146612 pairs aligned concordantly 0 times; of these: 8529 (5.82%) aligned discordantly 1 time ---- 138083 pairs aligned 0 times concordantly or discordantly; of these: 276166 mates make up the pairs; of these: 226669 (82.08%) aligned 0 times 14863 (5.38%) aligned exactly 1 time 34634 (12.54%) aligned >1 times 89.38% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 55025 / 921969 = 0.0597 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 01:42:30: # Command line: callpeak -t SRX2574966.bam -f BAM -g 12100000 -n SRX2574966.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2574966.05 # format = BAM # ChIP-seq file = ['SRX2574966.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 01:42:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:42:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:42:30: # Command line: callpeak -t SRX2574966.bam -f BAM -g 12100000 -n SRX2574966.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2574966.10 # format = BAM # ChIP-seq file = ['SRX2574966.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 01:42:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:42:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:42:30: # Command line: callpeak -t SRX2574966.bam -f BAM -g 12100000 -n SRX2574966.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2574966.20 # format = BAM # ChIP-seq file = ['SRX2574966.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 01:42:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:42:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:42:36: 1000000 INFO @ Wed, 28 Jun 2017 01:42:36: 1000000 INFO @ Wed, 28 Jun 2017 01:42:36: 1000000 INFO @ Wed, 28 Jun 2017 01:42:40: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:42:40: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:42:40: #1 total tags in treatment: 865451 INFO @ Wed, 28 Jun 2017 01:42:40: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:42:40: #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 01:42:40: #1 tags after filtering in treatment: 506345 INFO @ Wed, 28 Jun 2017 01:42:40: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 28 Jun 2017 01:42:40: #1 finished! INFO @ Wed, 28 Jun 2017 01:42:40: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:42:40: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:42:40: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:42:40: #1 total tags in treatment: 865451 INFO @ Wed, 28 Jun 2017 01:42:40: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:42:40: #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 01:42:40: #1 tags after filtering in treatment: 506345 INFO @ Wed, 28 Jun 2017 01:42:40: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 28 Jun 2017 01:42:40: #1 finished! INFO @ Wed, 28 Jun 2017 01:42:40: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:42:40: #2 number of paired peaks: 202 WARNING @ Wed, 28 Jun 2017 01:42:40: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Wed, 28 Jun 2017 01:42:40: start model_add_line... INFO @ Wed, 28 Jun 2017 01:42:40: start X-correlation... INFO @ Wed, 28 Jun 2017 01:42:40: end of X-cor INFO @ Wed, 28 Jun 2017 01:42:40: #2 finished! INFO @ Wed, 28 Jun 2017 01:42:40: #2 predicted fragment length is 233 bps INFO @ Wed, 28 Jun 2017 01:42:40: #2 alternative fragment length(s) may be 233 bps INFO @ Wed, 28 Jun 2017 01:42:40: #2.2 Generate R script for model : SRX2574966.10_model.r INFO @ Wed, 28 Jun 2017 01:42:40: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:42:40: #2 number of paired peaks: 202 WARNING @ Wed, 28 Jun 2017 01:42:40: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Wed, 28 Jun 2017 01:42:40: start model_add_line... INFO @ Wed, 28 Jun 2017 01:42:40: start X-correlation... INFO @ Wed, 28 Jun 2017 01:42:40: end of X-cor INFO @ Wed, 28 Jun 2017 01:42:40: #2 finished! INFO @ Wed, 28 Jun 2017 01:42:40: #2 predicted fragment length is 233 bps INFO @ Wed, 28 Jun 2017 01:42:40: #2 alternative fragment length(s) may be 233 bps INFO @ Wed, 28 Jun 2017 01:42:40: #2.2 Generate R script for model : SRX2574966.05_model.r INFO @ Wed, 28 Jun 2017 01:42:40: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:42:40: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:42:40: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:42:40: #1 total tags in treatment: 865451 INFO @ Wed, 28 Jun 2017 01:42:40: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:42:40: #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 01:42:40: #1 tags after filtering in treatment: 506345 INFO @ Wed, 28 Jun 2017 01:42:40: #1 Redundant rate of treatment: 0.41 INFO @ Wed, 28 Jun 2017 01:42:40: #1 finished! INFO @ Wed, 28 Jun 2017 01:42:40: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:42:40: #2 number of paired peaks: 202 WARNING @ Wed, 28 Jun 2017 01:42:40: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Wed, 28 Jun 2017 01:42:40: start model_add_line... INFO @ Wed, 28 Jun 2017 01:42:40: start X-correlation... INFO @ Wed, 28 Jun 2017 01:42:40: end of X-cor INFO @ Wed, 28 Jun 2017 01:42:40: #2 finished! INFO @ Wed, 28 Jun 2017 01:42:40: #2 predicted fragment length is 233 bps INFO @ Wed, 28 Jun 2017 01:42:40: #2 alternative fragment length(s) may be 233 bps INFO @ Wed, 28 Jun 2017 01:42:40: #2.2 Generate R script for model : SRX2574966.20_model.r INFO @ Wed, 28 Jun 2017 01:42:40: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:42:42: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:42:42: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:42:43: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:42:43: #4 Write output xls file... SRX2574966.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:42:43: #4 Write peak in narrowPeak format file... SRX2574966.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:42:43: #4 Write output xls file... SRX2574966.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:42:43: #4 Write summits bed file... SRX2574966.10_summits.bed INFO @ Wed, 28 Jun 2017 01:42:43: Done! INFO @ Wed, 28 Jun 2017 01:42:43: #4 Write peak in narrowPeak format file... SRX2574966.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:42:43: #4 Write summits bed file... SRX2574966.05_summits.bed INFO @ Wed, 28 Jun 2017 01:42:43: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (476 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (647 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:42:43: #4 Write output xls file... SRX2574966.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:42:43: #4 Write peak in narrowPeak format file... SRX2574966.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:42:43: #4 Write summits bed file... SRX2574966.20_summits.bed INFO @ Wed, 28 Jun 2017 01:42:43: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (221 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。