Job ID = 9160011 sra ファイルのダウンロード中... Completed: 1022476K bytes transferred in 12 seconds (675873K 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 10606621 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2402736/SRR5085181.sra Written 10606621 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: 00:11:13 10606621 reads; of these: 10606621 (100.00%) were paired; of these: 532239 (5.02%) aligned concordantly 0 times 7212712 (68.00%) aligned concordantly exactly 1 time 2861670 (26.98%) aligned concordantly >1 times ---- 532239 pairs aligned concordantly 0 times; of these: 30493 (5.73%) aligned discordantly 1 time ---- 501746 pairs aligned 0 times concordantly or discordantly; of these: 1003492 mates make up the pairs; of these: 887690 (88.46%) aligned 0 times 68981 (6.87%) aligned exactly 1 time 46821 (4.67%) aligned >1 times 95.82% overall alignment rate Time searching: 00:11:13 Overall time: 00:11:13 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] 7753042 / 10098831 = 0.7677 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 01:53:40: # Command line: callpeak -t SRX2402736.bam -f BAM -g 12100000 -n SRX2402736.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2402736.05 # format = BAM # ChIP-seq file = ['SRX2402736.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 01:53:40: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:53:40: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:53:40: # Command line: callpeak -t SRX2402736.bam -f BAM -g 12100000 -n SRX2402736.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2402736.10 # format = BAM # ChIP-seq file = ['SRX2402736.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 01:53:40: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:53:40: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:53:40: # Command line: callpeak -t SRX2402736.bam -f BAM -g 12100000 -n SRX2402736.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2402736.20 # format = BAM # ChIP-seq file = ['SRX2402736.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 01:53:40: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:53:40: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:53:50: 1000000 INFO @ Wed, 28 Jun 2017 01:53:50: 1000000 INFO @ Wed, 28 Jun 2017 01:53:50: 1000000 INFO @ Wed, 28 Jun 2017 01:53:59: 2000000 INFO @ Wed, 28 Jun 2017 01:53:59: 2000000 INFO @ Wed, 28 Jun 2017 01:53:59: 2000000 INFO @ Wed, 28 Jun 2017 01:54:09: 3000000 INFO @ Wed, 28 Jun 2017 01:54:09: 3000000 INFO @ Wed, 28 Jun 2017 01:54:09: 3000000 INFO @ Wed, 28 Jun 2017 01:54:18: 4000000 INFO @ Wed, 28 Jun 2017 01:54:18: 4000000 INFO @ Wed, 28 Jun 2017 01:54:18: 4000000 INFO @ Wed, 28 Jun 2017 01:54:26: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:54:26: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:54:26: #1 total tags in treatment: 2335242 INFO @ Wed, 28 Jun 2017 01:54:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:54:26: #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 01:54:26: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:54:26: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:54:26: #1 total tags in treatment: 2335242 INFO @ Wed, 28 Jun 2017 01:54:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:54:26: #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 01:54:26: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:54:26: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:54:26: #1 total tags in treatment: 2335242 INFO @ Wed, 28 Jun 2017 01:54:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:54:26: #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 01:54:26: #1 tags after filtering in treatment: 1587751 INFO @ Wed, 28 Jun 2017 01:54:26: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 01:54:26: #1 finished! INFO @ Wed, 28 Jun 2017 01:54:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:54:26: #1 tags after filtering in treatment: 1587751 INFO @ Wed, 28 Jun 2017 01:54:26: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 01:54:26: #1 finished! INFO @ Wed, 28 Jun 2017 01:54:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:54:26: #1 tags after filtering in treatment: 1587751 INFO @ Wed, 28 Jun 2017 01:54:26: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 28 Jun 2017 01:54:26: #1 finished! INFO @ Wed, 28 Jun 2017 01:54:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:54:26: #2 number of paired peaks: 144 WARNING @ Wed, 28 Jun 2017 01:54:26: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Wed, 28 Jun 2017 01:54:26: start model_add_line... INFO @ Wed, 28 Jun 2017 01:54:26: #2 number of paired peaks: 144 WARNING @ Wed, 28 Jun 2017 01:54:26: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Wed, 28 Jun 2017 01:54:26: start model_add_line... INFO @ Wed, 28 Jun 2017 01:54:26: #2 number of paired peaks: 144 WARNING @ Wed, 28 Jun 2017 01:54:26: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Wed, 28 Jun 2017 01:54:26: start model_add_line... INFO @ Wed, 28 Jun 2017 01:54:26: start X-correlation... INFO @ Wed, 28 Jun 2017 01:54:26: end of X-cor INFO @ Wed, 28 Jun 2017 01:54:26: #2 finished! INFO @ Wed, 28 Jun 2017 01:54:26: #2 predicted fragment length is 115 bps INFO @ Wed, 28 Jun 2017 01:54:26: #2 alternative fragment length(s) may be 2,34,43,67,76,94,115,167,187,200,287,553 bps INFO @ Wed, 28 Jun 2017 01:54:26: #2.2 Generate R script for model : SRX2402736.20_model.r INFO @ Wed, 28 Jun 2017 01:54:26: start X-correlation... INFO @ Wed, 28 Jun 2017 01:54:26: end of X-cor INFO @ Wed, 28 Jun 2017 01:54:26: #2 finished! INFO @ Wed, 28 Jun 2017 01:54:26: #2 predicted fragment length is 115 bps INFO @ Wed, 28 Jun 2017 01:54:26: #2 alternative fragment length(s) may be 2,34,43,67,76,94,115,167,187,200,287,553 bps INFO @ Wed, 28 Jun 2017 01:54:26: #2.2 Generate R script for model : SRX2402736.05_model.r WARNING @ Wed, 28 Jun 2017 01:54:26: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 01:54:26: #2 You may need to consider one of the other alternative d(s): 2,34,43,67,76,94,115,167,187,200,287,553 WARNING @ Wed, 28 Jun 2017 01:54:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 01:54:26: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:54:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:54:26: start X-correlation... INFO @ Wed, 28 Jun 2017 01:54:26: end of X-cor INFO @ Wed, 28 Jun 2017 01:54:26: #2 finished! INFO @ Wed, 28 Jun 2017 01:54:26: #2 predicted fragment length is 115 bps INFO @ Wed, 28 Jun 2017 01:54:26: #2 alternative fragment length(s) may be 2,34,43,67,76,94,115,167,187,200,287,553 bps INFO @ Wed, 28 Jun 2017 01:54:26: #2.2 Generate R script for model : SRX2402736.10_model.r WARNING @ Wed, 28 Jun 2017 01:54:26: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 01:54:26: #2 You may need to consider one of the other alternative d(s): 2,34,43,67,76,94,115,167,187,200,287,553 WARNING @ Wed, 28 Jun 2017 01:54:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 01:54:26: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:54:26: #3 Pre-compute pvalue-qvalue table... WARNING @ Wed, 28 Jun 2017 01:54:26: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 01:54:26: #2 You may need to consider one of the other alternative d(s): 2,34,43,67,76,94,115,167,187,200,287,553 WARNING @ Wed, 28 Jun 2017 01:54:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 01:54:26: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:54:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:54:31: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:54:31: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:54:31: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:54:33: #4 Write output xls file... SRX2402736.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:54:33: #4 Write peak in narrowPeak format file... SRX2402736.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:54:33: #4 Write summits bed file... SRX2402736.20_summits.bed INFO @ Wed, 28 Jun 2017 01:54:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (75 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:54:33: #4 Write output xls file... SRX2402736.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:54:33: #4 Write peak in narrowPeak format file... SRX2402736.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:54:33: #4 Write summits bed file... SRX2402736.10_summits.bed INFO @ Wed, 28 Jun 2017 01:54:33: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (304 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:54:33: #4 Write output xls file... SRX2402736.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:54:33: #4 Write peak in narrowPeak format file... SRX2402736.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:54:33: #4 Write summits bed file... SRX2402736.05_summits.bed INFO @ Wed, 28 Jun 2017 01:54:33: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (710 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。