Job ID = 9162129 sra ファイルのダウンロード中... Completed: 324371K bytes transferred in 5 seconds (525250K 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 2093609 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1639668/SRR3234031.sra Written 2093609 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: 00:03:32 2093609 reads; of these: 2093609 (100.00%) were paired; of these: 218918 (10.46%) aligned concordantly 0 times 1470511 (70.24%) aligned concordantly exactly 1 time 404180 (19.31%) aligned concordantly >1 times ---- 218918 pairs aligned concordantly 0 times; of these: 2260 (1.03%) aligned discordantly 1 time ---- 216658 pairs aligned 0 times concordantly or discordantly; of these: 433316 mates make up the pairs; of these: 420805 (97.11%) aligned 0 times 8733 (2.02%) aligned exactly 1 time 3778 (0.87%) aligned >1 times 89.95% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:32 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] 1548634 / 1750703 = 0.8846 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 06:11:34: # Command line: callpeak -t SRX1639668.bam -f BAM -g 12100000 -n SRX1639668.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1639668.20 # format = BAM # ChIP-seq file = ['SRX1639668.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 06:11:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:11:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:11:34: # Command line: callpeak -t SRX1639668.bam -f BAM -g 12100000 -n SRX1639668.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1639668.10 # format = BAM # ChIP-seq file = ['SRX1639668.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 06:11:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:11:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:11:34: # Command line: callpeak -t SRX1639668.bam -f BAM -g 12100000 -n SRX1639668.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1639668.05 # format = BAM # ChIP-seq file = ['SRX1639668.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 06:11:34: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:11:34: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:11:39: #1 tag size is determined as 138 bps INFO @ Wed, 28 Jun 2017 06:11:39: #1 tag size = 138 INFO @ Wed, 28 Jun 2017 06:11:39: #1 total tags in treatment: 326636 INFO @ Wed, 28 Jun 2017 06:11:39: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:11:39: #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 06:11:39: #1 tags after filtering in treatment: 186910 INFO @ Wed, 28 Jun 2017 06:11:39: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 28 Jun 2017 06:11:39: #1 finished! INFO @ Wed, 28 Jun 2017 06:11:39: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:11:39: #1 tag size is determined as 138 bps INFO @ Wed, 28 Jun 2017 06:11:39: #1 tag size = 138 INFO @ Wed, 28 Jun 2017 06:11:39: #1 total tags in treatment: 326636 INFO @ Wed, 28 Jun 2017 06:11:39: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:11:39: #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 06:11:39: #1 tags after filtering in treatment: 186910 INFO @ Wed, 28 Jun 2017 06:11:39: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 28 Jun 2017 06:11:39: #1 finished! INFO @ Wed, 28 Jun 2017 06:11:39: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:11:39: #2 number of paired peaks: 220 WARNING @ Wed, 28 Jun 2017 06:11:39: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Wed, 28 Jun 2017 06:11:39: start model_add_line... INFO @ Wed, 28 Jun 2017 06:11:39: start X-correlation... INFO @ Wed, 28 Jun 2017 06:11:39: end of X-cor INFO @ Wed, 28 Jun 2017 06:11:39: #2 finished! INFO @ Wed, 28 Jun 2017 06:11:39: #2 predicted fragment length is 263 bps INFO @ Wed, 28 Jun 2017 06:11:39: #2 alternative fragment length(s) may be 34,146,181,207,228,256,263,292,303,320,349,453,486,556,586 bps INFO @ Wed, 28 Jun 2017 06:11:39: #2.2 Generate R script for model : SRX1639668.05_model.r INFO @ Wed, 28 Jun 2017 06:11:39: #2 number of paired peaks: 220 WARNING @ Wed, 28 Jun 2017 06:11:39: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Wed, 28 Jun 2017 06:11:39: start model_add_line... INFO @ Wed, 28 Jun 2017 06:11:39: #1 tag size is determined as 138 bps INFO @ Wed, 28 Jun 2017 06:11:39: #1 tag size = 138 INFO @ Wed, 28 Jun 2017 06:11:39: #1 total tags in treatment: 326636 INFO @ Wed, 28 Jun 2017 06:11:39: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:11:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) WARNING @ Wed, 28 Jun 2017 06:11:39: #2 Since the d (263) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Wed, 28 Jun 2017 06:11:39: start X-correlation... WARNING @ Wed, 28 Jun 2017 06:11:39: #2 You may need to consider one of the other alternative d(s): 34,146,181,207,228,256,263,292,303,320,349,453,486,556,586 WARNING @ Wed, 28 Jun 2017 06:11:39: #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 06:11:39: #3 Call peaks... INFO @ Wed, 28 Jun 2017 06:11:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 06:11:39: end of X-cor INFO @ Wed, 28 Jun 2017 06:11:39: #2 finished! INFO @ Wed, 28 Jun 2017 06:11:39: #2 predicted fragment length is 263 bps INFO @ Wed, 28 Jun 2017 06:11:39: #2 alternative fragment length(s) may be 34,146,181,207,228,256,263,292,303,320,349,453,486,556,586 bps INFO @ Wed, 28 Jun 2017 06:11:39: #2.2 Generate R script for model : SRX1639668.10_model.r INFO @ Wed, 28 Jun 2017 06:11:39: #1 tags after filtering in treatment: 186910 INFO @ Wed, 28 Jun 2017 06:11:39: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 28 Jun 2017 06:11:39: #1 finished! INFO @ Wed, 28 Jun 2017 06:11:39: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:11:39: #2 looking for paired plus/minus strand peaks... WARNING @ Wed, 28 Jun 2017 06:11:39: #2 Since the d (263) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 06:11:39: #2 You may need to consider one of the other alternative d(s): 34,146,181,207,228,256,263,292,303,320,349,453,486,556,586 WARNING @ Wed, 28 Jun 2017 06:11:39: #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 06:11:39: #3 Call peaks... INFO @ Wed, 28 Jun 2017 06:11:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 06:11:39: #2 number of paired peaks: 220 WARNING @ Wed, 28 Jun 2017 06:11:39: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Wed, 28 Jun 2017 06:11:39: start model_add_line... INFO @ Wed, 28 Jun 2017 06:11:39: start X-correlation... INFO @ Wed, 28 Jun 2017 06:11:39: end of X-cor INFO @ Wed, 28 Jun 2017 06:11:39: #2 finished! INFO @ Wed, 28 Jun 2017 06:11:39: #2 predicted fragment length is 263 bps INFO @ Wed, 28 Jun 2017 06:11:39: #2 alternative fragment length(s) may be 34,146,181,207,228,256,263,292,303,320,349,453,486,556,586 bps INFO @ Wed, 28 Jun 2017 06:11:39: #2.2 Generate R script for model : SRX1639668.20_model.r WARNING @ Wed, 28 Jun 2017 06:11:39: #2 Since the d (263) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 06:11:39: #2 You may need to consider one of the other alternative d(s): 34,146,181,207,228,256,263,292,303,320,349,453,486,556,586 WARNING @ Wed, 28 Jun 2017 06:11:39: #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 06:11:39: #3 Call peaks... INFO @ Wed, 28 Jun 2017 06:11:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 06:11:40: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 06:11:40: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 06:11:40: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 06:11:40: #4 Write output xls file... SRX1639668.05_peaks.xls INFO @ Wed, 28 Jun 2017 06:11:40: #4 Write peak in narrowPeak format file... SRX1639668.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 06:11:40: #4 Write summits bed file... SRX1639668.05_summits.bed INFO @ Wed, 28 Jun 2017 06:11:40: Done! pass1 - making usageList (12 chroms): 1 millis INFO @ Wed, 28 Jun 2017 06:11:40: #4 Write output xls file... SRX1639668.20_peaks.xls pass2 - checking and writing primary data (20 records, 4 fields): 2 millis INFO @ Wed, 28 Jun 2017 06:11:40: #4 Write peak in narrowPeak format file... SRX1639668.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 06:11:40: #4 Write summits bed file... SRX1639668.20_summits.bed INFO @ Wed, 28 Jun 2017 06:11:40: Done! CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 06:11:40: #4 Write output xls file... SRX1639668.10_peaks.xls INFO @ Wed, 28 Jun 2017 06:11:40: #4 Write peak in narrowPeak format file... SRX1639668.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 06:11:40: #4 Write summits bed file... SRX1639668.10_summits.bed INFO @ Wed, 28 Jun 2017 06:11:40: Done! pass1 - making usageList (1 chroms): 2 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (5 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。