Job ID = 9162308 sra ファイルのダウンロード中... Completed: 563209K bytes transferred in 11 seconds (393400K 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 4608614 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1872753/SRR3713226.sra Written 4608614 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: 00:06:09 4608614 reads; of these: 4608614 (100.00%) were paired; of these: 1186677 (25.75%) aligned concordantly 0 times 1935927 (42.01%) aligned concordantly exactly 1 time 1486010 (32.24%) aligned concordantly >1 times ---- 1186677 pairs aligned concordantly 0 times; of these: 204459 (17.23%) aligned discordantly 1 time ---- 982218 pairs aligned 0 times concordantly or discordantly; of these: 1964436 mates make up the pairs; of these: 1556822 (79.25%) aligned 0 times 41102 (2.09%) aligned exactly 1 time 366512 (18.66%) aligned >1 times 83.11% overall alignment rate Time searching: 00:06:09 Overall time: 00:06:09 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] 447637 / 3604174 = 0.1242 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 07:24:58: # Command line: callpeak -t SRX1872753.bam -f BAM -g 12100000 -n SRX1872753.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872753.05 # format = BAM # ChIP-seq file = ['SRX1872753.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 07:24:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:24:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:24:58: # Command line: callpeak -t SRX1872753.bam -f BAM -g 12100000 -n SRX1872753.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872753.20 # format = BAM # ChIP-seq file = ['SRX1872753.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 07:24:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:24:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:24:58: # Command line: callpeak -t SRX1872753.bam -f BAM -g 12100000 -n SRX1872753.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872753.10 # format = BAM # ChIP-seq file = ['SRX1872753.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 07:24:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:24:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:25:05: 1000000 INFO @ Wed, 28 Jun 2017 07:25:05: 1000000 INFO @ Wed, 28 Jun 2017 07:25:05: 1000000 INFO @ Wed, 28 Jun 2017 07:25:12: 2000000 INFO @ Wed, 28 Jun 2017 07:25:12: 2000000 INFO @ Wed, 28 Jun 2017 07:25:12: 2000000 INFO @ Wed, 28 Jun 2017 07:25:20: 3000000 INFO @ Wed, 28 Jun 2017 07:25:20: 3000000 INFO @ Wed, 28 Jun 2017 07:25:20: 3000000 INFO @ Wed, 28 Jun 2017 07:25:26: 4000000 INFO @ Wed, 28 Jun 2017 07:25:27: 4000000 INFO @ Wed, 28 Jun 2017 07:25:27: 4000000 INFO @ Wed, 28 Jun 2017 07:25:33: 5000000 INFO @ Wed, 28 Jun 2017 07:25:35: 5000000 INFO @ Wed, 28 Jun 2017 07:25:35: 5000000 INFO @ Wed, 28 Jun 2017 07:25:40: 6000000 INFO @ Wed, 28 Jun 2017 07:25:42: 6000000 INFO @ Wed, 28 Jun 2017 07:25:43: 6000000 INFO @ Wed, 28 Jun 2017 07:25:46: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:25:46: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:25:46: #1 total tags in treatment: 2991398 INFO @ Wed, 28 Jun 2017 07:25:46: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:25:46: #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 07:25:46: #1 tags after filtering in treatment: 1575809 INFO @ Wed, 28 Jun 2017 07:25:46: #1 Redundant rate of treatment: 0.47 INFO @ Wed, 28 Jun 2017 07:25:46: #1 finished! INFO @ Wed, 28 Jun 2017 07:25:46: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:25:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:25:46: #2 number of paired peaks: 607 WARNING @ Wed, 28 Jun 2017 07:25:46: Fewer paired peaks (607) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 607 pairs to build model! INFO @ Wed, 28 Jun 2017 07:25:46: start model_add_line... INFO @ Wed, 28 Jun 2017 07:25:46: start X-correlation... INFO @ Wed, 28 Jun 2017 07:25:46: end of X-cor INFO @ Wed, 28 Jun 2017 07:25:46: #2 finished! INFO @ Wed, 28 Jun 2017 07:25:46: #2 predicted fragment length is 188 bps INFO @ Wed, 28 Jun 2017 07:25:46: #2 alternative fragment length(s) may be 0,17,45,57,91,114,136,155,172,188,204,215,244,263,285,329,370,557,576,583,590 bps INFO @ Wed, 28 Jun 2017 07:25:46: #2.2 Generate R script for model : SRX1872753.20_model.r WARNING @ Wed, 28 Jun 2017 07:25:46: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:25:46: #2 You may need to consider one of the other alternative d(s): 0,17,45,57,91,114,136,155,172,188,204,215,244,263,285,329,370,557,576,583,590 WARNING @ Wed, 28 Jun 2017 07:25:46: #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 07:25:46: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:25:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:25:49: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:25:49: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:25:49: #1 total tags in treatment: 2991398 INFO @ Wed, 28 Jun 2017 07:25:49: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:25:49: #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 07:25:49: #1 tags after filtering in treatment: 1575809 INFO @ Wed, 28 Jun 2017 07:25:49: #1 Redundant rate of treatment: 0.47 INFO @ Wed, 28 Jun 2017 07:25:49: #1 finished! INFO @ Wed, 28 Jun 2017 07:25:49: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:25:49: #2 number of paired peaks: 607 WARNING @ Wed, 28 Jun 2017 07:25:49: Fewer paired peaks (607) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 607 pairs to build model! INFO @ Wed, 28 Jun 2017 07:25:49: start model_add_line... INFO @ Wed, 28 Jun 2017 07:25:49: start X-correlation... INFO @ Wed, 28 Jun 2017 07:25:49: end of X-cor INFO @ Wed, 28 Jun 2017 07:25:49: #2 finished! INFO @ Wed, 28 Jun 2017 07:25:49: #2 predicted fragment length is 188 bps INFO @ Wed, 28 Jun 2017 07:25:49: #2 alternative fragment length(s) may be 0,17,45,57,91,114,136,155,172,188,204,215,244,263,285,329,370,557,576,583,590 bps INFO @ Wed, 28 Jun 2017 07:25:49: #2.2 Generate R script for model : SRX1872753.10_model.r WARNING @ Wed, 28 Jun 2017 07:25:49: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:25:49: #2 You may need to consider one of the other alternative d(s): 0,17,45,57,91,114,136,155,172,188,204,215,244,263,285,329,370,557,576,583,590 WARNING @ Wed, 28 Jun 2017 07:25:49: #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 07:25:49: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:25:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:25:49: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:25:49: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:25:49: #1 total tags in treatment: 2991398 INFO @ Wed, 28 Jun 2017 07:25:49: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:25:49: #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 07:25:49: #1 tags after filtering in treatment: 1575809 INFO @ Wed, 28 Jun 2017 07:25:49: #1 Redundant rate of treatment: 0.47 INFO @ Wed, 28 Jun 2017 07:25:49: #1 finished! INFO @ Wed, 28 Jun 2017 07:25:49: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:25:50: #2 number of paired peaks: 607 WARNING @ Wed, 28 Jun 2017 07:25:50: Fewer paired peaks (607) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 607 pairs to build model! INFO @ Wed, 28 Jun 2017 07:25:50: start model_add_line... INFO @ Wed, 28 Jun 2017 07:25:50: start X-correlation... INFO @ Wed, 28 Jun 2017 07:25:50: end of X-cor INFO @ Wed, 28 Jun 2017 07:25:50: #2 finished! INFO @ Wed, 28 Jun 2017 07:25:50: #2 predicted fragment length is 188 bps INFO @ Wed, 28 Jun 2017 07:25:50: #2 alternative fragment length(s) may be 0,17,45,57,91,114,136,155,172,188,204,215,244,263,285,329,370,557,576,583,590 bps INFO @ Wed, 28 Jun 2017 07:25:50: #2.2 Generate R script for model : SRX1872753.05_model.r WARNING @ Wed, 28 Jun 2017 07:25:50: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 07:25:50: #2 You may need to consider one of the other alternative d(s): 0,17,45,57,91,114,136,155,172,188,204,215,244,263,285,329,370,557,576,583,590 WARNING @ Wed, 28 Jun 2017 07:25:50: #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 07:25:50: #3 Call peaks... INFO @ Wed, 28 Jun 2017 07:25:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 07:25:54: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:25:56: #4 Write output xls file... SRX1872753.20_peaks.xls INFO @ Wed, 28 Jun 2017 07:25:56: #4 Write peak in narrowPeak format file... SRX1872753.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:25:56: #4 Write summits bed file... SRX1872753.20_summits.bed INFO @ Wed, 28 Jun 2017 07:25:56: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (21 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 07:25:57: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:25:58: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 07:25:59: #4 Write output xls file... SRX1872753.10_peaks.xls INFO @ Wed, 28 Jun 2017 07:25:59: #4 Write peak in narrowPeak format file... SRX1872753.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:25:59: #4 Write summits bed file... SRX1872753.10_summits.bed INFO @ Wed, 28 Jun 2017 07:25:59: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (122 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 07:26:00: #4 Write output xls file... SRX1872753.05_peaks.xls INFO @ Wed, 28 Jun 2017 07:26:00: #4 Write peak in narrowPeak format file... SRX1872753.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 07:26:00: #4 Write summits bed file... SRX1872753.05_summits.bed INFO @ Wed, 28 Jun 2017 07:26:00: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (228 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。