Job ID = 9160004 sra ファイルのダウンロード中... Completed: 733700K bytes transferred in 10 seconds (592101K 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 7729102 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2402729/SRR5085174.sra Written 7729102 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: 00:07:49 7729102 reads; of these: 7729102 (100.00%) were paired; of these: 644077 (8.33%) aligned concordantly 0 times 5212723 (67.44%) aligned concordantly exactly 1 time 1872302 (24.22%) aligned concordantly >1 times ---- 644077 pairs aligned concordantly 0 times; of these: 24783 (3.85%) aligned discordantly 1 time ---- 619294 pairs aligned 0 times concordantly or discordantly; of these: 1238588 mates make up the pairs; of these: 1046916 (84.52%) aligned 0 times 130018 (10.50%) aligned exactly 1 time 61654 (4.98%) aligned >1 times 93.23% overall alignment rate Time searching: 00:07:49 Overall time: 00:07:49 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 8 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] 6070039 / 7104521 = 0.8544 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 01:45:27: # Command line: callpeak -t SRX2402729.bam -f BAM -g 12100000 -n SRX2402729.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2402729.05 # format = BAM # ChIP-seq file = ['SRX2402729.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 01:45:27: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:45:27: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:45:27: # Command line: callpeak -t SRX2402729.bam -f BAM -g 12100000 -n SRX2402729.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2402729.10 # format = BAM # ChIP-seq file = ['SRX2402729.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 01:45:27: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:45:27: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:45:27: # Command line: callpeak -t SRX2402729.bam -f BAM -g 12100000 -n SRX2402729.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2402729.20 # format = BAM # ChIP-seq file = ['SRX2402729.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 01:45:27: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:45:27: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:45:36: 1000000 INFO @ Wed, 28 Jun 2017 01:45:36: 1000000 INFO @ Wed, 28 Jun 2017 01:45:36: 1000000 INFO @ Wed, 28 Jun 2017 01:45:45: 2000000 INFO @ Wed, 28 Jun 2017 01:45:45: 2000000 INFO @ Wed, 28 Jun 2017 01:45:45: 2000000 INFO @ Wed, 28 Jun 2017 01:45:47: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:45:47: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:45:47: #1 total tags in treatment: 1030792 INFO @ Wed, 28 Jun 2017 01:45:47: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:45:47: #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 01:45:47: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:45:47: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:45:47: #1 total tags in treatment: 1030792 INFO @ Wed, 28 Jun 2017 01:45:47: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:45:47: #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 01:45:47: #1 tag size is determined as 75 bps INFO @ Wed, 28 Jun 2017 01:45:47: #1 tag size = 75 INFO @ Wed, 28 Jun 2017 01:45:47: #1 total tags in treatment: 1030792 INFO @ Wed, 28 Jun 2017 01:45:47: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:45:47: #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 01:45:47: #1 tags after filtering in treatment: 737511 INFO @ Wed, 28 Jun 2017 01:45:47: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 01:45:47: #1 finished! INFO @ Wed, 28 Jun 2017 01:45:47: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:45:47: #1 tags after filtering in treatment: 737511 INFO @ Wed, 28 Jun 2017 01:45:47: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 01:45:47: #1 finished! INFO @ Wed, 28 Jun 2017 01:45:47: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:45:47: #1 tags after filtering in treatment: 737511 INFO @ Wed, 28 Jun 2017 01:45:47: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 01:45:47: #1 finished! INFO @ Wed, 28 Jun 2017 01:45:47: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:45:47: #2 number of paired peaks: 254 WARNING @ Wed, 28 Jun 2017 01:45:47: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Wed, 28 Jun 2017 01:45:47: start model_add_line... INFO @ Wed, 28 Jun 2017 01:45:47: #2 number of paired peaks: 254 WARNING @ Wed, 28 Jun 2017 01:45:47: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Wed, 28 Jun 2017 01:45:47: start model_add_line... INFO @ Wed, 28 Jun 2017 01:45:47: #2 number of paired peaks: 254 WARNING @ Wed, 28 Jun 2017 01:45:47: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Wed, 28 Jun 2017 01:45:47: start model_add_line... INFO @ Wed, 28 Jun 2017 01:45:47: start X-correlation... INFO @ Wed, 28 Jun 2017 01:45:47: start X-correlation... INFO @ Wed, 28 Jun 2017 01:45:47: start X-correlation... INFO @ Wed, 28 Jun 2017 01:45:47: end of X-cor INFO @ Wed, 28 Jun 2017 01:45:47: #2 finished! INFO @ Wed, 28 Jun 2017 01:45:47: end of X-cor INFO @ Wed, 28 Jun 2017 01:45:47: #2 predicted fragment length is 178 bps INFO @ Wed, 28 Jun 2017 01:45:47: #2 finished! INFO @ Wed, 28 Jun 2017 01:45:47: #2 alternative fragment length(s) may be 2,100,147,178,197,417,588 bps INFO @ Wed, 28 Jun 2017 01:45:47: #2.2 Generate R script for model : SRX2402729.10_model.r INFO @ Wed, 28 Jun 2017 01:45:47: #2 predicted fragment length is 178 bps INFO @ Wed, 28 Jun 2017 01:45:47: #2 alternative fragment length(s) may be 2,100,147,178,197,417,588 bps INFO @ Wed, 28 Jun 2017 01:45:47: #2.2 Generate R script for model : SRX2402729.05_model.r INFO @ Wed, 28 Jun 2017 01:45:47: end of X-cor INFO @ Wed, 28 Jun 2017 01:45:47: #2 finished! INFO @ Wed, 28 Jun 2017 01:45:47: #2 predicted fragment length is 178 bps INFO @ Wed, 28 Jun 2017 01:45:47: #2 alternative fragment length(s) may be 2,100,147,178,197,417,588 bps INFO @ Wed, 28 Jun 2017 01:45:47: #2.2 Generate R script for model : SRX2402729.20_model.r INFO @ Wed, 28 Jun 2017 01:45:47: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:45:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:45:47: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:45:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:45:47: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:45:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:45:50: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:45:50: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:45:50: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:45:51: #4 Write output xls file... SRX2402729.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:45:51: #4 Write peak in narrowPeak format file... SRX2402729.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:45:51: #4 Write summits bed file... SRX2402729.20_summits.bed INFO @ Wed, 28 Jun 2017 01:45:51: Done! INFO @ Wed, 28 Jun 2017 01:45:51: #4 Write output xls file... SRX2402729.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:45:51: #4 Write peak in narrowPeak format file... SRX2402729.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:45:51: #4 Write summits bed file... SRX2402729.10_summits.bed INFO @ Wed, 28 Jun 2017 01:45:51: Done! pass1 - making usageList (7 chroms): 0 millis INFO @ Wed, 28 Jun 2017 01:45:51: #4 Write output xls file... SRX2402729.05_peaks.xls pass2 - checking and writing primary data (14 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:45:51: #4 Write peak in narrowPeak format file... SRX2402729.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:45:51: #4 Write summits bed file... SRX2402729.05_summits.bed INFO @ Wed, 28 Jun 2017 01:45:51: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (99 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (331 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。