Job ID = 9161993 sra ファイルのダウンロード中... Completed: 962082K bytes transferred in 13 seconds (601709K 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 22255960 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423725/SRR2931014.sra Written 22255960 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: 00:12:13 22255960 reads; of these: 22255960 (100.00%) were paired; of these: 9150011 (41.11%) aligned concordantly 0 times 11861436 (53.30%) aligned concordantly exactly 1 time 1244513 (5.59%) aligned concordantly >1 times ---- 9150011 pairs aligned concordantly 0 times; of these: 14684 (0.16%) aligned discordantly 1 time ---- 9135327 pairs aligned 0 times concordantly or discordantly; of these: 18270654 mates make up the pairs; of these: 17800413 (97.43%) aligned 0 times 417893 (2.29%) aligned exactly 1 time 52348 (0.29%) aligned >1 times 60.01% overall alignment rate Time searching: 00:12:13 Overall time: 00:12:13 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] 12126672 / 13112967 = 0.9248 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 05:28:25: # Command line: callpeak -t SRX1423725.bam -f BAM -g 12100000 -n SRX1423725.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423725.20 # format = BAM # ChIP-seq file = ['SRX1423725.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 05:28:25: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:28:25: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:28:25: # Command line: callpeak -t SRX1423725.bam -f BAM -g 12100000 -n SRX1423725.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423725.05 # format = BAM # ChIP-seq file = ['SRX1423725.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 05:28:25: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:28:25: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:28:25: # Command line: callpeak -t SRX1423725.bam -f BAM -g 12100000 -n SRX1423725.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423725.10 # format = BAM # ChIP-seq file = ['SRX1423725.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 05:28:25: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:28:25: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:28:30: 1000000 INFO @ Wed, 28 Jun 2017 05:28:30: 1000000 INFO @ Wed, 28 Jun 2017 05:28:31: 1000000 INFO @ Wed, 28 Jun 2017 05:28:36: 2000000 INFO @ Wed, 28 Jun 2017 05:28:36: 2000000 INFO @ Wed, 28 Jun 2017 05:28:37: 2000000 INFO @ Wed, 28 Jun 2017 05:28:38: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:28:38: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:28:38: #1 total tags in treatment: 987423 INFO @ Wed, 28 Jun 2017 05:28:38: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:28:38: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:28:38: #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 05:28:38: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:28:38: #1 total tags in treatment: 987423 INFO @ Wed, 28 Jun 2017 05:28:38: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:28:38: #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 05:28:39: #1 tags after filtering in treatment: 916172 INFO @ Wed, 28 Jun 2017 05:28:39: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 05:28:39: #1 tags after filtering in treatment: 916172 INFO @ Wed, 28 Jun 2017 05:28:39: #1 finished! INFO @ Wed, 28 Jun 2017 05:28:39: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:28:39: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 05:28:39: #1 finished! INFO @ Wed, 28 Jun 2017 05:28:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:28:39: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:28:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:28:39: #2 number of paired peaks: 198 WARNING @ Wed, 28 Jun 2017 05:28:39: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Wed, 28 Jun 2017 05:28:39: start model_add_line... INFO @ Wed, 28 Jun 2017 05:28:39: #2 number of paired peaks: 198 WARNING @ Wed, 28 Jun 2017 05:28:39: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Wed, 28 Jun 2017 05:28:39: start model_add_line... INFO @ Wed, 28 Jun 2017 05:28:39: start X-correlation... INFO @ Wed, 28 Jun 2017 05:28:39: start X-correlation... INFO @ Wed, 28 Jun 2017 05:28:39: end of X-cor INFO @ Wed, 28 Jun 2017 05:28:39: #2 finished! INFO @ Wed, 28 Jun 2017 05:28:39: #2 predicted fragment length is 214 bps INFO @ Wed, 28 Jun 2017 05:28:39: #2 alternative fragment length(s) may be 4,160,199,214,234 bps INFO @ Wed, 28 Jun 2017 05:28:39: #2.2 Generate R script for model : SRX1423725.20_model.r INFO @ Wed, 28 Jun 2017 05:28:39: end of X-cor INFO @ Wed, 28 Jun 2017 05:28:39: #2 finished! INFO @ Wed, 28 Jun 2017 05:28:39: #2 predicted fragment length is 214 bps INFO @ Wed, 28 Jun 2017 05:28:39: #2 alternative fragment length(s) may be 4,160,199,214,234 bps INFO @ Wed, 28 Jun 2017 05:28:39: #2.2 Generate R script for model : SRX1423725.05_model.r INFO @ Wed, 28 Jun 2017 05:28:39: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:28:39: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:28:39: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:28:39: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:28:39: #1 total tags in treatment: 987423 INFO @ Wed, 28 Jun 2017 05:28:39: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:28:39: #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 05:28:40: #1 tags after filtering in treatment: 916172 INFO @ Wed, 28 Jun 2017 05:28:40: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 28 Jun 2017 05:28:40: #1 finished! INFO @ Wed, 28 Jun 2017 05:28:40: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:28:40: #2 number of paired peaks: 198 WARNING @ Wed, 28 Jun 2017 05:28:40: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Wed, 28 Jun 2017 05:28:40: start model_add_line... INFO @ Wed, 28 Jun 2017 05:28:40: start X-correlation... INFO @ Wed, 28 Jun 2017 05:28:40: end of X-cor INFO @ Wed, 28 Jun 2017 05:28:40: #2 finished! INFO @ Wed, 28 Jun 2017 05:28:40: #2 predicted fragment length is 214 bps INFO @ Wed, 28 Jun 2017 05:28:40: #2 alternative fragment length(s) may be 4,160,199,214,234 bps INFO @ Wed, 28 Jun 2017 05:28:40: #2.2 Generate R script for model : SRX1423725.10_model.r INFO @ Wed, 28 Jun 2017 05:28:40: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:28:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:28:42: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:28:42: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:28:43: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:28:43: #4 Write output xls file... SRX1423725.20_peaks.xls INFO @ Wed, 28 Jun 2017 05:28:43: #4 Write peak in narrowPeak format file... SRX1423725.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:28:43: #4 Write summits bed file... SRX1423725.20_summits.bed INFO @ Wed, 28 Jun 2017 05:28:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 05:28:43: #4 Write output xls file... SRX1423725.05_peaks.xls INFO @ Wed, 28 Jun 2017 05:28:43: #4 Write peak in narrowPeak format file... SRX1423725.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:28:43: #4 Write summits bed file... SRX1423725.05_summits.bed INFO @ Wed, 28 Jun 2017 05:28:43: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (564 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 05:28:44: #4 Write output xls file... SRX1423725.10_peaks.xls INFO @ Wed, 28 Jun 2017 05:28:44: #4 Write peak in narrowPeak format file... SRX1423725.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:28:44: #4 Write summits bed file... SRX1423725.10_summits.bed INFO @ Wed, 28 Jun 2017 05:28:44: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (301 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。