Job ID = 2165926 sra ファイルのダウンロード中... Completed: 866062K bytes transferred in 9 seconds (739886K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 16381 0 16381 0 0 22357 0 --:--:-- --:--:-- --:--:-- 30223 100 36861 0 36861 0 0 50243 0 --:--:-- --:--:-- --:--:-- 67883 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 16928006 spots for /home/okishinya/chipatlas/results/sacCer3/SRX065608/SRR217311.sra Written 16928006 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: 00:07:44 16928006 reads; of these: 16928006 (100.00%) were paired; of these: 5134492 (30.33%) aligned concordantly 0 times 3417041 (20.19%) aligned concordantly exactly 1 time 8376473 (49.48%) aligned concordantly >1 times ---- 5134492 pairs aligned concordantly 0 times; of these: 3315 (0.06%) aligned discordantly 1 time ---- 5131177 pairs aligned 0 times concordantly or discordantly; of these: 10262354 mates make up the pairs; of these: 10025354 (97.69%) aligned 0 times 193545 (1.89%) aligned exactly 1 time 43455 (0.42%) aligned >1 times 70.39% overall alignment rate Time searching: 00:07:44 Overall time: 00:07:44 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] 8496971 / 11793646 = 0.7205 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, 22 Apr 2015 09:39:13: # Command line: callpeak -t SRX065608.bam -f BAM -g 12100000 -n SRX065608.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX065608.10 # format = BAM # ChIP-seq file = ['SRX065608.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 INFO @ Wed, 22 Apr 2015 09:39:13: # Command line: callpeak -t SRX065608.bam -f BAM -g 12100000 -n SRX065608.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX065608.05 # format = BAM # ChIP-seq file = ['SRX065608.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 INFO @ Wed, 22 Apr 2015 09:39:13: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:39:13: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:39:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:39:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:39:13: # Command line: callpeak -t SRX065608.bam -f BAM -g 12100000 -n SRX065608.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX065608.20 # format = BAM # ChIP-seq file = ['SRX065608.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 INFO @ Wed, 22 Apr 2015 09:39:13: #1 read tag files... INFO @ Wed, 22 Apr 2015 09:39:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2015 09:39:19: 1000000 INFO @ Wed, 22 Apr 2015 09:39:19: 1000000 INFO @ Wed, 22 Apr 2015 09:39:19: 1000000 INFO @ Wed, 22 Apr 2015 09:39:24: 2000000 INFO @ Wed, 22 Apr 2015 09:39:24: 2000000 INFO @ Wed, 22 Apr 2015 09:39:24: 2000000 INFO @ Wed, 22 Apr 2015 09:39:30: 3000000 INFO @ Wed, 22 Apr 2015 09:39:30: 3000000 INFO @ Wed, 22 Apr 2015 09:39:30: 3000000 INFO @ Wed, 22 Apr 2015 09:39:35: 4000000 INFO @ Wed, 22 Apr 2015 09:39:36: 4000000 INFO @ Wed, 22 Apr 2015 09:39:36: 4000000 INFO @ Wed, 22 Apr 2015 09:39:40: 5000000 INFO @ Wed, 22 Apr 2015 09:39:42: 5000000 INFO @ Wed, 22 Apr 2015 09:39:42: 5000000 INFO @ Wed, 22 Apr 2015 09:39:46: 6000000 INFO @ Wed, 22 Apr 2015 09:39:47: 6000000 INFO @ Wed, 22 Apr 2015 09:39:47: 6000000 INFO @ Wed, 22 Apr 2015 09:39:50: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2015 09:39:50: #1 tag size = 36 INFO @ Wed, 22 Apr 2015 09:39:50: #1 total tags in treatment: 3298800 INFO @ Wed, 22 Apr 2015 09:39:50: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:39:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2015 09:39:51: #1 tags after filtering in treatment: 1232138 INFO @ Wed, 22 Apr 2015 09:39:51: #1 Redundant rate of treatment: 0.63 INFO @ Wed, 22 Apr 2015 09:39:51: #1 finished! INFO @ Wed, 22 Apr 2015 09:39:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:39:51: #2 number of paired peaks: 245 WARNING @ Wed, 22 Apr 2015 09:39:51: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Wed, 22 Apr 2015 09:39:51: start model_add_line... INFO @ Wed, 22 Apr 2015 09:39:52: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2015 09:39:52: #1 tag size = 36 INFO @ Wed, 22 Apr 2015 09:39:52: #1 total tags in treatment: 3298800 INFO @ Wed, 22 Apr 2015 09:39:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:39:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2015 09:39:52: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2015 09:39:52: #1 tag size = 36 INFO @ Wed, 22 Apr 2015 09:39:52: #1 total tags in treatment: 3298800 INFO @ Wed, 22 Apr 2015 09:39:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2015 09:39:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2015 09:39:53: #1 tags after filtering in treatment: 1232138 INFO @ Wed, 22 Apr 2015 09:39:53: #1 Redundant rate of treatment: 0.63 INFO @ Wed, 22 Apr 2015 09:39:53: #1 finished! INFO @ Wed, 22 Apr 2015 09:39:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:39:53: #1 tags after filtering in treatment: 1232138 INFO @ Wed, 22 Apr 2015 09:39:53: #1 Redundant rate of treatment: 0.63 INFO @ Wed, 22 Apr 2015 09:39:53: #1 finished! INFO @ Wed, 22 Apr 2015 09:39:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2015 09:39:53: #2 number of paired peaks: 245 WARNING @ Wed, 22 Apr 2015 09:39:53: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Wed, 22 Apr 2015 09:39:53: start model_add_line... INFO @ Wed, 22 Apr 2015 09:39:53: #2 number of paired peaks: 245 WARNING @ Wed, 22 Apr 2015 09:39:53: Fewer paired peaks (245) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 245 pairs to build model! INFO @ Wed, 22 Apr 2015 09:39:53: start model_add_line... INFO @ Wed, 22 Apr 2015 09:39:53: start X-correlation... INFO @ Wed, 22 Apr 2015 09:39:53: end of X-cor INFO @ Wed, 22 Apr 2015 09:39:53: #2 finished! INFO @ Wed, 22 Apr 2015 09:39:53: #2 predicted fragment length is 141 bps INFO @ Wed, 22 Apr 2015 09:39:53: #2 alternative fragment length(s) may be 141 bps INFO @ Wed, 22 Apr 2015 09:39:53: #2.2 Generate R script for model : SRX065608.20_model.r INFO @ Wed, 22 Apr 2015 09:39:53: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:39:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:39:55: start X-correlation... INFO @ Wed, 22 Apr 2015 09:39:55: end of X-cor INFO @ Wed, 22 Apr 2015 09:39:55: #2 finished! INFO @ Wed, 22 Apr 2015 09:39:55: #2 predicted fragment length is 141 bps INFO @ Wed, 22 Apr 2015 09:39:55: #2 alternative fragment length(s) may be 141 bps INFO @ Wed, 22 Apr 2015 09:39:55: #2.2 Generate R script for model : SRX065608.10_model.r INFO @ Wed, 22 Apr 2015 09:39:55: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:39:55: start X-correlation... INFO @ Wed, 22 Apr 2015 09:39:55: end of X-cor INFO @ Wed, 22 Apr 2015 09:39:55: #2 finished! INFO @ Wed, 22 Apr 2015 09:39:55: #2 predicted fragment length is 141 bps INFO @ Wed, 22 Apr 2015 09:39:55: #2 alternative fragment length(s) may be 141 bps INFO @ Wed, 22 Apr 2015 09:39:55: #2.2 Generate R script for model : SRX065608.05_model.r INFO @ Wed, 22 Apr 2015 09:39:55: #3 Call peaks... INFO @ Wed, 22 Apr 2015 09:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2015 09:40:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:40:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:40:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2015 09:40:06: #4 Write output xls file... SRX065608.20_peaks.xls INFO @ Wed, 22 Apr 2015 09:40:06: #4 Write peak in narrowPeak format file... SRX065608.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:40:06: #4 Write summits bed file... SRX065608.20_summits.bed INFO @ Wed, 22 Apr 2015 09:40:06: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (467 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2015 09:40:08: #4 Write output xls file... SRX065608.10_peaks.xls INFO @ Wed, 22 Apr 2015 09:40:08: #4 Write peak in narrowPeak format file... SRX065608.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:40:08: #4 Write summits bed file... SRX065608.10_summits.bed INFO @ Wed, 22 Apr 2015 09:40:08: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (848 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2015 09:40:09: #4 Write output xls file... SRX065608.05_peaks.xls INFO @ Wed, 22 Apr 2015 09:40:09: #4 Write peak in narrowPeak format file... SRX065608.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2015 09:40:09: #4 Write summits bed file... SRX065608.05_summits.bed INFO @ Wed, 22 Apr 2015 09:40:09: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1314 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。