Job ID = 9036405 sra ファイルのダウンロード中... Completed: 354797K bytes transferred in 6 seconds (422672K 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 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:10 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:11 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:12 --:--:-- 0 100 20109 0 20109 0 0 1529 0 --:--:-- 0:00:13 --:--:-- 4260 100 49901 0 49901 0 0 3528 0 --:--:-- 0:00:14 --:--:-- 10587 100 54656 0 54656 0 0 3864 0 --:--:-- 0:00:14 --:--:-- 14724 sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 10861435 spots for /home/okishinya/chipatlas/results/sacCer3/SRX211416/SRR636667.sra Written 10861435 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: 00:02:07 10861435 reads; of these: 10861435 (100.00%) were unpaired; of these: 1307663 (12.04%) aligned 0 times 8186165 (75.37%) aligned exactly 1 time 1367607 (12.59%) aligned >1 times 87.96% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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_rmdupse_core] 8083714 / 9553772 = 0.8461 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 @ Sun, 04 Jun 2017 03:07:46: # Command line: callpeak -t SRX211416.bam -f BAM -g 12100000 -n SRX211416.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX211416.20 # format = BAM # ChIP-seq file = ['SRX211416.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 @ Sun, 04 Jun 2017 03:07:46: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:07:46: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:07:46: # Command line: callpeak -t SRX211416.bam -f BAM -g 12100000 -n SRX211416.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX211416.05 # format = BAM # ChIP-seq file = ['SRX211416.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 @ Sun, 04 Jun 2017 03:07:46: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:07:46: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:07:46: # Command line: callpeak -t SRX211416.bam -f BAM -g 12100000 -n SRX211416.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX211416.10 # format = BAM # ChIP-seq file = ['SRX211416.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 @ Sun, 04 Jun 2017 03:07:46: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:07:46: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:07:52: 1000000 INFO @ Sun, 04 Jun 2017 03:07:52: 1000000 INFO @ Sun, 04 Jun 2017 03:07:52: 1000000 INFO @ Sun, 04 Jun 2017 03:07:54: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:07:54: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:07:54: #1 total tags in treatment: 1470058 INFO @ Sun, 04 Jun 2017 03:07:54: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:07:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 03:07:54: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:07:54: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:07:54: #1 total tags in treatment: 1470058 INFO @ Sun, 04 Jun 2017 03:07:54: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:07:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 03:07:55: #1 tags after filtering in treatment: 1469324 INFO @ Sun, 04 Jun 2017 03:07:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:07:55: #1 finished! INFO @ Sun, 04 Jun 2017 03:07:55: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:07:55: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:07:55: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:07:55: #1 total tags in treatment: 1470058 INFO @ Sun, 04 Jun 2017 03:07:55: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:07:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 03:07:55: #1 tags after filtering in treatment: 1469324 INFO @ Sun, 04 Jun 2017 03:07:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:07:55: #1 finished! INFO @ Sun, 04 Jun 2017 03:07:55: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:07:55: #2 number of paired peaks: 268 WARNING @ Sun, 04 Jun 2017 03:07:55: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Sun, 04 Jun 2017 03:07:55: start model_add_line... INFO @ Sun, 04 Jun 2017 03:07:55: #1 tags after filtering in treatment: 1469324 INFO @ Sun, 04 Jun 2017 03:07:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:07:55: #1 finished! INFO @ Sun, 04 Jun 2017 03:07:55: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:07:55: #2 number of paired peaks: 268 WARNING @ Sun, 04 Jun 2017 03:07:55: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Sun, 04 Jun 2017 03:07:55: start model_add_line... INFO @ Sun, 04 Jun 2017 03:07:55: #2 number of paired peaks: 268 WARNING @ Sun, 04 Jun 2017 03:07:55: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Sun, 04 Jun 2017 03:07:55: start model_add_line... INFO @ Sun, 04 Jun 2017 03:07:58: start X-correlation... INFO @ Sun, 04 Jun 2017 03:07:58: end of X-cor INFO @ Sun, 04 Jun 2017 03:07:58: #2 finished! INFO @ Sun, 04 Jun 2017 03:07:58: #2 predicted fragment length is 140 bps INFO @ Sun, 04 Jun 2017 03:07:58: #2 alternative fragment length(s) may be 4,140 bps INFO @ Sun, 04 Jun 2017 03:07:58: #2.2 Generate R script for model : SRX211416.05_model.r INFO @ Sun, 04 Jun 2017 03:07:58: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:07:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:07:58: start X-correlation... INFO @ Sun, 04 Jun 2017 03:07:58: end of X-cor INFO @ Sun, 04 Jun 2017 03:07:58: #2 finished! INFO @ Sun, 04 Jun 2017 03:07:58: #2 predicted fragment length is 140 bps INFO @ Sun, 04 Jun 2017 03:07:58: #2 alternative fragment length(s) may be 4,140 bps INFO @ Sun, 04 Jun 2017 03:07:58: #2.2 Generate R script for model : SRX211416.10_model.r INFO @ Sun, 04 Jun 2017 03:07:58: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:07:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:07:58: start X-correlation... INFO @ Sun, 04 Jun 2017 03:07:58: end of X-cor INFO @ Sun, 04 Jun 2017 03:07:58: #2 finished! INFO @ Sun, 04 Jun 2017 03:07:58: #2 predicted fragment length is 140 bps INFO @ Sun, 04 Jun 2017 03:07:58: #2 alternative fragment length(s) may be 4,140 bps INFO @ Sun, 04 Jun 2017 03:07:58: #2.2 Generate R script for model : SRX211416.20_model.r INFO @ Sun, 04 Jun 2017 03:07:58: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:07:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:08:07: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:08:07: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:08:08: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:08:13: #4 Write output xls file... SRX211416.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:08:13: #4 Write peak in narrowPeak format file... SRX211416.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:08:13: #4 Write summits bed file... SRX211416.20_summits.bed INFO @ Sun, 04 Jun 2017 03:08:13: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (265 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:08:14: #4 Write output xls file... SRX211416.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:08:14: #4 Write peak in narrowPeak format file... SRX211416.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:08:14: #4 Write summits bed file... SRX211416.10_summits.bed INFO @ Sun, 04 Jun 2017 03:08:14: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (557 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:08:14: #4 Write output xls file... SRX211416.05_peaks.xls INFO @ Sun, 04 Jun 2017 03:08:14: #4 Write peak in narrowPeak format file... SRX211416.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:08:14: #4 Write summits bed file... SRX211416.05_summits.bed INFO @ Sun, 04 Jun 2017 03:08:14: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (971 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。