Job ID = 9036322 sra ファイルのダウンロード中... Completed: 20297K bytes transferred in 3 seconds (52003K 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 --:--:-- 0 100 7663 0 7663 0 0 998 0 --:--:-- 0:00:07 --:--:-- 6110 100 30318 0 30318 0 0 3497 0 --:--:-- 0:00:08 --:--:-- 13474 100 50023 0 50023 0 0 5360 0 --:--:-- 0:00:09 --:--:-- 17166 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 720269 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1810791/SRR3611451.sra Written 720269 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: 00:00:10 720269 reads; of these: 720269 (100.00%) were unpaired; of these: 372705 (51.75%) aligned 0 times 272002 (37.76%) aligned exactly 1 time 75562 (10.49%) aligned >1 times 48.25% overall alignment rate Time searching: 00:00:10 Overall time: 00:00:10 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] 88479 / 347564 = 0.2546 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 02:54:03: # Command line: callpeak -t SRX1810791.bam -f BAM -g 12100000 -n SRX1810791.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1810791.05 # format = BAM # ChIP-seq file = ['SRX1810791.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 02:54:03: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:54:03: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:54:03: # Command line: callpeak -t SRX1810791.bam -f BAM -g 12100000 -n SRX1810791.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1810791.10 # format = BAM # ChIP-seq file = ['SRX1810791.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 02:54:03: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:54:03: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:54:03: # Command line: callpeak -t SRX1810791.bam -f BAM -g 12100000 -n SRX1810791.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1810791.20 # format = BAM # ChIP-seq file = ['SRX1810791.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 02:54:03: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:54:03: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:54:04: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 02:54:04: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 02:54:04: #1 total tags in treatment: 259085 INFO @ Sun, 04 Jun 2017 02:54:04: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:54:04: #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 02:54:04: #1 tags after filtering in treatment: 258960 INFO @ Sun, 04 Jun 2017 02:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:54:04: #1 finished! INFO @ Sun, 04 Jun 2017 02:54:04: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:54:04: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 02:54:04: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 02:54:04: #1 total tags in treatment: 259085 INFO @ Sun, 04 Jun 2017 02:54:04: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:54:04: #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 02:54:04: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 02:54:04: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 02:54:04: #1 total tags in treatment: 259085 INFO @ Sun, 04 Jun 2017 02:54:04: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:54:04: #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 02:54:05: #1 tags after filtering in treatment: 258960 INFO @ Sun, 04 Jun 2017 02:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:54:05: #1 finished! INFO @ Sun, 04 Jun 2017 02:54:05: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:54:05: #1 tags after filtering in treatment: 258960 INFO @ Sun, 04 Jun 2017 02:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:54:05: #1 finished! INFO @ Sun, 04 Jun 2017 02:54:05: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:54:05: #2 number of paired peaks: 106 WARNING @ Sun, 04 Jun 2017 02:54:05: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sun, 04 Jun 2017 02:54:05: start model_add_line... INFO @ Sun, 04 Jun 2017 02:54:05: #2 number of paired peaks: 106 WARNING @ Sun, 04 Jun 2017 02:54:05: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sun, 04 Jun 2017 02:54:05: start model_add_line... INFO @ Sun, 04 Jun 2017 02:54:05: #2 number of paired peaks: 106 WARNING @ Sun, 04 Jun 2017 02:54:05: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sun, 04 Jun 2017 02:54:05: start model_add_line... INFO @ Sun, 04 Jun 2017 02:54:05: start X-correlation... INFO @ Sun, 04 Jun 2017 02:54:05: end of X-cor INFO @ Sun, 04 Jun 2017 02:54:05: #2 finished! INFO @ Sun, 04 Jun 2017 02:54:05: #2 predicted fragment length is 188 bps INFO @ Sun, 04 Jun 2017 02:54:05: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 04 Jun 2017 02:54:05: #2.2 Generate R script for model : SRX1810791.05_model.r INFO @ Sun, 04 Jun 2017 02:54:05: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:54:05: start X-correlation... INFO @ Sun, 04 Jun 2017 02:54:05: end of X-cor INFO @ Sun, 04 Jun 2017 02:54:05: #2 finished! INFO @ Sun, 04 Jun 2017 02:54:05: #2 predicted fragment length is 188 bps INFO @ Sun, 04 Jun 2017 02:54:05: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 04 Jun 2017 02:54:05: #2.2 Generate R script for model : SRX1810791.10_model.r INFO @ Sun, 04 Jun 2017 02:54:05: start X-correlation... INFO @ Sun, 04 Jun 2017 02:54:05: end of X-cor INFO @ Sun, 04 Jun 2017 02:54:05: #2 finished! INFO @ Sun, 04 Jun 2017 02:54:05: #2 predicted fragment length is 188 bps INFO @ Sun, 04 Jun 2017 02:54:05: #2 alternative fragment length(s) may be 188 bps INFO @ Sun, 04 Jun 2017 02:54:05: #2.2 Generate R script for model : SRX1810791.20_model.r INFO @ Sun, 04 Jun 2017 02:54:05: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:54:05: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:54:07: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:54:07: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:54:07: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:54:08: #4 Write output xls file... SRX1810791.20_peaks.xls INFO @ Sun, 04 Jun 2017 02:54:08: #4 Write peak in narrowPeak format file... SRX1810791.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:54:08: #4 Write summits bed file... SRX1810791.20_summits.bed INFO @ Sun, 04 Jun 2017 02:54:08: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:54:08: #4 Write output xls file... SRX1810791.05_peaks.xls INFO @ Sun, 04 Jun 2017 02:54:08: #4 Write peak in narrowPeak format file... SRX1810791.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:54:08: #4 Write summits bed file... SRX1810791.05_summits.bed INFO @ Sun, 04 Jun 2017 02:54:08: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (172 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:54:08: #4 Write output xls file... SRX1810791.10_peaks.xls INFO @ Sun, 04 Jun 2017 02:54:08: #4 Write peak in narrowPeak format file... SRX1810791.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:54:08: #4 Write summits bed file... SRX1810791.10_summits.bed INFO @ Sun, 04 Jun 2017 02:54:08: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (73 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。