Job ID = 9036420 sra ファイルのダウンロード中... Completed: 230167K bytes transferred in 5 seconds (327239K 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 --:--:-- 0:00:06 --:--:-- 0 100 22317 0 22317 0 0 2930 0 --:--:-- 0:00:07 --:--:-- 18337 100 46246 0 46246 0 0 5585 0 --:--:-- 0:00:08 --:--:-- 24585 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 7219758 spots for /home/okishinya/chipatlas/results/sacCer3/SRX211431/SRR636682.sra Written 7219758 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:24 7219758 reads; of these: 7219758 (100.00%) were unpaired; of these: 1301716 (18.03%) aligned 0 times 5305419 (73.48%) aligned exactly 1 time 612623 (8.49%) aligned >1 times 81.97% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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] 4968240 / 5918042 = 0.8395 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 03:07:03: # Command line: callpeak -t SRX211431.bam -f BAM -g 12100000 -n SRX211431.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX211431.05 # format = BAM # ChIP-seq file = ['SRX211431.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 03:07:03: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:07:03: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:07:03: # Command line: callpeak -t SRX211431.bam -f BAM -g 12100000 -n SRX211431.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX211431.10 # format = BAM # ChIP-seq file = ['SRX211431.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 03:07:03: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:07:03: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:07:03: # Command line: callpeak -t SRX211431.bam -f BAM -g 12100000 -n SRX211431.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX211431.20 # format = BAM # ChIP-seq file = ['SRX211431.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 03:07:03: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:07:03: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:07:09: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:07:09: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:07:09: #1 total tags in treatment: 949802 INFO @ Sun, 04 Jun 2017 03:07:09: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:07:09: #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 03:07:09: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:07:09: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:07:09: #1 total tags in treatment: 949802 INFO @ Sun, 04 Jun 2017 03:07:09: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:07:09: #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 03:07:09: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:07:09: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:07:09: #1 total tags in treatment: 949802 INFO @ Sun, 04 Jun 2017 03:07:09: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:07:09: #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 03:07:09: #1 tags after filtering in treatment: 949047 INFO @ Sun, 04 Jun 2017 03:07:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:07:09: #1 finished! INFO @ Sun, 04 Jun 2017 03:07:09: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:07:09: #1 tags after filtering in treatment: 949047 INFO @ Sun, 04 Jun 2017 03:07:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:07:09: #1 finished! INFO @ Sun, 04 Jun 2017 03:07:09: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:07:09: #1 tags after filtering in treatment: 949047 INFO @ Sun, 04 Jun 2017 03:07:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:07:09: #1 finished! INFO @ Sun, 04 Jun 2017 03:07:09: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:07:09: #2 number of paired peaks: 178 WARNING @ Sun, 04 Jun 2017 03:07:09: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sun, 04 Jun 2017 03:07:09: start model_add_line... INFO @ Sun, 04 Jun 2017 03:07:09: #2 number of paired peaks: 178 WARNING @ Sun, 04 Jun 2017 03:07:09: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sun, 04 Jun 2017 03:07:09: start model_add_line... INFO @ Sun, 04 Jun 2017 03:07:09: #2 number of paired peaks: 178 WARNING @ Sun, 04 Jun 2017 03:07:09: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sun, 04 Jun 2017 03:07:09: start model_add_line... INFO @ Sun, 04 Jun 2017 03:07:11: start X-correlation... INFO @ Sun, 04 Jun 2017 03:07:11: end of X-cor INFO @ Sun, 04 Jun 2017 03:07:11: #2 finished! INFO @ Sun, 04 Jun 2017 03:07:11: #2 predicted fragment length is 135 bps INFO @ Sun, 04 Jun 2017 03:07:11: #2 alternative fragment length(s) may be 4,135 bps INFO @ Sun, 04 Jun 2017 03:07:11: #2.2 Generate R script for model : SRX211431.20_model.r INFO @ Sun, 04 Jun 2017 03:07:11: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:07:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:07:11: start X-correlation... INFO @ Sun, 04 Jun 2017 03:07:11: end of X-cor INFO @ Sun, 04 Jun 2017 03:07:11: #2 finished! INFO @ Sun, 04 Jun 2017 03:07:11: #2 predicted fragment length is 135 bps INFO @ Sun, 04 Jun 2017 03:07:11: #2 alternative fragment length(s) may be 4,135 bps INFO @ Sun, 04 Jun 2017 03:07:11: #2.2 Generate R script for model : SRX211431.10_model.r INFO @ Sun, 04 Jun 2017 03:07:11: start X-correlation... INFO @ Sun, 04 Jun 2017 03:07:11: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:07:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:07:11: end of X-cor INFO @ Sun, 04 Jun 2017 03:07:11: #2 finished! INFO @ Sun, 04 Jun 2017 03:07:11: #2 predicted fragment length is 135 bps INFO @ Sun, 04 Jun 2017 03:07:11: #2 alternative fragment length(s) may be 4,135 bps INFO @ Sun, 04 Jun 2017 03:07:11: #2.2 Generate R script for model : SRX211431.05_model.r INFO @ Sun, 04 Jun 2017 03:07:11: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:07:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:07:17: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:07:17: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:07:17: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:07:21: #4 Write output xls file... SRX211431.05_peaks.xls INFO @ Sun, 04 Jun 2017 03:07:21: #4 Write peak in narrowPeak format file... SRX211431.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:07:21: #4 Write summits bed file... SRX211431.05_summits.bed INFO @ Sun, 04 Jun 2017 03:07:21: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (148 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:07:21: #4 Write output xls file... SRX211431.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:07:21: #4 Write peak in narrowPeak format file... SRX211431.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:07:21: #4 Write summits bed file... SRX211431.10_summits.bed INFO @ Sun, 04 Jun 2017 03:07:21: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (54 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:07:21: #4 Write output xls file... SRX211431.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:07:21: #4 Write peak in narrowPeak format file... SRX211431.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:07:21: #4 Write summits bed file... SRX211431.20_summits.bed INFO @ Sun, 04 Jun 2017 03:07:21: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (18 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。