Job ID = 9036414 sra ファイルのダウンロード中... Completed: 382103K bytes transferred in 6 seconds (474496K 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 --:--:-- 0 100 7663 0 7663 0 0 1044 0 --:--:-- 0:00:07 --:--:-- 7940 100 38317 0 38317 0 0 4576 0 --:--:-- 0:00:08 --:--:-- 19158 100 58998 0 58998 0 0 6778 0 --:--:-- 0:00:08 --:--:-- 25299 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 11586362 spots for /home/okishinya/chipatlas/results/sacCer3/SRX211425/SRR636676.sra Written 11586362 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: 00:01:39 11586362 reads; of these: 11586362 (100.00%) were unpaired; of these: 3993646 (34.47%) aligned 0 times 6338745 (54.71%) aligned exactly 1 time 1253971 (10.82%) aligned >1 times 65.53% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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] 7008789 / 7592716 = 0.9231 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 03:07:34: # Command line: callpeak -t SRX211425.bam -f BAM -g 12100000 -n SRX211425.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX211425.10 # format = BAM # ChIP-seq file = ['SRX211425.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 03:07:34: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:07:34: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:07:34: # Command line: callpeak -t SRX211425.bam -f BAM -g 12100000 -n SRX211425.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX211425.05 # format = BAM # ChIP-seq file = ['SRX211425.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 03:07:34: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:07:34: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:07:34: # Command line: callpeak -t SRX211425.bam -f BAM -g 12100000 -n SRX211425.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX211425.20 # format = BAM # ChIP-seq file = ['SRX211425.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 03:07:34: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:07:34: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:07:38: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:07:38: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:07:38: #1 total tags in treatment: 583927 INFO @ Sun, 04 Jun 2017 03:07:38: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:07:38: #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 03:07:38: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:07:38: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:07:38: #1 total tags in treatment: 583927 INFO @ Sun, 04 Jun 2017 03:07:38: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:07:38: #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 03:07:38: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:07:38: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:07:38: #1 total tags in treatment: 583927 INFO @ Sun, 04 Jun 2017 03:07:38: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:07:38: #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 03:07:38: #1 tags after filtering in treatment: 583666 INFO @ Sun, 04 Jun 2017 03:07:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:07:38: #1 finished! INFO @ Sun, 04 Jun 2017 03:07:38: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:07:38: #1 tags after filtering in treatment: 583666 INFO @ Sun, 04 Jun 2017 03:07:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:07:38: #1 finished! INFO @ Sun, 04 Jun 2017 03:07:38: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:07:38: #1 tags after filtering in treatment: 583666 INFO @ Sun, 04 Jun 2017 03:07:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:07:38: #1 finished! INFO @ Sun, 04 Jun 2017 03:07:38: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:07:38: #2 number of paired peaks: 424 INFO @ Sun, 04 Jun 2017 03:07:38: #2 number of paired peaks: 424 WARNING @ Sun, 04 Jun 2017 03:07:38: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! WARNING @ Sun, 04 Jun 2017 03:07:38: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sun, 04 Jun 2017 03:07:38: start model_add_line... INFO @ Sun, 04 Jun 2017 03:07:38: start model_add_line... INFO @ Sun, 04 Jun 2017 03:07:38: #2 number of paired peaks: 424 WARNING @ Sun, 04 Jun 2017 03:07:38: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sun, 04 Jun 2017 03:07:38: start model_add_line... INFO @ Sun, 04 Jun 2017 03:07:40: start X-correlation... INFO @ Sun, 04 Jun 2017 03:07:40: end of X-cor INFO @ Sun, 04 Jun 2017 03:07:40: #2 finished! INFO @ Sun, 04 Jun 2017 03:07:40: #2 predicted fragment length is 138 bps INFO @ Sun, 04 Jun 2017 03:07:40: #2 alternative fragment length(s) may be 1,94,105,138,157,173,193,215,246,399,517,539,553,587 bps INFO @ Sun, 04 Jun 2017 03:07:40: #2.2 Generate R script for model : SRX211425.10_model.r INFO @ Sun, 04 Jun 2017 03:07:40: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:07:40: start X-correlation... INFO @ Sun, 04 Jun 2017 03:07:40: start X-correlation... INFO @ Sun, 04 Jun 2017 03:07:40: end of X-cor INFO @ Sun, 04 Jun 2017 03:07:40: #2 finished! INFO @ Sun, 04 Jun 2017 03:07:40: #2 predicted fragment length is 138 bps INFO @ Sun, 04 Jun 2017 03:07:40: #2 alternative fragment length(s) may be 1,94,105,138,157,173,193,215,246,399,517,539,553,587 bps INFO @ Sun, 04 Jun 2017 03:07:40: #2.2 Generate R script for model : SRX211425.20_model.r INFO @ Sun, 04 Jun 2017 03:07:40: end of X-cor INFO @ Sun, 04 Jun 2017 03:07:40: #2 finished! INFO @ Sun, 04 Jun 2017 03:07:40: #2 predicted fragment length is 138 bps INFO @ Sun, 04 Jun 2017 03:07:40: #2 alternative fragment length(s) may be 1,94,105,138,157,173,193,215,246,399,517,539,553,587 bps INFO @ Sun, 04 Jun 2017 03:07:40: #2.2 Generate R script for model : SRX211425.05_model.r INFO @ Sun, 04 Jun 2017 03:07:40: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:07:40: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:07:44: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:07:44: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:07:44: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:07:46: #4 Write output xls file... SRX211425.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:07:46: #4 Write peak in narrowPeak format file... SRX211425.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:07:46: #4 Write summits bed file... SRX211425.10_summits.bed INFO @ Sun, 04 Jun 2017 03:07:46: Done! INFO @ Sun, 04 Jun 2017 03:07:46: #4 Write output xls file... SRX211425.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:07:46: #4 Write peak in narrowPeak format file... SRX211425.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:07:46: #4 Write summits bed file... SRX211425.20_summits.bed INFO @ Sun, 04 Jun 2017 03:07:46: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (67 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (27 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:07:47: #4 Write output xls file... SRX211425.05_peaks.xls INFO @ Sun, 04 Jun 2017 03:07:47: #4 Write peak in narrowPeak format file... SRX211425.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:07:47: #4 Write summits bed file... SRX211425.05_summits.bed INFO @ Sun, 04 Jun 2017 03:07:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (215 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。