Job ID = 9036425 sra ファイルのダウンロード中... Completed: 234756K bytes transferred in 5 seconds (382126K 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 8351 0 8351 0 0 964 0 --:--:-- 0:00:08 --:--:-- 4091 100 30245 0 30245 0 0 3186 0 --:--:-- 0:00:09 --:--:-- 10530 100 43896 0 43896 0 0 4468 0 --:--:-- 0:00:09 --:--:-- 13704 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 7709035 spots for /home/okishinya/chipatlas/results/sacCer3/SRX211436/SRR636687.sra Written 7709035 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: 00:01:30 7709035 reads; of these: 7709035 (100.00%) were unpaired; of these: 681673 (8.84%) aligned 0 times 6073133 (78.78%) aligned exactly 1 time 954229 (12.38%) aligned >1 times 91.16% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 4700173 / 7027362 = 0.6688 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 03:08:04: # Command line: callpeak -t SRX211436.bam -f BAM -g 12100000 -n SRX211436.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX211436.10 # format = BAM # ChIP-seq file = ['SRX211436.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 03:08:04: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:08:04: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:08:04: # Command line: callpeak -t SRX211436.bam -f BAM -g 12100000 -n SRX211436.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX211436.05 # format = BAM # ChIP-seq file = ['SRX211436.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 03:08:04: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:08:04: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:08:04: # Command line: callpeak -t SRX211436.bam -f BAM -g 12100000 -n SRX211436.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX211436.20 # format = BAM # ChIP-seq file = ['SRX211436.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 03:08:04: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:08:04: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:08:11: 1000000 INFO @ Sun, 04 Jun 2017 03:08:11: 1000000 INFO @ Sun, 04 Jun 2017 03:08:11: 1000000 INFO @ Sun, 04 Jun 2017 03:08:17: 2000000 INFO @ Sun, 04 Jun 2017 03:08:17: 2000000 INFO @ Sun, 04 Jun 2017 03:08:17: 2000000 INFO @ Sun, 04 Jun 2017 03:08:19: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:08:19: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:08:19: #1 total tags in treatment: 2327189 INFO @ Sun, 04 Jun 2017 03:08:19: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:08:19: #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 03:08:19: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:08:19: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:08:19: #1 total tags in treatment: 2327189 INFO @ Sun, 04 Jun 2017 03:08:19: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:08:19: #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 03:08:19: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:08:19: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:08:19: #1 total tags in treatment: 2327189 INFO @ Sun, 04 Jun 2017 03:08:19: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:08:19: #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 03:08:20: #1 tags after filtering in treatment: 2325052 INFO @ Sun, 04 Jun 2017 03:08:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:08:20: #1 finished! INFO @ Sun, 04 Jun 2017 03:08:20: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:08:20: #1 tags after filtering in treatment: 2325052 INFO @ Sun, 04 Jun 2017 03:08:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:08:20: #1 finished! INFO @ Sun, 04 Jun 2017 03:08:20: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:08:20: #1 tags after filtering in treatment: 2325052 INFO @ Sun, 04 Jun 2017 03:08:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:08:20: #1 finished! INFO @ Sun, 04 Jun 2017 03:08:20: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:08:20: #2 number of paired peaks: 145 WARNING @ Sun, 04 Jun 2017 03:08:20: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sun, 04 Jun 2017 03:08:20: start model_add_line... INFO @ Sun, 04 Jun 2017 03:08:20: #2 number of paired peaks: 145 WARNING @ Sun, 04 Jun 2017 03:08:20: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sun, 04 Jun 2017 03:08:20: start model_add_line... INFO @ Sun, 04 Jun 2017 03:08:20: #2 number of paired peaks: 145 WARNING @ Sun, 04 Jun 2017 03:08:20: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sun, 04 Jun 2017 03:08:20: start model_add_line... INFO @ Sun, 04 Jun 2017 03:08:22: start X-correlation... INFO @ Sun, 04 Jun 2017 03:08:22: end of X-cor INFO @ Sun, 04 Jun 2017 03:08:22: #2 finished! INFO @ Sun, 04 Jun 2017 03:08:22: #2 predicted fragment length is 145 bps INFO @ Sun, 04 Jun 2017 03:08:22: #2 alternative fragment length(s) may be 0,18,36,80,103,145,170,192,208,229,263,286,338,365,395,454,484,521,540,557,597 bps INFO @ Sun, 04 Jun 2017 03:08:22: #2.2 Generate R script for model : SRX211436.05_model.r INFO @ Sun, 04 Jun 2017 03:08:22: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:08:22: start X-correlation... INFO @ Sun, 04 Jun 2017 03:08:22: end of X-cor INFO @ Sun, 04 Jun 2017 03:08:22: #2 finished! INFO @ Sun, 04 Jun 2017 03:08:22: #2 predicted fragment length is 145 bps INFO @ Sun, 04 Jun 2017 03:08:22: #2 alternative fragment length(s) may be 0,18,36,80,103,145,170,192,208,229,263,286,338,365,395,454,484,521,540,557,597 bps INFO @ Sun, 04 Jun 2017 03:08:22: #2.2 Generate R script for model : SRX211436.10_model.r INFO @ Sun, 04 Jun 2017 03:08:22: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:08:22: start X-correlation... INFO @ Sun, 04 Jun 2017 03:08:22: end of X-cor INFO @ Sun, 04 Jun 2017 03:08:22: #2 finished! INFO @ Sun, 04 Jun 2017 03:08:22: #2 predicted fragment length is 145 bps INFO @ Sun, 04 Jun 2017 03:08:22: #2 alternative fragment length(s) may be 0,18,36,80,103,145,170,192,208,229,263,286,338,365,395,454,484,521,540,557,597 bps INFO @ Sun, 04 Jun 2017 03:08:22: #2.2 Generate R script for model : SRX211436.20_model.r INFO @ Sun, 04 Jun 2017 03:08:22: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:08:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:08:34: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:08:34: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:08:34: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:08:42: #4 Write output xls file... SRX211436.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:08:42: #4 Write peak in narrowPeak format file... SRX211436.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:08:42: #4 Write summits bed file... SRX211436.20_summits.bed INFO @ Sun, 04 Jun 2017 03:08:42: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:08:42: #4 Write output xls file... SRX211436.05_peaks.xls INFO @ Sun, 04 Jun 2017 03:08:42: #4 Write peak in narrowPeak format file... SRX211436.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:08:42: #4 Write summits bed file... SRX211436.05_summits.bed INFO @ Sun, 04 Jun 2017 03:08:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (51 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:08:43: #4 Write output xls file... SRX211436.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:08:43: #4 Write peak in narrowPeak format file... SRX211436.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:08:43: #4 Write summits bed file... SRX211436.10_summits.bed INFO @ Sun, 04 Jun 2017 03:08:43: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (27 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。