Job ID = 9036424 sra ファイルのダウンロード中... Completed: 203612K bytes transferred in 4 seconds (337226K 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 --:--:-- 0 100 22317 0 22317 0 0 2449 0 --:--:-- 0:00:09 --:--:-- 8232 100 45093 0 45093 0 0 4613 0 --:--:-- 0:00:09 --:--:-- 13360 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 6650029 spots for /home/okishinya/chipatlas/results/sacCer3/SRX211435/SRR636686.sra Written 6650029 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: 00:01:16 6650029 reads; of these: 6650029 (100.00%) were unpaired; of these: 430632 (6.48%) aligned 0 times 5375802 (80.84%) aligned exactly 1 time 843595 (12.69%) aligned >1 times 93.52% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 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] 3976785 / 6219397 = 0.6394 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 03:07:19: # Command line: callpeak -t SRX211435.bam -f BAM -g 12100000 -n SRX211435.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX211435.10 # format = BAM # ChIP-seq file = ['SRX211435.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 03:07:19: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:07:19: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:07:19: # Command line: callpeak -t SRX211435.bam -f BAM -g 12100000 -n SRX211435.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX211435.20 # format = BAM # ChIP-seq file = ['SRX211435.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 03:07:19: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:07:19: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:07:19: # Command line: callpeak -t SRX211435.bam -f BAM -g 12100000 -n SRX211435.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX211435.05 # format = BAM # ChIP-seq file = ['SRX211435.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 03:07:19: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:07:19: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:07:25: 1000000 INFO @ Sun, 04 Jun 2017 03:07:26: 1000000 INFO @ Sun, 04 Jun 2017 03:07:26: 1000000 INFO @ Sun, 04 Jun 2017 03:07:33: 2000000 INFO @ Sun, 04 Jun 2017 03:07:34: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:07:34: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:07:34: #1 total tags in treatment: 2242612 INFO @ Sun, 04 Jun 2017 03:07:34: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:07:34: #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 03:07:34: 2000000 INFO @ Sun, 04 Jun 2017 03:07:34: 2000000 INFO @ Sun, 04 Jun 2017 03:07:35: #1 tags after filtering in treatment: 2241990 INFO @ Sun, 04 Jun 2017 03:07:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:07:35: #1 finished! INFO @ Sun, 04 Jun 2017 03:07:35: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:07:35: #2 number of paired peaks: 144 WARNING @ Sun, 04 Jun 2017 03:07:35: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sun, 04 Jun 2017 03:07:35: start model_add_line... INFO @ Sun, 04 Jun 2017 03:07:36: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:07:36: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:07:36: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:07:36: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:07:36: #1 total tags in treatment: 2242612 INFO @ Sun, 04 Jun 2017 03:07:36: #1 total tags in treatment: 2242612 INFO @ Sun, 04 Jun 2017 03:07:36: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:07:36: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:07:36: #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 03:07:36: #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 03:07:37: #1 tags after filtering in treatment: 2241990 INFO @ Sun, 04 Jun 2017 03:07:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:07:37: #1 finished! INFO @ Sun, 04 Jun 2017 03:07:37: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:07:37: #1 tags after filtering in treatment: 2241990 INFO @ Sun, 04 Jun 2017 03:07:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:07:37: #1 finished! INFO @ Sun, 04 Jun 2017 03:07:37: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:07:37: #2 number of paired peaks: 144 WARNING @ Sun, 04 Jun 2017 03:07:37: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sun, 04 Jun 2017 03:07:37: start model_add_line... INFO @ Sun, 04 Jun 2017 03:07:37: #2 number of paired peaks: 144 WARNING @ Sun, 04 Jun 2017 03:07:37: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sun, 04 Jun 2017 03:07:37: start model_add_line... INFO @ Sun, 04 Jun 2017 03:07:37: start X-correlation... INFO @ Sun, 04 Jun 2017 03:07:37: end of X-cor INFO @ Sun, 04 Jun 2017 03:07:37: #2 finished! INFO @ Sun, 04 Jun 2017 03:07:37: #2 predicted fragment length is 163 bps INFO @ Sun, 04 Jun 2017 03:07:37: #2 alternative fragment length(s) may be 14,43,86,113,163,195,229,261,297,313,336,356,399,417,444,469,483,533,554,577,582 bps INFO @ Sun, 04 Jun 2017 03:07:37: #2.2 Generate R script for model : SRX211435.10_model.r INFO @ Sun, 04 Jun 2017 03:07:37: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:07:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:07:39: start X-correlation... INFO @ Sun, 04 Jun 2017 03:07:39: end of X-cor INFO @ Sun, 04 Jun 2017 03:07:39: #2 finished! INFO @ Sun, 04 Jun 2017 03:07:39: #2 predicted fragment length is 163 bps INFO @ Sun, 04 Jun 2017 03:07:39: #2 alternative fragment length(s) may be 14,43,86,113,163,195,229,261,297,313,336,356,399,417,444,469,483,533,554,577,582 bps INFO @ Sun, 04 Jun 2017 03:07:39: #2.2 Generate R script for model : SRX211435.05_model.r INFO @ Sun, 04 Jun 2017 03:07:39: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:07:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:07:39: start X-correlation... INFO @ Sun, 04 Jun 2017 03:07:39: end of X-cor INFO @ Sun, 04 Jun 2017 03:07:39: #2 finished! INFO @ Sun, 04 Jun 2017 03:07:39: #2 predicted fragment length is 163 bps INFO @ Sun, 04 Jun 2017 03:07:39: #2 alternative fragment length(s) may be 14,43,86,113,163,195,229,261,297,313,336,356,399,417,444,469,483,533,554,577,582 bps INFO @ Sun, 04 Jun 2017 03:07:39: #2.2 Generate R script for model : SRX211435.20_model.r INFO @ Sun, 04 Jun 2017 03:07:39: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:07:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:07:50: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:07:51: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:07:51: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:07:57: #4 Write output xls file... SRX211435.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:07:57: #4 Write peak in narrowPeak format file... SRX211435.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:07:57: #4 Write summits bed file... SRX211435.10_summits.bed INFO @ Sun, 04 Jun 2017 03:07:57: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (28 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:07:59: #4 Write output xls file... SRX211435.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:07:59: #4 Write peak in narrowPeak format file... SRX211435.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:07:59: #4 Write summits bed file... SRX211435.20_summits.bed INFO @ Sun, 04 Jun 2017 03:07:59: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:07:59: #4 Write output xls file... SRX211435.05_peaks.xls INFO @ Sun, 04 Jun 2017 03:07:59: #4 Write peak in narrowPeak format file... SRX211435.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:07:59: #4 Write summits bed file... SRX211435.05_summits.bed INFO @ Sun, 04 Jun 2017 03:07:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (40 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。