Job ID = 2236878 sra ファイルのダウンロード中... Completed: 225223K bytes transferred in 17 seconds (106676K 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 --:--:-- --:--:-- --:--:-- 0 100 35225 0 35225 0 0 47137 0 --:--:-- --:--:-- --:--:-- 63468 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 11592789 spots for /home/okishinya/chipatlas/results/ce10/SRX059254/SRR190694.sra Written 11592789 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: 00:02:12 11592789 reads; of these: 11592789 (100.00%) were unpaired; of these: 1265727 (10.92%) aligned 0 times 9036486 (77.95%) aligned exactly 1 time 1290576 (11.13%) aligned >1 times 89.08% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2172499 / 10327062 = 0.2104 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 @ Thu, 30 Apr 2015 11:15:37: # Command line: callpeak -t SRX059254.bam -f BAM -g ce -n SRX059254.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059254.20 # format = BAM # ChIP-seq file = ['SRX059254.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 30 Apr 2015 11:15:37: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:15:37: # Command line: callpeak -t SRX059254.bam -f BAM -g ce -n SRX059254.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059254.10 # format = BAM # ChIP-seq file = ['SRX059254.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 30 Apr 2015 11:15:37: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:15:37: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:15:37: # Command line: callpeak -t SRX059254.bam -f BAM -g ce -n SRX059254.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059254.05 # format = BAM # ChIP-seq file = ['SRX059254.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 30 Apr 2015 11:15:37: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:15:37: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:15:37: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:15:42: 1000000 INFO @ Thu, 30 Apr 2015 11:15:42: 1000000 INFO @ Thu, 30 Apr 2015 11:15:42: 1000000 INFO @ Thu, 30 Apr 2015 11:15:48: 2000000 INFO @ Thu, 30 Apr 2015 11:15:48: 2000000 INFO @ Thu, 30 Apr 2015 11:15:48: 2000000 INFO @ Thu, 30 Apr 2015 11:15:53: 3000000 INFO @ Thu, 30 Apr 2015 11:15:53: 3000000 INFO @ Thu, 30 Apr 2015 11:15:53: 3000000 INFO @ Thu, 30 Apr 2015 11:15:58: 4000000 INFO @ Thu, 30 Apr 2015 11:15:59: 4000000 INFO @ Thu, 30 Apr 2015 11:15:59: 4000000 INFO @ Thu, 30 Apr 2015 11:16:04: 5000000 INFO @ Thu, 30 Apr 2015 11:16:04: 5000000 INFO @ Thu, 30 Apr 2015 11:16:04: 5000000 INFO @ Thu, 30 Apr 2015 11:16:09: 6000000 INFO @ Thu, 30 Apr 2015 11:16:09: 6000000 INFO @ Thu, 30 Apr 2015 11:16:10: 6000000 INFO @ Thu, 30 Apr 2015 11:16:14: 7000000 INFO @ Thu, 30 Apr 2015 11:16:15: 7000000 INFO @ Thu, 30 Apr 2015 11:16:15: 7000000 INFO @ Thu, 30 Apr 2015 11:16:19: 8000000 INFO @ Thu, 30 Apr 2015 11:16:20: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:16:20: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:16:20: #1 total tags in treatment: 8154563 INFO @ Thu, 30 Apr 2015 11:16:20: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:16:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:16:20: 8000000 INFO @ Thu, 30 Apr 2015 11:16:21: 8000000 INFO @ Thu, 30 Apr 2015 11:16:21: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:16:21: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:16:21: #1 total tags in treatment: 8154563 INFO @ Thu, 30 Apr 2015 11:16:21: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:16:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:16:22: #1 tags after filtering in treatment: 8153821 INFO @ Thu, 30 Apr 2015 11:16:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:16:22: #1 finished! INFO @ Thu, 30 Apr 2015 11:16:22: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:16:22: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:16:22: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:16:22: #1 total tags in treatment: 8154563 INFO @ Thu, 30 Apr 2015 11:16:22: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:16:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:16:23: #1 tags after filtering in treatment: 8153821 INFO @ Thu, 30 Apr 2015 11:16:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:16:23: #1 finished! INFO @ Thu, 30 Apr 2015 11:16:23: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:16:23: #1 tags after filtering in treatment: 8153821 INFO @ Thu, 30 Apr 2015 11:16:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:16:23: #1 finished! INFO @ Thu, 30 Apr 2015 11:16:23: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:16:24: #2 number of paired peaks: 3596 INFO @ Thu, 30 Apr 2015 11:16:24: start model_add_line... INFO @ Thu, 30 Apr 2015 11:16:24: #2 number of paired peaks: 3596 INFO @ Thu, 30 Apr 2015 11:16:24: start model_add_line... INFO @ Thu, 30 Apr 2015 11:16:25: #2 number of paired peaks: 3596 INFO @ Thu, 30 Apr 2015 11:16:25: start model_add_line... INFO @ Thu, 30 Apr 2015 11:16:54: start X-correlation... INFO @ Thu, 30 Apr 2015 11:16:54: end of X-cor INFO @ Thu, 30 Apr 2015 11:16:54: #2 finished! INFO @ Thu, 30 Apr 2015 11:16:54: #2 predicted fragment length is 137 bps INFO @ Thu, 30 Apr 2015 11:16:54: #2 alternative fragment length(s) may be 137 bps INFO @ Thu, 30 Apr 2015 11:16:54: #2.2 Generate R script for model : SRX059254.20_model.r INFO @ Thu, 30 Apr 2015 11:16:54: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:16:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:16:54: start X-correlation... INFO @ Thu, 30 Apr 2015 11:16:54: end of X-cor INFO @ Thu, 30 Apr 2015 11:16:54: #2 finished! INFO @ Thu, 30 Apr 2015 11:16:54: #2 predicted fragment length is 137 bps INFO @ Thu, 30 Apr 2015 11:16:54: #2 alternative fragment length(s) may be 137 bps INFO @ Thu, 30 Apr 2015 11:16:54: #2.2 Generate R script for model : SRX059254.05_model.r INFO @ Thu, 30 Apr 2015 11:16:54: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:16:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:16:55: start X-correlation... INFO @ Thu, 30 Apr 2015 11:16:55: end of X-cor INFO @ Thu, 30 Apr 2015 11:16:55: #2 finished! INFO @ Thu, 30 Apr 2015 11:16:55: #2 predicted fragment length is 137 bps INFO @ Thu, 30 Apr 2015 11:16:55: #2 alternative fragment length(s) may be 137 bps INFO @ Thu, 30 Apr 2015 11:16:55: #2.2 Generate R script for model : SRX059254.10_model.r INFO @ Thu, 30 Apr 2015 11:16:55: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:16:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:17:41: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:17:42: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:17:43: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:18:19: #4 Write output xls file... SRX059254.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:18:19: #4 Write peak in narrowPeak format file... SRX059254.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:18:19: #4 Write summits bed file... SRX059254.20_summits.bed INFO @ Thu, 30 Apr 2015 11:18:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3519 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:18:20: #4 Write output xls file... SRX059254.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:18:20: #4 Write peak in narrowPeak format file... SRX059254.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:18:20: #4 Write summits bed file... SRX059254.10_summits.bed INFO @ Thu, 30 Apr 2015 11:18:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4725 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:18:23: #4 Write output xls file... SRX059254.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:18:23: #4 Write peak in narrowPeak format file... SRX059254.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:18:23: #4 Write summits bed file... SRX059254.05_summits.bed INFO @ Thu, 30 Apr 2015 11:18:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6128 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。