Job ID = 2236867 sra ファイルのダウンロード中... Completed: 122662K bytes transferred in 6 seconds (161088K 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 20024 0 20024 0 0 27574 0 --:--:-- --:--:-- --:--:-- 37428 100 35282 0 35282 0 0 48526 0 --:--:-- --:--:-- --:--:-- 65824 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 7751700 spots for /home/okishinya/chipatlas/results/ce10/SRX059243/SRR190683.sra Written 7751700 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: 00:01:13 7751700 reads; of these: 7751700 (100.00%) were unpaired; of these: 975646 (12.59%) aligned 0 times 5727424 (73.89%) aligned exactly 1 time 1048630 (13.53%) aligned >1 times 87.41% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 2569506 / 6776054 = 0.3792 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 11:13:06: # Command line: callpeak -t SRX059243.bam -f BAM -g ce -n SRX059243.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059243.05 # format = BAM # ChIP-seq file = ['SRX059243.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 11:13:06: # Command line: callpeak -t SRX059243.bam -f BAM -g ce -n SRX059243.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059243.10 # format = BAM # ChIP-seq file = ['SRX059243.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 11:13:06: # Command line: callpeak -t SRX059243.bam -f BAM -g ce -n SRX059243.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059243.20 # format = BAM # ChIP-seq file = ['SRX059243.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 11:13:06: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:13:06: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:13:06: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:13:06: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:13:06: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:13:06: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:13:12: 1000000 INFO @ Thu, 30 Apr 2015 11:13:12: 1000000 INFO @ Thu, 30 Apr 2015 11:13:12: 1000000 INFO @ Thu, 30 Apr 2015 11:13:18: 2000000 INFO @ Thu, 30 Apr 2015 11:13:18: 2000000 INFO @ Thu, 30 Apr 2015 11:13:18: 2000000 INFO @ Thu, 30 Apr 2015 11:13:24: 3000000 INFO @ Thu, 30 Apr 2015 11:13:24: 3000000 INFO @ Thu, 30 Apr 2015 11:13:25: 3000000 INFO @ Thu, 30 Apr 2015 11:13:30: 4000000 INFO @ Thu, 30 Apr 2015 11:13:30: 4000000 INFO @ Thu, 30 Apr 2015 11:13:31: 4000000 INFO @ Thu, 30 Apr 2015 11:13:31: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:13:31: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:13:31: #1 total tags in treatment: 4206548 INFO @ Thu, 30 Apr 2015 11:13:31: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:13:31: #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 11:13:31: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:13:31: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:13:31: #1 total tags in treatment: 4206548 INFO @ Thu, 30 Apr 2015 11:13:31: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:13:31: #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 11:13:32: #1 tags after filtering in treatment: 4206519 INFO @ Thu, 30 Apr 2015 11:13:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:13:32: #1 finished! INFO @ Thu, 30 Apr 2015 11:13:32: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:13:32: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:13:32: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:13:32: #1 total tags in treatment: 4206548 INFO @ Thu, 30 Apr 2015 11:13:32: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:13:32: #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 11:13:32: #1 tags after filtering in treatment: 4206519 INFO @ Thu, 30 Apr 2015 11:13:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:13:32: #1 finished! INFO @ Thu, 30 Apr 2015 11:13:32: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:13:32: #2 number of paired peaks: 1103 INFO @ Thu, 30 Apr 2015 11:13:32: start model_add_line... INFO @ Thu, 30 Apr 2015 11:13:33: #1 tags after filtering in treatment: 4206519 INFO @ Thu, 30 Apr 2015 11:13:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:13:33: #1 finished! INFO @ Thu, 30 Apr 2015 11:13:33: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:13:33: #2 number of paired peaks: 1103 INFO @ Thu, 30 Apr 2015 11:13:33: start model_add_line... INFO @ Thu, 30 Apr 2015 11:13:33: #2 number of paired peaks: 1103 INFO @ Thu, 30 Apr 2015 11:13:33: start model_add_line... INFO @ Thu, 30 Apr 2015 11:13:39: start X-correlation... INFO @ Thu, 30 Apr 2015 11:13:39: end of X-cor INFO @ Thu, 30 Apr 2015 11:13:39: #2 finished! INFO @ Thu, 30 Apr 2015 11:13:39: #2 predicted fragment length is 139 bps INFO @ Thu, 30 Apr 2015 11:13:39: #2 alternative fragment length(s) may be 139 bps INFO @ Thu, 30 Apr 2015 11:13:39: #2.2 Generate R script for model : SRX059243.20_model.r INFO @ Thu, 30 Apr 2015 11:13:39: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:13:40: start X-correlation... INFO @ Thu, 30 Apr 2015 11:13:40: end of X-cor INFO @ Thu, 30 Apr 2015 11:13:40: #2 finished! INFO @ Thu, 30 Apr 2015 11:13:40: #2 predicted fragment length is 139 bps INFO @ Thu, 30 Apr 2015 11:13:40: #2 alternative fragment length(s) may be 139 bps INFO @ Thu, 30 Apr 2015 11:13:40: #2.2 Generate R script for model : SRX059243.05_model.r INFO @ Thu, 30 Apr 2015 11:13:40: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:13:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:13:40: start X-correlation... INFO @ Thu, 30 Apr 2015 11:13:40: end of X-cor INFO @ Thu, 30 Apr 2015 11:13:40: #2 finished! INFO @ Thu, 30 Apr 2015 11:13:40: #2 predicted fragment length is 139 bps INFO @ Thu, 30 Apr 2015 11:13:40: #2 alternative fragment length(s) may be 139 bps INFO @ Thu, 30 Apr 2015 11:13:40: #2.2 Generate R script for model : SRX059243.10_model.r INFO @ Thu, 30 Apr 2015 11:13:40: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:13:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:14:06: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:14:06: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:14:07: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:14:22: #4 Write output xls file... SRX059243.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:14:22: #4 Write peak in narrowPeak format file... SRX059243.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:14:22: #4 Write summits bed file... SRX059243.20_summits.bed INFO @ Thu, 30 Apr 2015 11:14:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (313 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:14:23: #4 Write output xls file... SRX059243.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:14:23: #4 Write peak in narrowPeak format file... SRX059243.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:14:23: #4 Write summits bed file... SRX059243.05_summits.bed INFO @ Thu, 30 Apr 2015 11:14:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1056 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:14:24: #4 Write output xls file... SRX059243.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:14:24: #4 Write peak in narrowPeak format file... SRX059243.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:14:24: #4 Write summits bed file... SRX059243.10_summits.bed INFO @ Thu, 30 Apr 2015 11:14:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (666 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。