Job ID = 2236870 sra ファイルのダウンロード中... Completed: 62253K bytes transferred in 4 seconds (108503K 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 35038 0 35038 0 0 47345 0 --:--:-- --:--:-- --:--:-- 63937 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 4391606 spots for /home/okishinya/chipatlas/results/ce10/SRX059246/SRR190686.sra Written 4391606 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: 00:00:42 4391606 reads; of these: 4391606 (100.00%) were unpaired; of these: 70850 (1.61%) aligned 0 times 3569102 (81.27%) aligned exactly 1 time 751654 (17.12%) aligned >1 times 98.39% overall alignment rate Time searching: 00:00:42 Overall time: 00:00:42 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] 1027782 / 4320756 = 0.2379 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 11:11:56: # Command line: callpeak -t SRX059246.bam -f BAM -g ce -n SRX059246.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059246.10 # format = BAM # ChIP-seq file = ['SRX059246.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 11:11:56: # Command line: callpeak -t SRX059246.bam -f BAM -g ce -n SRX059246.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059246.20 # format = BAM # ChIP-seq file = ['SRX059246.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 11:11:56: # Command line: callpeak -t SRX059246.bam -f BAM -g ce -n SRX059246.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059246.05 # format = BAM # ChIP-seq file = ['SRX059246.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 11:11:56: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:11:56: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:11:56: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:11:56: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:11:56: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:11:56: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:12:00: 1000000 INFO @ Thu, 30 Apr 2015 11:12:00: 1000000 INFO @ Thu, 30 Apr 2015 11:12:01: 1000000 INFO @ Thu, 30 Apr 2015 11:12:05: 2000000 INFO @ Thu, 30 Apr 2015 11:12:05: 2000000 INFO @ Thu, 30 Apr 2015 11:12:05: 2000000 INFO @ Thu, 30 Apr 2015 11:12:09: 3000000 INFO @ Thu, 30 Apr 2015 11:12:10: 3000000 INFO @ Thu, 30 Apr 2015 11:12:10: 3000000 INFO @ Thu, 30 Apr 2015 11:12:11: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:12:11: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:12:11: #1 total tags in treatment: 3292974 INFO @ Thu, 30 Apr 2015 11:12:11: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:12:11: #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 11:12:11: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:12:11: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:12:11: #1 total tags in treatment: 3292974 INFO @ Thu, 30 Apr 2015 11:12:11: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:12:11: #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 11:12:11: #1 tags after filtering in treatment: 3292946 INFO @ Thu, 30 Apr 2015 11:12:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:12:11: #1 finished! INFO @ Thu, 30 Apr 2015 11:12:11: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:12:12: #1 tags after filtering in treatment: 3292946 INFO @ Thu, 30 Apr 2015 11:12:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:12:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:12:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:12:12: #1 tag size is determined as 28 bps INFO @ Thu, 30 Apr 2015 11:12:12: #1 tag size = 28 INFO @ Thu, 30 Apr 2015 11:12:12: #1 total tags in treatment: 3292974 INFO @ Thu, 30 Apr 2015 11:12:12: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:12:12: #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 11:12:12: #2 number of paired peaks: 1848 INFO @ Thu, 30 Apr 2015 11:12:12: start model_add_line... INFO @ Thu, 30 Apr 2015 11:12:12: #1 tags after filtering in treatment: 3292946 INFO @ Thu, 30 Apr 2015 11:12:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:12:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:12:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:12:13: #2 number of paired peaks: 1848 INFO @ Thu, 30 Apr 2015 11:12:13: start model_add_line... INFO @ Thu, 30 Apr 2015 11:12:13: #2 number of paired peaks: 1848 INFO @ Thu, 30 Apr 2015 11:12:13: start model_add_line... INFO @ Thu, 30 Apr 2015 11:12:18: start X-correlation... INFO @ Thu, 30 Apr 2015 11:12:18: end of X-cor INFO @ Thu, 30 Apr 2015 11:12:18: #2 finished! INFO @ Thu, 30 Apr 2015 11:12:18: #2 predicted fragment length is 240 bps INFO @ Thu, 30 Apr 2015 11:12:18: #2 alternative fragment length(s) may be 240 bps INFO @ Thu, 30 Apr 2015 11:12:18: #2.2 Generate R script for model : SRX059246.10_model.r INFO @ Thu, 30 Apr 2015 11:12:18: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:12:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:12:19: start X-correlation... INFO @ Thu, 30 Apr 2015 11:12:19: end of X-cor INFO @ Thu, 30 Apr 2015 11:12:19: #2 finished! INFO @ Thu, 30 Apr 2015 11:12:19: #2 predicted fragment length is 240 bps INFO @ Thu, 30 Apr 2015 11:12:19: #2 alternative fragment length(s) may be 240 bps INFO @ Thu, 30 Apr 2015 11:12:19: #2.2 Generate R script for model : SRX059246.20_model.r INFO @ Thu, 30 Apr 2015 11:12:19: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:12:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:12:20: start X-correlation... INFO @ Thu, 30 Apr 2015 11:12:20: end of X-cor INFO @ Thu, 30 Apr 2015 11:12:20: #2 finished! INFO @ Thu, 30 Apr 2015 11:12:20: #2 predicted fragment length is 240 bps INFO @ Thu, 30 Apr 2015 11:12:20: #2 alternative fragment length(s) may be 240 bps INFO @ Thu, 30 Apr 2015 11:12:20: #2.2 Generate R script for model : SRX059246.05_model.r INFO @ Thu, 30 Apr 2015 11:12:20: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:12:40: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:12:41: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:12:41: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:12:57: #4 Write output xls file... SRX059246.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:12:57: #4 Write peak in narrowPeak format file... SRX059246.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:12:57: #4 Write summits bed file... SRX059246.20_summits.bed INFO @ Thu, 30 Apr 2015 11:12:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1198 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:12:57: #4 Write output xls file... SRX059246.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:12:57: #4 Write peak in narrowPeak format file... SRX059246.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:12:57: #4 Write summits bed file... SRX059246.10_summits.bed INFO @ Thu, 30 Apr 2015 11:12:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2069 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:12:58: #4 Write output xls file... SRX059246.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:12:58: #4 Write peak in narrowPeak format file... SRX059246.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:12:58: #4 Write summits bed file... SRX059246.05_summits.bed INFO @ Thu, 30 Apr 2015 11:12:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3113 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。