Job ID = 2236858 sra ファイルのダウンロード中... Completed: 79326K bytes transferred in 7 seconds (84399K 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 --:--:-- --:--:-- --:--:-- 0 101 2547 0 2547 0 0 4741 0 --:--:-- --:--:-- --:--:-- 7361 100 34604 0 34604 0 0 47562 0 --:--:-- --:--:-- --:--:-- 64439 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 3402069 spots for /home/okishinya/chipatlas/results/ce10/SRX059234/SRR190674.sra Written 3402069 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: 00:00:36 3402069 reads; of these: 3402069 (100.00%) were unpaired; of these: 913155 (26.84%) aligned 0 times 1995627 (58.66%) aligned exactly 1 time 493287 (14.50%) aligned >1 times 73.16% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 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] 304970 / 2488914 = 0.1225 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 11:11:29: # Command line: callpeak -t SRX059234.bam -f BAM -g ce -n SRX059234.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059234.20 # format = BAM # ChIP-seq file = ['SRX059234.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 11:11:29: # Command line: callpeak -t SRX059234.bam -f BAM -g ce -n SRX059234.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059234.05 # format = BAM # ChIP-seq file = ['SRX059234.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 11:11:29: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:11:29: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:11:29: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:11:29: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:11:29: # Command line: callpeak -t SRX059234.bam -f BAM -g ce -n SRX059234.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059234.10 # format = BAM # ChIP-seq file = ['SRX059234.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 11:11:29: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:11:29: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:11:35: 1000000 INFO @ Thu, 30 Apr 2015 11:11:35: 1000000 INFO @ Thu, 30 Apr 2015 11:11:35: 1000000 INFO @ Thu, 30 Apr 2015 11:11:40: 2000000 INFO @ Thu, 30 Apr 2015 11:11:41: 2000000 INFO @ Thu, 30 Apr 2015 11:11:41: 2000000 INFO @ Thu, 30 Apr 2015 11:11:41: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:11:41: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:11:41: #1 total tags in treatment: 2183944 INFO @ Thu, 30 Apr 2015 11:11:41: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:11:41: #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 11:11:42: #1 tags after filtering in treatment: 2183736 INFO @ Thu, 30 Apr 2015 11:11:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:11:42: #1 finished! INFO @ Thu, 30 Apr 2015 11:11:42: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:11:42: #2 number of paired peaks: 1415 INFO @ Thu, 30 Apr 2015 11:11:42: start model_add_line... INFO @ Thu, 30 Apr 2015 11:11:42: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:11:42: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:11:42: #1 total tags in treatment: 2183944 INFO @ Thu, 30 Apr 2015 11:11:42: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:11:42: #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 11:11:42: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:11:42: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:11:42: #1 total tags in treatment: 2183944 INFO @ Thu, 30 Apr 2015 11:11:42: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:11:42: #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 11:11:43: #1 tags after filtering in treatment: 2183736 INFO @ Thu, 30 Apr 2015 11:11:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:11:43: #1 finished! INFO @ Thu, 30 Apr 2015 11:11:43: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:11:43: #1 tags after filtering in treatment: 2183736 INFO @ Thu, 30 Apr 2015 11:11:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:11:43: #1 finished! INFO @ Thu, 30 Apr 2015 11:11:43: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:11:43: #2 number of paired peaks: 1415 INFO @ Thu, 30 Apr 2015 11:11:43: start model_add_line... INFO @ Thu, 30 Apr 2015 11:11:43: #2 number of paired peaks: 1415 INFO @ Thu, 30 Apr 2015 11:11:43: start model_add_line... INFO @ Thu, 30 Apr 2015 11:11:46: start X-correlation... INFO @ Thu, 30 Apr 2015 11:11:46: end of X-cor INFO @ Thu, 30 Apr 2015 11:11:46: #2 finished! INFO @ Thu, 30 Apr 2015 11:11:46: #2 predicted fragment length is 119 bps INFO @ Thu, 30 Apr 2015 11:11:46: #2 alternative fragment length(s) may be 119 bps INFO @ Thu, 30 Apr 2015 11:11:46: #2.2 Generate R script for model : SRX059234.10_model.r INFO @ Thu, 30 Apr 2015 11:11:46: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:11:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:11:47: start X-correlation... INFO @ Thu, 30 Apr 2015 11:11:47: end of X-cor INFO @ Thu, 30 Apr 2015 11:11:47: #2 finished! INFO @ Thu, 30 Apr 2015 11:11:47: #2 predicted fragment length is 119 bps INFO @ Thu, 30 Apr 2015 11:11:47: #2 alternative fragment length(s) may be 119 bps INFO @ Thu, 30 Apr 2015 11:11:47: #2.2 Generate R script for model : SRX059234.20_model.r INFO @ Thu, 30 Apr 2015 11:11:47: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:11:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:11:47: start X-correlation... INFO @ Thu, 30 Apr 2015 11:11:47: end of X-cor INFO @ Thu, 30 Apr 2015 11:11:47: #2 finished! INFO @ Thu, 30 Apr 2015 11:11:47: #2 predicted fragment length is 119 bps INFO @ Thu, 30 Apr 2015 11:11:47: #2 alternative fragment length(s) may be 119 bps INFO @ Thu, 30 Apr 2015 11:11:47: #2.2 Generate R script for model : SRX059234.05_model.r INFO @ Thu, 30 Apr 2015 11:11:47: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:11:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:12:01: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:12:01: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:12:01: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:12:11: #4 Write output xls file... SRX059234.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:12:11: #4 Write peak in narrowPeak format file... SRX059234.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:12:11: #4 Write summits bed file... SRX059234.10_summits.bed INFO @ Thu, 30 Apr 2015 11:12:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1334 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:12:12: #4 Write output xls file... SRX059234.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:12:12: #4 Write peak in narrowPeak format file... SRX059234.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:12:12: #4 Write summits bed file... SRX059234.05_summits.bed INFO @ Thu, 30 Apr 2015 11:12:12: #4 Write output xls file... SRX059234.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:12:12: Done! INFO @ Thu, 30 Apr 2015 11:12:12: #4 Write peak in narrowPeak format file... SRX059234.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:12:12: #4 Write summits bed file... SRX059234.20_summits.bed INFO @ Thu, 30 Apr 2015 11:12:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1941 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (899 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。