Job ID = 2237003 sra ファイルのダウンロード中... Completed: 72768K bytes transferred in 4 seconds (139714K 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 38130 0 38130 0 0 48301 0 --:--:-- --:--:-- --:--:-- 63762 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 3638904 spots for /home/okishinya/chipatlas/results/ce10/SRX080059/SRR298879.sra Written 3638904 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: 00:00:30 3638904 reads; of these: 3638904 (100.00%) were unpaired; of these: 1427664 (39.23%) aligned 0 times 1819137 (49.99%) aligned exactly 1 time 392103 (10.78%) aligned >1 times 60.77% overall alignment rate Time searching: 00:00:30 Overall time: 00:00:30 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] 301399 / 2211240 = 0.1363 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 11:23:10: # Command line: callpeak -t SRX080059.bam -f BAM -g ce -n SRX080059.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080059.20 # format = BAM # ChIP-seq file = ['SRX080059.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 11:23:10: # Command line: callpeak -t SRX080059.bam -f BAM -g ce -n SRX080059.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080059.10 # format = BAM # ChIP-seq file = ['SRX080059.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 11:23:10: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:23:10: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:23:10: # Command line: callpeak -t SRX080059.bam -f BAM -g ce -n SRX080059.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080059.05 # format = BAM # ChIP-seq file = ['SRX080059.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 11:23:10: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:23:10: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:23:10: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:23:10: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:23:15: 1000000 INFO @ Thu, 30 Apr 2015 11:23:15: 1000000 INFO @ Thu, 30 Apr 2015 11:23:15: 1000000 INFO @ Thu, 30 Apr 2015 11:23:21: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:23:21: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:23:21: #1 total tags in treatment: 1909841 INFO @ Thu, 30 Apr 2015 11:23:21: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:23:21: #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 11:23:21: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:23:21: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:23:21: #1 total tags in treatment: 1909841 INFO @ Thu, 30 Apr 2015 11:23:21: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:23:21: #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 11:23:21: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:23:21: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:23:21: #1 total tags in treatment: 1909841 INFO @ Thu, 30 Apr 2015 11:23:21: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:23:21: #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 11:23:21: #1 tags after filtering in treatment: 1909792 INFO @ Thu, 30 Apr 2015 11:23:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:23:21: #1 finished! INFO @ Thu, 30 Apr 2015 11:23:21: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:23:21: #1 tags after filtering in treatment: 1909792 INFO @ Thu, 30 Apr 2015 11:23:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:23:21: #1 finished! INFO @ Thu, 30 Apr 2015 11:23:21: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:23:21: #1 tags after filtering in treatment: 1909792 INFO @ Thu, 30 Apr 2015 11:23:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:23:21: #1 finished! INFO @ Thu, 30 Apr 2015 11:23:21: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:23:21: #2 number of paired peaks: 879 WARNING @ Thu, 30 Apr 2015 11:23:21: Fewer paired peaks (879) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 879 pairs to build model! INFO @ Thu, 30 Apr 2015 11:23:21: start model_add_line... INFO @ Thu, 30 Apr 2015 11:23:21: #2 number of paired peaks: 879 WARNING @ Thu, 30 Apr 2015 11:23:21: Fewer paired peaks (879) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 879 pairs to build model! INFO @ Thu, 30 Apr 2015 11:23:21: start model_add_line... INFO @ Thu, 30 Apr 2015 11:23:22: #2 number of paired peaks: 879 WARNING @ Thu, 30 Apr 2015 11:23:22: Fewer paired peaks (879) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 879 pairs to build model! INFO @ Thu, 30 Apr 2015 11:23:22: start model_add_line... INFO @ Thu, 30 Apr 2015 11:23:24: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:24: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:24: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:24: #2 predicted fragment length is 148 bps INFO @ Thu, 30 Apr 2015 11:23:24: #2 alternative fragment length(s) may be 148 bps INFO @ Thu, 30 Apr 2015 11:23:24: #2.2 Generate R script for model : SRX080059.20_model.r INFO @ Thu, 30 Apr 2015 11:23:24: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:24: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:24: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:24: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:24: #2 predicted fragment length is 148 bps INFO @ Thu, 30 Apr 2015 11:23:24: #2 alternative fragment length(s) may be 148 bps INFO @ Thu, 30 Apr 2015 11:23:24: #2.2 Generate R script for model : SRX080059.05_model.r INFO @ Thu, 30 Apr 2015 11:23:24: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:24: start X-correlation... INFO @ Thu, 30 Apr 2015 11:23:24: end of X-cor INFO @ Thu, 30 Apr 2015 11:23:24: #2 finished! INFO @ Thu, 30 Apr 2015 11:23:24: #2 predicted fragment length is 148 bps INFO @ Thu, 30 Apr 2015 11:23:24: #2 alternative fragment length(s) may be 148 bps INFO @ Thu, 30 Apr 2015 11:23:24: #2.2 Generate R script for model : SRX080059.10_model.r INFO @ Thu, 30 Apr 2015 11:23:24: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:23:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:23:35: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:35: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:35: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:23:44: #4 Write output xls file... SRX080059.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:23:44: #4 Write peak in narrowPeak format file... SRX080059.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:23:44: #4 Write summits bed file... SRX080059.20_summits.bed INFO @ Thu, 30 Apr 2015 11:23:44: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (329 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:23:44: #4 Write output xls file... SRX080059.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:23:44: #4 Write peak in narrowPeak format file... SRX080059.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:23:44: #4 Write summits bed file... SRX080059.10_summits.bed INFO @ Thu, 30 Apr 2015 11:23:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (721 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:23:45: #4 Write output xls file... SRX080059.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:23:45: #4 Write peak in narrowPeak format file... SRX080059.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:23:45: #4 Write summits bed file... SRX080059.05_summits.bed INFO @ Thu, 30 Apr 2015 11:23:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1242 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。