Job ID = 2237043 sra ファイルのダウンロード中... Completed: 126163K bytes transferred in 4 seconds (211382K 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 4214 0 --:--:-- --:--:-- --:--:-- 6152 100 38015 0 38015 0 0 35488 0 --:--:-- 0:00:01 --:--:-- 43198 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 7035155 spots for /home/okishinya/chipatlas/results/ce10/SRX080098/SRR298918.sra Written 7035155 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: 00:01:07 7035155 reads; of these: 7035155 (100.00%) were unpaired; of these: 748779 (10.64%) aligned 0 times 5499430 (78.17%) aligned exactly 1 time 786946 (11.19%) aligned >1 times 89.36% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 1147565 / 6286376 = 0.1825 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 11:27:18: # Command line: callpeak -t SRX080098.bam -f BAM -g ce -n SRX080098.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080098.05 # format = BAM # ChIP-seq file = ['SRX080098.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 11:27:18: # Command line: callpeak -t SRX080098.bam -f BAM -g ce -n SRX080098.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080098.20 # format = BAM # ChIP-seq file = ['SRX080098.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 11:27:18: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:27:18: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:27:18: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:27:18: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:27:18: # Command line: callpeak -t SRX080098.bam -f BAM -g ce -n SRX080098.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080098.10 # format = BAM # ChIP-seq file = ['SRX080098.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 11:27:18: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:27:18: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:27:24: 1000000 INFO @ Thu, 30 Apr 2015 11:27:24: 1000000 INFO @ Thu, 30 Apr 2015 11:27:24: 1000000 INFO @ Thu, 30 Apr 2015 11:27:29: 2000000 INFO @ Thu, 30 Apr 2015 11:27:29: 2000000 INFO @ Thu, 30 Apr 2015 11:27:29: 2000000 INFO @ Thu, 30 Apr 2015 11:27:34: 3000000 INFO @ Thu, 30 Apr 2015 11:27:35: 3000000 INFO @ Thu, 30 Apr 2015 11:27:35: 3000000 INFO @ Thu, 30 Apr 2015 11:27:39: 4000000 INFO @ Thu, 30 Apr 2015 11:27:40: 4000000 INFO @ Thu, 30 Apr 2015 11:27:40: 4000000 INFO @ Thu, 30 Apr 2015 11:27:45: 5000000 INFO @ Thu, 30 Apr 2015 11:27:45: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:27:45: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:27:45: #1 total tags in treatment: 5138811 INFO @ Thu, 30 Apr 2015 11:27:45: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:27:45: #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 11:27:45: 5000000 INFO @ Thu, 30 Apr 2015 11:27:46: 5000000 INFO @ Thu, 30 Apr 2015 11:27:46: #1 tags after filtering in treatment: 5138566 INFO @ Thu, 30 Apr 2015 11:27:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:27:46: #1 finished! INFO @ Thu, 30 Apr 2015 11:27:46: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:27:46: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:27:46: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:27:46: #1 total tags in treatment: 5138811 INFO @ Thu, 30 Apr 2015 11:27:46: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:27:46: #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 11:27:46: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:27:46: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:27:46: #1 total tags in treatment: 5138811 INFO @ Thu, 30 Apr 2015 11:27:46: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:27:46: #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 11:27:47: #1 tags after filtering in treatment: 5138566 INFO @ Thu, 30 Apr 2015 11:27:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:27:47: #1 finished! INFO @ Thu, 30 Apr 2015 11:27:47: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:27:47: #1 tags after filtering in treatment: 5138566 INFO @ Thu, 30 Apr 2015 11:27:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:27:47: #1 finished! INFO @ Thu, 30 Apr 2015 11:27:47: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:27:48: #2 number of paired peaks: 3294 INFO @ Thu, 30 Apr 2015 11:27:48: start model_add_line... INFO @ Thu, 30 Apr 2015 11:27:48: #2 number of paired peaks: 3294 INFO @ Thu, 30 Apr 2015 11:27:48: start model_add_line... INFO @ Thu, 30 Apr 2015 11:27:49: #2 number of paired peaks: 3294 INFO @ Thu, 30 Apr 2015 11:27:49: start model_add_line... INFO @ Thu, 30 Apr 2015 11:28:02: start X-correlation... INFO @ Thu, 30 Apr 2015 11:28:02: end of X-cor INFO @ Thu, 30 Apr 2015 11:28:02: #2 finished! INFO @ Thu, 30 Apr 2015 11:28:02: #2 predicted fragment length is 153 bps INFO @ Thu, 30 Apr 2015 11:28:02: #2 alternative fragment length(s) may be 153 bps INFO @ Thu, 30 Apr 2015 11:28:02: #2.2 Generate R script for model : SRX080098.10_model.r INFO @ Thu, 30 Apr 2015 11:28:02: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:28:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:28:03: start X-correlation... INFO @ Thu, 30 Apr 2015 11:28:03: end of X-cor INFO @ Thu, 30 Apr 2015 11:28:03: #2 finished! INFO @ Thu, 30 Apr 2015 11:28:03: #2 predicted fragment length is 153 bps INFO @ Thu, 30 Apr 2015 11:28:03: #2 alternative fragment length(s) may be 153 bps INFO @ Thu, 30 Apr 2015 11:28:03: #2.2 Generate R script for model : SRX080098.20_model.r INFO @ Thu, 30 Apr 2015 11:28:03: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:28:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:28:03: start X-correlation... INFO @ Thu, 30 Apr 2015 11:28:03: end of X-cor INFO @ Thu, 30 Apr 2015 11:28:03: #2 finished! INFO @ Thu, 30 Apr 2015 11:28:03: #2 predicted fragment length is 153 bps INFO @ Thu, 30 Apr 2015 11:28:03: #2 alternative fragment length(s) may be 153 bps INFO @ Thu, 30 Apr 2015 11:28:03: #2.2 Generate R script for model : SRX080098.05_model.r INFO @ Thu, 30 Apr 2015 11:28:03: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:28:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:28:35: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:28:36: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:28:36: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:29:00: #4 Write output xls file... SRX080098.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:29:00: #4 Write peak in narrowPeak format file... SRX080098.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:29:00: #4 Write summits bed file... SRX080098.20_summits.bed INFO @ Thu, 30 Apr 2015 11:29:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3733 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:29:03: #4 Write output xls file... SRX080098.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:29:03: #4 Write peak in narrowPeak format file... SRX080098.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:29:03: #4 Write summits bed file... SRX080098.10_summits.bed INFO @ Thu, 30 Apr 2015 11:29:03: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5772 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:29:03: #4 Write output xls file... SRX080098.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:29:03: #4 Write peak in narrowPeak format file... SRX080098.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:29:04: #4 Write summits bed file... SRX080098.05_summits.bed INFO @ Thu, 30 Apr 2015 11:29:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8042 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。