Job ID = 2237052 sra ファイルのダウンロード中... Completed: 368197K bytes transferred in 6 seconds (451681K 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 32510 0 32510 0 0 45473 0 --:--:-- --:--:-- --:--:-- 62160 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 10356199 spots for /home/okishinya/chipatlas/results/ce10/SRX094473/SRR340085.sra Written 10356199 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: 00:01:45 10356199 reads; of these: 10356199 (100.00%) were unpaired; of these: 2485970 (24.00%) aligned 0 times 7121578 (68.77%) aligned exactly 1 time 748651 (7.23%) aligned >1 times 76.00% overall alignment rate Time searching: 00:01:45 Overall time: 00:01:45 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] 4914817 / 7870229 = 0.6245 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 11:28:46: # Command line: callpeak -t SRX094473.bam -f BAM -g ce -n SRX094473.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX094473.20 # format = BAM # ChIP-seq file = ['SRX094473.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 11:28:46: # Command line: callpeak -t SRX094473.bam -f BAM -g ce -n SRX094473.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX094473.10 # format = BAM # ChIP-seq file = ['SRX094473.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 11:28:46: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:28:46: # Command line: callpeak -t SRX094473.bam -f BAM -g ce -n SRX094473.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX094473.05 # format = BAM # ChIP-seq file = ['SRX094473.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 11:28:46: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:28:46: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:28:46: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:28:46: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:28:46: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:28:51: 1000000 INFO @ Thu, 30 Apr 2015 11:28:51: 1000000 INFO @ Thu, 30 Apr 2015 11:28:51: 1000000 INFO @ Thu, 30 Apr 2015 11:28:56: 2000000 INFO @ Thu, 30 Apr 2015 11:28:56: 2000000 INFO @ Thu, 30 Apr 2015 11:28:56: 2000000 INFO @ Thu, 30 Apr 2015 11:29:00: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:29:00: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:29:00: #1 total tags in treatment: 2955412 INFO @ Thu, 30 Apr 2015 11:29:00: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:29:00: #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 11:29:00: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:29:00: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:29:00: #1 total tags in treatment: 2955412 INFO @ Thu, 30 Apr 2015 11:29:00: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:29:00: #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 11:29:01: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:29:01: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:29:01: #1 total tags in treatment: 2955412 INFO @ Thu, 30 Apr 2015 11:29:01: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:29:01: #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 11:29:01: #1 tags after filtering in treatment: 2955178 INFO @ Thu, 30 Apr 2015 11:29:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:29:01: #1 finished! INFO @ Thu, 30 Apr 2015 11:29:01: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:29:01: #1 tags after filtering in treatment: 2955178 INFO @ Thu, 30 Apr 2015 11:29:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:29:01: #1 finished! INFO @ Thu, 30 Apr 2015 11:29:01: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:29:01: #1 tags after filtering in treatment: 2955178 INFO @ Thu, 30 Apr 2015 11:29:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:29:01: #1 finished! INFO @ Thu, 30 Apr 2015 11:29:01: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:29:02: #2 number of paired peaks: 4925 INFO @ Thu, 30 Apr 2015 11:29:02: start model_add_line... INFO @ Thu, 30 Apr 2015 11:29:02: #2 number of paired peaks: 4925 INFO @ Thu, 30 Apr 2015 11:29:02: start model_add_line... INFO @ Thu, 30 Apr 2015 11:29:02: #2 number of paired peaks: 4925 INFO @ Thu, 30 Apr 2015 11:29:02: start model_add_line... INFO @ Thu, 30 Apr 2015 11:29:13: start X-correlation... INFO @ Thu, 30 Apr 2015 11:29:13: end of X-cor INFO @ Thu, 30 Apr 2015 11:29:13: #2 finished! INFO @ Thu, 30 Apr 2015 11:29:13: #2 predicted fragment length is 176 bps INFO @ Thu, 30 Apr 2015 11:29:13: #2 alternative fragment length(s) may be 4,176 bps INFO @ Thu, 30 Apr 2015 11:29:13: #2.2 Generate R script for model : SRX094473.20_model.r INFO @ Thu, 30 Apr 2015 11:29:13: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:29:13: start X-correlation... INFO @ Thu, 30 Apr 2015 11:29:13: end of X-cor INFO @ Thu, 30 Apr 2015 11:29:13: #2 finished! INFO @ Thu, 30 Apr 2015 11:29:13: #2 predicted fragment length is 176 bps INFO @ Thu, 30 Apr 2015 11:29:13: #2 alternative fragment length(s) may be 4,176 bps INFO @ Thu, 30 Apr 2015 11:29:13: #2.2 Generate R script for model : SRX094473.10_model.r INFO @ Thu, 30 Apr 2015 11:29:13: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:29:13: start X-correlation... INFO @ Thu, 30 Apr 2015 11:29:13: end of X-cor INFO @ Thu, 30 Apr 2015 11:29:13: #2 finished! INFO @ Thu, 30 Apr 2015 11:29:13: #2 predicted fragment length is 176 bps INFO @ Thu, 30 Apr 2015 11:29:13: #2 alternative fragment length(s) may be 4,176 bps INFO @ Thu, 30 Apr 2015 11:29:13: #2.2 Generate R script for model : SRX094473.05_model.r INFO @ Thu, 30 Apr 2015 11:29:13: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:29:30: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:29:31: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:29:32: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:29:42: #4 Write output xls file... SRX094473.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:29:42: #4 Write peak in narrowPeak format file... SRX094473.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:29:42: #4 Write summits bed file... SRX094473.20_summits.bed INFO @ Thu, 30 Apr 2015 11:29:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (54 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:29:43: #4 Write output xls file... SRX094473.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:29:43: #4 Write peak in narrowPeak format file... SRX094473.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:29:43: #4 Write summits bed file... SRX094473.10_summits.bed INFO @ Thu, 30 Apr 2015 11:29:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (899 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:29:48: #4 Write output xls file... SRX094473.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:29:48: #4 Write peak in narrowPeak format file... SRX094473.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:29:48: #4 Write summits bed file... SRX094473.05_summits.bed INFO @ Thu, 30 Apr 2015 11:29:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3996 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。