Job ID = 2237033 sra ファイルのダウンロード中... Completed: 94299K bytes transferred in 4 seconds (174887K 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 10530 0 10530 0 0 19429 0 --:--:-- --:--:-- --:--:-- 30000 100 38006 0 38006 0 0 51931 0 --:--:-- --:--:-- --:--:-- 70251 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 5992012 spots for /home/okishinya/chipatlas/results/ce10/SRX080088/SRR298908.sra Written 5992012 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: 00:00:01 Multiseed full-index search: 00:00:41 5992012 reads; of these: 5992012 (100.00%) were unpaired; of these: 3288226 (54.88%) aligned 0 times 2335525 (38.98%) aligned exactly 1 time 368261 (6.15%) aligned >1 times 45.12% 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] 656437 / 2703786 = 0.2428 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 11:25:29: # Command line: callpeak -t SRX080088.bam -f BAM -g ce -n SRX080088.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080088.10 # format = BAM # ChIP-seq file = ['SRX080088.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 11:25:29: # Command line: callpeak -t SRX080088.bam -f BAM -g ce -n SRX080088.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080088.05 # format = BAM # ChIP-seq file = ['SRX080088.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 11:25:29: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:29: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:29: # Command line: callpeak -t SRX080088.bam -f BAM -g ce -n SRX080088.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080088.20 # format = BAM # ChIP-seq file = ['SRX080088.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 11:25:29: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:29: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:29: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:25:29: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:25:34: 1000000 INFO @ Thu, 30 Apr 2015 11:25:34: 1000000 INFO @ Thu, 30 Apr 2015 11:25:34: 1000000 INFO @ Thu, 30 Apr 2015 11:25:39: 2000000 INFO @ Thu, 30 Apr 2015 11:25:39: 2000000 INFO @ Thu, 30 Apr 2015 11:25:39: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:39: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:39: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:39: #1 total tags in treatment: 2047349 INFO @ Thu, 30 Apr 2015 11:25:39: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:39: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:39: #1 total tags in treatment: 2047349 INFO @ Thu, 30 Apr 2015 11:25:39: #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 11:25:39: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:39: #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 11:25:39: 2000000 INFO @ Thu, 30 Apr 2015 11:25:39: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:25:39: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:25:39: #1 total tags in treatment: 2047349 INFO @ Thu, 30 Apr 2015 11:25:39: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:25:39: #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 11:25:39: #1 tags after filtering in treatment: 2047303 INFO @ Thu, 30 Apr 2015 11:25:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:39: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:39: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:39: #1 tags after filtering in treatment: 2047303 INFO @ Thu, 30 Apr 2015 11:25:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:39: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:39: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:40: #1 tags after filtering in treatment: 2047303 INFO @ Thu, 30 Apr 2015 11:25:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:25:40: #1 finished! INFO @ Thu, 30 Apr 2015 11:25:40: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:25:40: #2 number of paired peaks: 2260 INFO @ Thu, 30 Apr 2015 11:25:40: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:40: #2 number of paired peaks: 2260 INFO @ Thu, 30 Apr 2015 11:25:40: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:40: #2 number of paired peaks: 2260 INFO @ Thu, 30 Apr 2015 11:25:40: start model_add_line... INFO @ Thu, 30 Apr 2015 11:25:44: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:44: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:44: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:44: #2 predicted fragment length is 139 bps INFO @ Thu, 30 Apr 2015 11:25:44: #2 alternative fragment length(s) may be 139 bps INFO @ Thu, 30 Apr 2015 11:25:44: #2.2 Generate R script for model : SRX080088.05_model.r INFO @ Thu, 30 Apr 2015 11:25:44: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:44: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:44: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:44: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:44: #2 predicted fragment length is 139 bps INFO @ Thu, 30 Apr 2015 11:25:44: #2 alternative fragment length(s) may be 139 bps INFO @ Thu, 30 Apr 2015 11:25:44: #2.2 Generate R script for model : SRX080088.10_model.r INFO @ Thu, 30 Apr 2015 11:25:44: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:44: start X-correlation... INFO @ Thu, 30 Apr 2015 11:25:44: end of X-cor INFO @ Thu, 30 Apr 2015 11:25:44: #2 finished! INFO @ Thu, 30 Apr 2015 11:25:44: #2 predicted fragment length is 139 bps INFO @ Thu, 30 Apr 2015 11:25:44: #2 alternative fragment length(s) may be 139 bps INFO @ Thu, 30 Apr 2015 11:25:44: #2.2 Generate R script for model : SRX080088.20_model.r INFO @ Thu, 30 Apr 2015 11:25:44: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:25:57: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:57: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:25:57: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:26:07: #4 Write output xls file... SRX080088.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:07: #4 Write peak in narrowPeak format file... SRX080088.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:07: #4 Write summits bed file... SRX080088.20_summits.bed INFO @ Thu, 30 Apr 2015 11:26:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1432 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:26:08: #4 Write output xls file... SRX080088.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:08: #4 Write peak in narrowPeak format file... SRX080088.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:08: #4 Write summits bed file... SRX080088.10_summits.bed INFO @ Thu, 30 Apr 2015 11:26:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2541 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:26:09: #4 Write output xls file... SRX080088.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:26:09: #4 Write peak in narrowPeak format file... SRX080088.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:26:09: #4 Write summits bed file... SRX080088.05_summits.bed INFO @ Thu, 30 Apr 2015 11:26:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3776 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。