Job ID = 2237005 sra ファイルのダウンロード中... Completed: 100948K bytes transferred in 4 seconds (189599K 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 5460 0 5460 0 0 9610 0 --:--:-- --:--:-- --:--:-- 14482 100 37999 0 37999 0 0 50135 0 --:--:-- --:--:-- --:--:-- 67017 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 5371132 spots for /home/okishinya/chipatlas/results/ce10/SRX080061/SRR298881.sra Written 5371132 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: 00:00:45 5371132 reads; of these: 5371132 (100.00%) were unpaired; of these: 2301223 (42.84%) aligned 0 times 2541072 (47.31%) aligned exactly 1 time 528837 (9.85%) aligned >1 times 57.16% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 700478 / 3069909 = 0.2282 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 11:23:57: # Command line: callpeak -t SRX080061.bam -f BAM -g ce -n SRX080061.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX080061.05 # format = BAM # ChIP-seq file = ['SRX080061.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 11:23:57: # Command line: callpeak -t SRX080061.bam -f BAM -g ce -n SRX080061.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX080061.20 # format = BAM # ChIP-seq file = ['SRX080061.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 11:23:57: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:23:57: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:23:57: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:23:57: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:23:57: # Command line: callpeak -t SRX080061.bam -f BAM -g ce -n SRX080061.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX080061.10 # format = BAM # ChIP-seq file = ['SRX080061.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 11:23:57: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:23:57: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:24:03: 1000000 INFO @ Thu, 30 Apr 2015 11:24:03: 1000000 INFO @ Thu, 30 Apr 2015 11:24:03: 1000000 INFO @ Thu, 30 Apr 2015 11:24:08: 2000000 INFO @ Thu, 30 Apr 2015 11:24:09: 2000000 INFO @ Thu, 30 Apr 2015 11:24:09: 2000000 INFO @ Thu, 30 Apr 2015 11:24:10: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:24:10: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:24:10: #1 total tags in treatment: 2369431 INFO @ Thu, 30 Apr 2015 11:24:10: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:24:10: #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 11:24:10: #1 tags after filtering in treatment: 2369369 INFO @ Thu, 30 Apr 2015 11:24:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:24:10: #1 finished! INFO @ Thu, 30 Apr 2015 11:24:10: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:24:11: #2 number of paired peaks: 1592 INFO @ Thu, 30 Apr 2015 11:24:11: start model_add_line... INFO @ Thu, 30 Apr 2015 11:24:11: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:24:11: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:24:11: #1 total tags in treatment: 2369431 INFO @ Thu, 30 Apr 2015 11:24:11: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:24:11: #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 11:24:11: #1 tag size is determined as 32 bps INFO @ Thu, 30 Apr 2015 11:24:11: #1 tag size = 32 INFO @ Thu, 30 Apr 2015 11:24:11: #1 total tags in treatment: 2369431 INFO @ Thu, 30 Apr 2015 11:24:11: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:24:11: #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 11:24:12: #1 tags after filtering in treatment: 2369369 INFO @ Thu, 30 Apr 2015 11:24:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:24:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:24:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:24:12: #1 tags after filtering in treatment: 2369369 INFO @ Thu, 30 Apr 2015 11:24:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:24:12: #1 finished! INFO @ Thu, 30 Apr 2015 11:24:12: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:24:12: #2 number of paired peaks: 1592 INFO @ Thu, 30 Apr 2015 11:24:12: start model_add_line... INFO @ Thu, 30 Apr 2015 11:24:12: #2 number of paired peaks: 1592 INFO @ Thu, 30 Apr 2015 11:24:12: start model_add_line... INFO @ Thu, 30 Apr 2015 11:24:15: start X-correlation... INFO @ Thu, 30 Apr 2015 11:24:15: end of X-cor INFO @ Thu, 30 Apr 2015 11:24:15: #2 finished! INFO @ Thu, 30 Apr 2015 11:24:15: #2 predicted fragment length is 171 bps INFO @ Thu, 30 Apr 2015 11:24:15: #2 alternative fragment length(s) may be 171 bps INFO @ Thu, 30 Apr 2015 11:24:15: #2.2 Generate R script for model : SRX080061.10_model.r INFO @ Thu, 30 Apr 2015 11:24:15: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:24:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:24:16: start X-correlation... INFO @ Thu, 30 Apr 2015 11:24:16: end of X-cor INFO @ Thu, 30 Apr 2015 11:24:16: #2 finished! INFO @ Thu, 30 Apr 2015 11:24:16: #2 predicted fragment length is 171 bps INFO @ Thu, 30 Apr 2015 11:24:16: #2 alternative fragment length(s) may be 171 bps INFO @ Thu, 30 Apr 2015 11:24:16: #2.2 Generate R script for model : SRX080061.05_model.r INFO @ Thu, 30 Apr 2015 11:24:16: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:24:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:24:16: start X-correlation... INFO @ Thu, 30 Apr 2015 11:24:16: end of X-cor INFO @ Thu, 30 Apr 2015 11:24:16: #2 finished! INFO @ Thu, 30 Apr 2015 11:24:16: #2 predicted fragment length is 171 bps INFO @ Thu, 30 Apr 2015 11:24:16: #2 alternative fragment length(s) may be 171 bps INFO @ Thu, 30 Apr 2015 11:24:16: #2.2 Generate R script for model : SRX080061.20_model.r INFO @ Thu, 30 Apr 2015 11:24:16: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:24:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:24:29: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:24:31: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:24:32: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:24:40: #4 Write output xls file... SRX080061.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:24:40: #4 Write peak in narrowPeak format file... SRX080061.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:24:40: #4 Write summits bed file... SRX080061.10_summits.bed INFO @ Thu, 30 Apr 2015 11:24:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1508 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:24:43: #4 Write output xls file... SRX080061.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:24:43: #4 Write peak in narrowPeak format file... SRX080061.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:24:43: #4 Write summits bed file... SRX080061.05_summits.bed INFO @ Thu, 30 Apr 2015 11:24:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2451 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:24:43: #4 Write output xls file... SRX080061.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:24:43: #4 Write peak in narrowPeak format file... SRX080061.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:24:43: #4 Write summits bed file... SRX080061.20_summits.bed INFO @ Thu, 30 Apr 2015 11:24:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (839 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。