Job ID = 3001505 sra ファイルのダウンロード中... Completed: 84037K bytes transferred in 4 seconds (140699K 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 14953 0 14953 0 0 8819 0 --:--:-- 0:00:01 --:--:-- 9942 100 14953 0 14953 0 0 5543 0 --:--:-- 0:00:02 --:--:-- 5966 100 14953 0 14953 0 0 4041 0 --:--:-- 0:00:03 --:--:-- 4262 100 14953 0 14953 0 0 3180 0 --:--:-- 0:00:04 --:--:-- 3315 100 14953 0 14953 0 0 2622 0 --:--:-- 0:00:05 --:--:-- 2713 100 14953 0 14953 0 0 2230 0 --:--:-- 0:00:06 --:--:-- 0 100 16400 0 16400 0 0 2179 0 --:--:-- 0:00:07 --:--:-- 299 100 34949 0 34949 0 0 4530 0 --:--:-- 0:00:07 --:--:-- 4981 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 5286180 spots for /home/okishinya/chipatlas/results/ce10/SRX005639/SRR017608.sra Written 5286180 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: 00:00:35 5286180 reads; of these: 5286180 (100.00%) were unpaired; of these: 3361796 (63.60%) aligned 0 times 1609365 (30.44%) aligned exactly 1 time 315019 (5.96%) aligned >1 times 36.40% overall alignment rate Time searching: 00:00:35 Overall time: 00:00:35 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] 219811 / 1924384 = 0.1142 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 @ Mon, 07 Sep 2015 18:46:00: # Command line: callpeak -t SRX005639.bam -f BAM -g ce -n SRX005639.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005639.20 # format = BAM # ChIP-seq file = ['SRX005639.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 @ Mon, 07 Sep 2015 18:46:00: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:00: # Command line: callpeak -t SRX005639.bam -f BAM -g ce -n SRX005639.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005639.10 # format = BAM # ChIP-seq file = ['SRX005639.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 @ Mon, 07 Sep 2015 18:46:00: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:00: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:00: # Command line: callpeak -t SRX005639.bam -f BAM -g ce -n SRX005639.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005639.05 # format = BAM # ChIP-seq file = ['SRX005639.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 @ Mon, 07 Sep 2015 18:46:00: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:00: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:00: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:06: 1000000 INFO @ Mon, 07 Sep 2015 18:46:06: 1000000 INFO @ Mon, 07 Sep 2015 18:46:06: 1000000 INFO @ Mon, 07 Sep 2015 18:46:09: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:09: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:09: #1 total tags in treatment: 1704573 INFO @ Mon, 07 Sep 2015 18:46:09: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:46:09: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:09: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:09: #1 total tags in treatment: 1704573 INFO @ Mon, 07 Sep 2015 18:46:09: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:46:09: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:09: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:09: #1 total tags in treatment: 1704573 INFO @ Mon, 07 Sep 2015 18:46:09: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 Sep 2015 18:46:10: #1 tags after filtering in treatment: 1704562 INFO @ Mon, 07 Sep 2015 18:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:10: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:10: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:10: #1 tags after filtering in treatment: 1704562 INFO @ Mon, 07 Sep 2015 18:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:10: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:10: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:10: #1 tags after filtering in treatment: 1704562 INFO @ Mon, 07 Sep 2015 18:46:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:10: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:10: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:10: #2 number of paired peaks: 1101 INFO @ Mon, 07 Sep 2015 18:46:10: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:10: #2 number of paired peaks: 1101 INFO @ Mon, 07 Sep 2015 18:46:10: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:10: #2 number of paired peaks: 1101 INFO @ Mon, 07 Sep 2015 18:46:10: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:12: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:12: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:12: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:12: #2 predicted fragment length is 111 bps INFO @ Mon, 07 Sep 2015 18:46:12: #2 alternative fragment length(s) may be 111 bps INFO @ Mon, 07 Sep 2015 18:46:12: #2.2 Generate R script for model : SRX005639.10_model.r INFO @ Mon, 07 Sep 2015 18:46:12: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:12: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:12: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:12: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:12: #2 predicted fragment length is 111 bps INFO @ Mon, 07 Sep 2015 18:46:12: #2 alternative fragment length(s) may be 111 bps INFO @ Mon, 07 Sep 2015 18:46:12: #2.2 Generate R script for model : SRX005639.20_model.r INFO @ Mon, 07 Sep 2015 18:46:12: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:12: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:12: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:12: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:12: #2 predicted fragment length is 111 bps INFO @ Mon, 07 Sep 2015 18:46:12: #2 alternative fragment length(s) may be 111 bps INFO @ Mon, 07 Sep 2015 18:46:12: #2.2 Generate R script for model : SRX005639.05_model.r INFO @ Mon, 07 Sep 2015 18:46:12: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:22: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:22: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:23: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:29: #4 Write output xls file... SRX005639.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:29: #4 Write peak in narrowPeak format file... SRX005639.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:29: #4 Write summits bed file... SRX005639.10_summits.bed INFO @ Mon, 07 Sep 2015 18:46:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (829 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:30: #4 Write output xls file... SRX005639.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:30: #4 Write peak in narrowPeak format file... SRX005639.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:30: #4 Write summits bed file... SRX005639.20_summits.bed INFO @ Mon, 07 Sep 2015 18:46:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (181 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:46:30: #4 Write output xls file... SRX005639.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:46:30: #4 Write peak in narrowPeak format file... SRX005639.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:46:30: #4 Write summits bed file... SRX005639.05_summits.bed INFO @ Mon, 07 Sep 2015 18:46:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2200 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。