Job ID = 2161286 sra ファイルのダウンロード中... Completed: 259608K bytes transferred in 5 seconds (372673K bits/sec), in 2 files, 3 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 4000 0 4000 0 0 8158 0 --:--:-- --:--:-- --:--:-- 13377 100 34370 0 34370 0 0 50544 0 --:--:-- --:--:-- --:--:-- 70286 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 4838167 spots for /home/okishinya/chipatlas/results/dm3/SRX016152/SRR034713.sra Written 4838167 spots total Written 5311031 spots for /home/okishinya/chipatlas/results/dm3/SRX016152/SRR034712.sra Written 5311031 spots total 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: 00:02:40 10149198 reads; of these: 10149198 (100.00%) were unpaired; of these: 1067184 (10.51%) aligned 0 times 7622826 (75.11%) aligned exactly 1 time 1459188 (14.38%) aligned >1 times 89.49% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 4330093 / 9082014 = 0.4768 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 @ Tue, 21 Apr 2015 12:16:42: # Command line: callpeak -t SRX016152.bam -f BAM -g dm -n SRX016152.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX016152.20 # format = BAM # ChIP-seq file = ['SRX016152.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:16:42: # Command line: callpeak -t SRX016152.bam -f BAM -g dm -n SRX016152.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX016152.05 # format = BAM # ChIP-seq file = ['SRX016152.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:16:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:16:42: # Command line: callpeak -t SRX016152.bam -f BAM -g dm -n SRX016152.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX016152.10 # format = BAM # ChIP-seq file = ['SRX016152.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 21 Apr 2015 12:16:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:16:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:16:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:16:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:16:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:16:49: 1000000 INFO @ Tue, 21 Apr 2015 12:16:49: 1000000 INFO @ Tue, 21 Apr 2015 12:16:49: 1000000 INFO @ Tue, 21 Apr 2015 12:16:56: 2000000 INFO @ Tue, 21 Apr 2015 12:16:56: 2000000 INFO @ Tue, 21 Apr 2015 12:16:56: 2000000 INFO @ Tue, 21 Apr 2015 12:17:01: 3000000 INFO @ Tue, 21 Apr 2015 12:17:01: 3000000 INFO @ Tue, 21 Apr 2015 12:17:01: 3000000 INFO @ Tue, 21 Apr 2015 12:17:06: 4000000 INFO @ Tue, 21 Apr 2015 12:17:06: 4000000 INFO @ Tue, 21 Apr 2015 12:17:07: 4000000 INFO @ Tue, 21 Apr 2015 12:17:10: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:17:10: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:17:10: #1 total tags in treatment: 4751921 INFO @ Tue, 21 Apr 2015 12:17:10: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:17:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:17:10: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:17:10: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:17:10: #1 total tags in treatment: 4751921 INFO @ Tue, 21 Apr 2015 12:17:10: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:17:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:17:11: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:17:11: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:17:11: #1 total tags in treatment: 4751921 INFO @ Tue, 21 Apr 2015 12:17:11: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:17:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:17:11: #1 tags after filtering in treatment: 4751530 INFO @ Tue, 21 Apr 2015 12:17:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:17:11: #1 finished! INFO @ Tue, 21 Apr 2015 12:17:11: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:17:11: #1 tags after filtering in treatment: 4751530 INFO @ Tue, 21 Apr 2015 12:17:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:17:11: #1 finished! INFO @ Tue, 21 Apr 2015 12:17:11: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:17:12: #1 tags after filtering in treatment: 4751530 INFO @ Tue, 21 Apr 2015 12:17:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:17:12: #1 finished! INFO @ Tue, 21 Apr 2015 12:17:12: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:17:12: #2 number of paired peaks: 2086 INFO @ Tue, 21 Apr 2015 12:17:12: start model_add_line... INFO @ Tue, 21 Apr 2015 12:17:12: #2 number of paired peaks: 2086 INFO @ Tue, 21 Apr 2015 12:17:12: start model_add_line... INFO @ Tue, 21 Apr 2015 12:17:13: #2 number of paired peaks: 2086 INFO @ Tue, 21 Apr 2015 12:17:13: start model_add_line... INFO @ Tue, 21 Apr 2015 12:17:18: start X-correlation... INFO @ Tue, 21 Apr 2015 12:17:18: end of X-cor INFO @ Tue, 21 Apr 2015 12:17:18: #2 finished! INFO @ Tue, 21 Apr 2015 12:17:18: #2 predicted fragment length is 180 bps INFO @ Tue, 21 Apr 2015 12:17:18: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 21 Apr 2015 12:17:18: #2.2 Generate R script for model : SRX016152.05_model.r INFO @ Tue, 21 Apr 2015 12:17:18: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:17:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:17:18: start X-correlation... INFO @ Tue, 21 Apr 2015 12:17:18: end of X-cor INFO @ Tue, 21 Apr 2015 12:17:18: #2 finished! INFO @ Tue, 21 Apr 2015 12:17:18: #2 predicted fragment length is 180 bps INFO @ Tue, 21 Apr 2015 12:17:18: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 21 Apr 2015 12:17:18: #2.2 Generate R script for model : SRX016152.10_model.r INFO @ Tue, 21 Apr 2015 12:17:18: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:17:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:17:19: start X-correlation... INFO @ Tue, 21 Apr 2015 12:17:19: end of X-cor INFO @ Tue, 21 Apr 2015 12:17:19: #2 finished! INFO @ Tue, 21 Apr 2015 12:17:19: #2 predicted fragment length is 180 bps INFO @ Tue, 21 Apr 2015 12:17:19: #2 alternative fragment length(s) may be 180 bps INFO @ Tue, 21 Apr 2015 12:17:19: #2.2 Generate R script for model : SRX016152.20_model.r INFO @ Tue, 21 Apr 2015 12:17:19: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:17:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:17:46: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:17:46: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:17:48: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:18:08: #4 Write output xls file... SRX016152.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:18:08: #4 Write peak in narrowPeak format file... SRX016152.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:18:08: #4 Write summits bed file... SRX016152.20_summits.bed INFO @ Tue, 21 Apr 2015 12:18:08: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1013 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:18:10: #4 Write output xls file... SRX016152.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:18:10: #4 Write peak in narrowPeak format file... SRX016152.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:18:10: #4 Write summits bed file... SRX016152.10_summits.bed INFO @ Tue, 21 Apr 2015 12:18:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2768 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:18:11: #4 Write output xls file... SRX016152.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:18:11: #4 Write peak in narrowPeak format file... SRX016152.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:18:11: #4 Write summits bed file... SRX016152.05_summits.bed INFO @ Tue, 21 Apr 2015 12:18:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5065 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。