Job ID = 3001508 sra ファイルのダウンロード中... Completed: 74862K bytes transferred in 5 seconds (117288K 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 8885 0 --:--:-- 0:00:01 --:--:-- 10035 100 14953 0 14953 0 0 5569 0 --:--:-- 0:00:02 --:--:-- 6000 100 14953 0 14953 0 0 4056 0 --:--:-- 0:00:03 --:--:-- 4279 100 14953 0 14953 0 0 3189 0 --:--:-- 0:00:04 --:--:-- 3325 100 14953 0 14953 0 0 2628 0 --:--:-- 0:00:05 --:--:-- 2720 100 14953 0 14953 0 0 2234 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1943 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1719 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1541 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1397 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1277 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1177 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1091 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1016 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 951 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 894 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 844 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 798 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 758 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 721 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 688 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 658 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 630 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 604 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 581 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 559 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 539 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 520 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 502 0 --:--:-- 0:00:29 --:--:-- 0 100 16407 0 16407 0 0 537 0 --:--:-- 0:00:30 --:--:-- 301 100 34802 0 34802 0 0 1132 0 --:--:-- 0:00:30 --:--:-- 4951 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 5019687 spots for /home/okishinya/chipatlas/results/ce10/SRX005649/SRR017618.sra Written 5019687 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: 00:00:43 5019687 reads; of these: 5019687 (100.00%) were unpaired; of these: 1777261 (35.41%) aligned 0 times 2640626 (52.61%) aligned exactly 1 time 601800 (11.99%) aligned >1 times 64.59% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 333468 / 3242426 = 0.1028 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 18:47:01: # Command line: callpeak -t SRX005649.bam -f BAM -g ce -n SRX005649.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005649.05 # format = BAM # ChIP-seq file = ['SRX005649.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 18:47:01: # Command line: callpeak -t SRX005649.bam -f BAM -g ce -n SRX005649.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005649.10 # format = BAM # ChIP-seq file = ['SRX005649.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 18:47:01: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:47:01: # Command line: callpeak -t SRX005649.bam -f BAM -g ce -n SRX005649.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005649.20 # format = BAM # ChIP-seq file = ['SRX005649.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 18:47:01: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:47:01: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:47:01: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:47:01: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:47:01: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:47:06: 1000000 INFO @ Mon, 07 Sep 2015 18:47:07: 1000000 INFO @ Mon, 07 Sep 2015 18:47:07: 1000000 INFO @ Mon, 07 Sep 2015 18:47:12: 2000000 INFO @ Mon, 07 Sep 2015 18:47:13: 2000000 INFO @ Mon, 07 Sep 2015 18:47:13: 2000000 INFO @ Mon, 07 Sep 2015 18:47:17: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:47:17: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:47:17: #1 total tags in treatment: 2908958 INFO @ Mon, 07 Sep 2015 18:47:17: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:47:17: #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 18:47:18: #1 tags after filtering in treatment: 2908947 INFO @ Mon, 07 Sep 2015 18:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:47:18: #1 finished! INFO @ Mon, 07 Sep 2015 18:47:18: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:47:18: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:47:18: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:47:18: #1 total tags in treatment: 2908958 INFO @ Mon, 07 Sep 2015 18:47:18: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:47:18: #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 18:47:18: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:47:18: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:47:18: #1 total tags in treatment: 2908958 INFO @ Mon, 07 Sep 2015 18:47:18: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:47:18: #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 18:47:18: #1 tags after filtering in treatment: 2908947 INFO @ Mon, 07 Sep 2015 18:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:47:18: #1 finished! INFO @ Mon, 07 Sep 2015 18:47:18: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:47:18: #1 tags after filtering in treatment: 2908947 INFO @ Mon, 07 Sep 2015 18:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:47:18: #1 finished! INFO @ Mon, 07 Sep 2015 18:47:18: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:47:19: #2 number of paired peaks: 864 WARNING @ Mon, 07 Sep 2015 18:47:19: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Mon, 07 Sep 2015 18:47:19: start model_add_line... INFO @ Mon, 07 Sep 2015 18:47:19: #2 number of paired peaks: 864 WARNING @ Mon, 07 Sep 2015 18:47:19: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Mon, 07 Sep 2015 18:47:19: start model_add_line... INFO @ Mon, 07 Sep 2015 18:47:19: #2 number of paired peaks: 864 WARNING @ Mon, 07 Sep 2015 18:47:19: Fewer paired peaks (864) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 864 pairs to build model! INFO @ Mon, 07 Sep 2015 18:47:19: start model_add_line... INFO @ Mon, 07 Sep 2015 18:47:22: start X-correlation... INFO @ Mon, 07 Sep 2015 18:47:22: end of X-cor INFO @ Mon, 07 Sep 2015 18:47:22: #2 finished! INFO @ Mon, 07 Sep 2015 18:47:22: #2 predicted fragment length is 102 bps INFO @ Mon, 07 Sep 2015 18:47:22: #2 alternative fragment length(s) may be 102 bps INFO @ Mon, 07 Sep 2015 18:47:22: #2.2 Generate R script for model : SRX005649.05_model.r INFO @ Mon, 07 Sep 2015 18:47:22: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:47:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:47:22: start X-correlation... INFO @ Mon, 07 Sep 2015 18:47:22: end of X-cor INFO @ Mon, 07 Sep 2015 18:47:22: #2 finished! INFO @ Mon, 07 Sep 2015 18:47:22: #2 predicted fragment length is 102 bps INFO @ Mon, 07 Sep 2015 18:47:22: #2 alternative fragment length(s) may be 102 bps INFO @ Mon, 07 Sep 2015 18:47:22: #2.2 Generate R script for model : SRX005649.10_model.r INFO @ Mon, 07 Sep 2015 18:47:22: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:47:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:47:22: start X-correlation... INFO @ Mon, 07 Sep 2015 18:47:22: end of X-cor INFO @ Mon, 07 Sep 2015 18:47:22: #2 finished! INFO @ Mon, 07 Sep 2015 18:47:22: #2 predicted fragment length is 102 bps INFO @ Mon, 07 Sep 2015 18:47:22: #2 alternative fragment length(s) may be 102 bps INFO @ Mon, 07 Sep 2015 18:47:22: #2.2 Generate R script for model : SRX005649.20_model.r INFO @ Mon, 07 Sep 2015 18:47:22: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:47:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:47:39: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:47:40: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:47:41: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:47:53: #4 Write output xls file... SRX005649.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:53: #4 Write peak in narrowPeak format file... SRX005649.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:53: #4 Write summits bed file... SRX005649.05_summits.bed INFO @ Mon, 07 Sep 2015 18:47:53: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1330 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:47:53: #4 Write output xls file... SRX005649.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:53: #4 Write peak in narrowPeak format file... SRX005649.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:54: #4 Write summits bed file... SRX005649.20_summits.bed INFO @ Mon, 07 Sep 2015 18:47:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (199 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:47:54: #4 Write output xls file... SRX005649.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:54: #4 Write peak in narrowPeak format file... SRX005649.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:54: #4 Write summits bed file... SRX005649.10_summits.bed INFO @ Mon, 07 Sep 2015 18:47:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (480 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。