Job ID = 3001496 sra ファイルのダウンロード中... Completed: 75244K bytes transferred in 5 seconds (117117K 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 8513 0 --:--:-- 0:00:01 --:--:-- 9554 100 14953 0 14953 0 0 5420 0 --:--:-- 0:00:02 --:--:-- 5825 100 14953 0 14953 0 0 3976 0 --:--:-- 0:00:03 --:--:-- 4189 100 14953 0 14953 0 0 3139 0 --:--:-- 0:00:04 --:--:-- 3271 100 14953 0 14953 0 0 2594 0 --:--:-- 0:00:05 --:--:-- 2683 100 14953 0 14953 0 0 2210 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1925 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1705 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1530 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1387 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1269 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1170 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1085 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1011 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 947 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 890 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 840 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 795 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 755 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 719 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 686 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 656 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 628 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 602 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 579 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 557 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 537 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 519 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 501 0 --:--:-- 0:00:29 --:--:-- 0 100 17867 0 17867 0 0 583 0 --:--:-- 0:00:30 --:--:-- 604 100 34962 0 34962 0 0 1134 0 --:--:-- 0:00:30 --:--:-- 4992 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 4436069 spots for /home/okishinya/chipatlas/results/ce10/SRX005630/SRR017599.sra Written 4436069 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: 00:00:33 4436069 reads; of these: 4436069 (100.00%) were unpaired; of these: 2039774 (45.98%) aligned 0 times 1983627 (44.72%) aligned exactly 1 time 412668 (9.30%) aligned >1 times 54.02% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 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] 140521 / 2396295 = 0.0586 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 18:46:27: # Command line: callpeak -t SRX005630.bam -f BAM -g ce -n SRX005630.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005630.10 # format = BAM # ChIP-seq file = ['SRX005630.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 18:46:27: # Command line: callpeak -t SRX005630.bam -f BAM -g ce -n SRX005630.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005630.20 # format = BAM # ChIP-seq file = ['SRX005630.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 18:46:27: # Command line: callpeak -t SRX005630.bam -f BAM -g ce -n SRX005630.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005630.05 # format = BAM # ChIP-seq file = ['SRX005630.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 18:46:27: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:27: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:27: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:27: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:27: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:27: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:33: 1000000 INFO @ Mon, 07 Sep 2015 18:46:33: 1000000 INFO @ Mon, 07 Sep 2015 18:46:33: 1000000 INFO @ Mon, 07 Sep 2015 18:46:38: 2000000 INFO @ Mon, 07 Sep 2015 18:46:39: 2000000 INFO @ Mon, 07 Sep 2015 18:46:39: 2000000 INFO @ Mon, 07 Sep 2015 18:46:40: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:40: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:40: #1 total tags in treatment: 2255774 INFO @ Mon, 07 Sep 2015 18:46:40: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:40: #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 18:46:40: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:40: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:40: #1 total tags in treatment: 2255774 INFO @ Mon, 07 Sep 2015 18:46:40: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:40: #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 18:46:40: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:40: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:40: #1 total tags in treatment: 2255774 INFO @ Mon, 07 Sep 2015 18:46:40: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:40: #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 18:46:40: #1 tags after filtering in treatment: 2255766 INFO @ Mon, 07 Sep 2015 18:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:40: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:40: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:40: #1 tags after filtering in treatment: 2255766 INFO @ Mon, 07 Sep 2015 18:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:40: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:40: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:40: #1 tags after filtering in treatment: 2255766 INFO @ Mon, 07 Sep 2015 18:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:40: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:40: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:41: #2 number of paired peaks: 355 WARNING @ Mon, 07 Sep 2015 18:46:41: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Mon, 07 Sep 2015 18:46:41: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:41: #2 number of paired peaks: 355 WARNING @ Mon, 07 Sep 2015 18:46:41: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Mon, 07 Sep 2015 18:46:41: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:41: #2 number of paired peaks: 355 WARNING @ Mon, 07 Sep 2015 18:46:41: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Mon, 07 Sep 2015 18:46:41: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:42: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:42: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:42: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:42: #2 predicted fragment length is 60 bps INFO @ Mon, 07 Sep 2015 18:46:42: #2 alternative fragment length(s) may be 60,527,530 bps INFO @ Mon, 07 Sep 2015 18:46:42: #2.2 Generate R script for model : SRX005630.05_model.r INFO @ Mon, 07 Sep 2015 18:46:42: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:42: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:42: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:42: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:42: #2 predicted fragment length is 60 bps INFO @ Mon, 07 Sep 2015 18:46:42: #2 alternative fragment length(s) may be 60,527,530 bps INFO @ Mon, 07 Sep 2015 18:46:42: #2.2 Generate R script for model : SRX005630.10_model.r INFO @ Mon, 07 Sep 2015 18:46:42: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:42: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:42: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:42: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:42: #2 predicted fragment length is 60 bps INFO @ Mon, 07 Sep 2015 18:46:42: #2 alternative fragment length(s) may be 60,527,530 bps INFO @ Mon, 07 Sep 2015 18:46:42: #2.2 Generate R script for model : SRX005630.20_model.r INFO @ Mon, 07 Sep 2015 18:46:42: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:56: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:56: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:46:56: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:47:05: #4 Write output xls file... SRX005630.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:05: #4 Write peak in narrowPeak format file... SRX005630.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:05: #4 Write summits bed file... SRX005630.10_summits.bed INFO @ Mon, 07 Sep 2015 18:47:05: Done! pass1 - making usageList (7 chroms): 6 millis pass2 - checking and writing primary data (160 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:47:05: #4 Write output xls file... SRX005630.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:05: #4 Write peak in narrowPeak format file... SRX005630.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:05: #4 Write summits bed file... SRX005630.05_summits.bed INFO @ Mon, 07 Sep 2015 18:47:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (606 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:47:06: #4 Write output xls file... SRX005630.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:06: #4 Write peak in narrowPeak format file... SRX005630.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:06: #4 Write summits bed file... SRX005630.20_summits.bed INFO @ Mon, 07 Sep 2015 18:47:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。