Job ID = 3001485 sra ファイルのダウンロード中... Completed: 233188K bytes transferred in 6 seconds (274091K 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 10548 0 10548 0 0 13011 0 --:--:-- --:--:-- --:--:-- 26044 100 14953 0 14953 0 0 7381 0 --:--:-- 0:00:02 --:--:-- 9230 100 14953 0 14953 0 0 4938 0 --:--:-- 0:00:03 --:--:-- 5702 100 14953 0 14953 0 0 3711 0 --:--:-- 0:00:04 --:--:-- 4127 100 14953 0 14953 0 0 2972 0 --:--:-- 0:00:05 --:--:-- 3233 100 14953 0 14953 0 0 2479 0 --:--:-- 0:00:06 --:--:-- 843 100 14953 0 14953 0 0 2126 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1861 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1655 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1489 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1354 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1241 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1146 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1064 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 993 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 931 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 877 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 828 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 784 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 745 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 710 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 678 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 648 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 621 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 596 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 573 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 552 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 532 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 514 0 --:--:-- 0:00:29 --:--:-- 0 100 14953 0 14953 0 0 497 0 --:--:-- 0:00:30 --:--:-- 0 100 17867 0 17867 0 0 579 0 --:--:-- 0:00:30 --:--:-- 609 100 40446 0 40446 0 0 1303 0 --:--:-- 0:00:31 --:--:-- 6427 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 1008815 spots for /home/okishinya/chipatlas/results/ce10/SRX003828/SRR015068.sra Written 1008815 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: 00:00:10 1008815 reads; of these: 1008815 (100.00%) were unpaired; of these: 302704 (30.01%) aligned 0 times 575859 (57.08%) aligned exactly 1 time 130252 (12.91%) aligned >1 times 69.99% overall alignment rate Time searching: 00:00:10 Overall time: 00:00:10 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] 19956 / 706111 = 0.0283 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 18:45:19: # Command line: callpeak -t SRX003828.bam -f BAM -g ce -n SRX003828.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003828.20 # format = BAM # ChIP-seq file = ['SRX003828.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 18:45:19: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:19: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:19: # Command line: callpeak -t SRX003828.bam -f BAM -g ce -n SRX003828.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003828.10 # format = BAM # ChIP-seq file = ['SRX003828.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 18:45:19: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:19: # Command line: callpeak -t SRX003828.bam -f BAM -g ce -n SRX003828.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003828.05 # format = BAM # ChIP-seq file = ['SRX003828.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 18:45:19: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:19: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:45:19: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:45:22: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:45:22: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:45:22: #1 total tags in treatment: 686155 INFO @ Mon, 07 Sep 2015 18:45:22: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:22: #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 18:45:22: #1 tags after filtering in treatment: 686111 INFO @ Mon, 07 Sep 2015 18:45:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:22: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:22: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:22: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:45:22: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:45:22: #1 total tags in treatment: 686155 INFO @ Mon, 07 Sep 2015 18:45:22: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:22: #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 18:45:22: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:45:22: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:45:22: #1 total tags in treatment: 686155 INFO @ Mon, 07 Sep 2015 18:45:22: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:45:22: #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 18:45:23: #1 tags after filtering in treatment: 686111 INFO @ Mon, 07 Sep 2015 18:45:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:23: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:23: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:23: #1 tags after filtering in treatment: 686111 INFO @ Mon, 07 Sep 2015 18:45:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:45:23: #1 finished! INFO @ Mon, 07 Sep 2015 18:45:23: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:45:23: #2 number of paired peaks: 481 WARNING @ Mon, 07 Sep 2015 18:45:23: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:23: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:23: #2 number of paired peaks: 481 WARNING @ Mon, 07 Sep 2015 18:45:23: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:23: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:23: #2 number of paired peaks: 481 WARNING @ Mon, 07 Sep 2015 18:45:23: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Mon, 07 Sep 2015 18:45:23: start model_add_line... INFO @ Mon, 07 Sep 2015 18:45:23: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:23: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:23: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:23: #2 predicted fragment length is 86 bps INFO @ Mon, 07 Sep 2015 18:45:23: #2 alternative fragment length(s) may be 45,86,476 bps INFO @ Mon, 07 Sep 2015 18:45:23: #2.2 Generate R script for model : SRX003828.05_model.r INFO @ Mon, 07 Sep 2015 18:45:23: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:23: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:23: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:23: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:23: #2 predicted fragment length is 86 bps INFO @ Mon, 07 Sep 2015 18:45:23: #2 alternative fragment length(s) may be 45,86,476 bps INFO @ Mon, 07 Sep 2015 18:45:23: #2.2 Generate R script for model : SRX003828.10_model.r INFO @ Mon, 07 Sep 2015 18:45:23: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:23: start X-correlation... INFO @ Mon, 07 Sep 2015 18:45:23: end of X-cor INFO @ Mon, 07 Sep 2015 18:45:23: #2 finished! INFO @ Mon, 07 Sep 2015 18:45:23: #2 predicted fragment length is 86 bps INFO @ Mon, 07 Sep 2015 18:45:23: #2 alternative fragment length(s) may be 45,86,476 bps INFO @ Mon, 07 Sep 2015 18:45:23: #2.2 Generate R script for model : SRX003828.20_model.r INFO @ Mon, 07 Sep 2015 18:45:23: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:45:28: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:28: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:28: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:45:31: #4 Write output xls file... SRX003828.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:31: #4 Write peak in narrowPeak format file... SRX003828.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:31: #4 Write summits bed file... SRX003828.05_summits.bed INFO @ Mon, 07 Sep 2015 18:45:31: #4 Write output xls file... SRX003828.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:31: #4 Write peak in narrowPeak format file... SRX003828.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:31: #4 Write summits bed file... SRX003828.20_summits.bed INFO @ Mon, 07 Sep 2015 18:45:31: #4 Write output xls file... SRX003828.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:45:31: #4 Write peak in narrowPeak format file... SRX003828.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:45:31: Done! INFO @ Mon, 07 Sep 2015 18:45:31: #4 Write summits bed file... SRX003828.10_summits.bed INFO @ Mon, 07 Sep 2015 18:45:31: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 1 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (57 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:45:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。