Job ID = 3001507 sra ファイルのダウンロード中... Completed: 63693K bytes transferred in 5 seconds (99429K 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 21427 0 --:--:-- --:--:-- --:--:-- 29493 100 14953 0 14953 0 0 8796 0 --:--:-- 0:00:01 --:--:-- 9909 100 14953 0 14953 0 0 5535 0 --:--:-- 0:00:02 --:--:-- 5957 100 14953 0 14953 0 0 4037 0 --:--:-- 0:00:03 --:--:-- 4257 100 14953 0 14953 0 0 3178 0 --:--:-- 0:00:04 --:--:-- 3312 100 14953 0 14953 0 0 2620 0 --:--:-- 0:00:05 --:--:-- 0 100 14953 0 14953 0 0 2228 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1939 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1716 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1539 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1395 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1275 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1175 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1089 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 1015 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 950 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 893 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 843 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 798 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 757 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 721 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 687 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 657 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 629 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 604 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 580 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 559 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 538 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 34509 0 34509 0 0 1122 0 --:--:-- 0:00:30 --:--:-- 3908 100 34509 0 34509 0 0 1122 0 --:--:-- 0:00:30 --:--:-- 4887 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 4134711 spots for /home/okishinya/chipatlas/results/ce10/SRX005648/SRR017617.sra Written 4134711 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 4134711 reads; of these: 4134711 (100.00%) were unpaired; of these: 1919324 (46.42%) aligned 0 times 1775646 (42.94%) aligned exactly 1 time 439741 (10.64%) aligned >1 times 53.58% 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] 277847 / 2215387 = 0.1254 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 18:46:35: # Command line: callpeak -t SRX005648.bam -f BAM -g ce -n SRX005648.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005648.10 # format = BAM # ChIP-seq file = ['SRX005648.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 18:46:35: # Command line: callpeak -t SRX005648.bam -f BAM -g ce -n SRX005648.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005648.05 # format = BAM # ChIP-seq file = ['SRX005648.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 18:46:35: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:35: # Command line: callpeak -t SRX005648.bam -f BAM -g ce -n SRX005648.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005648.20 # format = BAM # ChIP-seq file = ['SRX005648.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 18:46:35: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:35: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:35: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:35: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:35: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:41: 1000000 INFO @ Mon, 07 Sep 2015 18:46:41: 1000000 INFO @ Mon, 07 Sep 2015 18:46:41: 1000000 INFO @ Mon, 07 Sep 2015 18:46:47: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:47: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:47: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:47: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:47: #1 total tags in treatment: 1937540 INFO @ Mon, 07 Sep 2015 18:46:47: #1 total tags in treatment: 1937540 INFO @ Mon, 07 Sep 2015 18:46:47: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:47: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:47: #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 18:46:47: #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 18:46:47: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:47: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:47: #1 total tags in treatment: 1937540 INFO @ Mon, 07 Sep 2015 18:46:47: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:47: #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 18:46:47: #1 tags after filtering in treatment: 1937535 INFO @ Mon, 07 Sep 2015 18:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:47: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:47: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:47: #1 tags after filtering in treatment: 1937535 INFO @ Mon, 07 Sep 2015 18:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:47: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:47: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:47: #1 tags after filtering in treatment: 1937535 INFO @ Mon, 07 Sep 2015 18:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:47: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:47: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:46:48: #2 number of paired peaks: 808 WARNING @ Mon, 07 Sep 2015 18:46:48: Fewer paired peaks (808) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 808 pairs to build model! INFO @ Mon, 07 Sep 2015 18:46:48: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:48: #2 number of paired peaks: 808 WARNING @ Mon, 07 Sep 2015 18:46:48: Fewer paired peaks (808) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 808 pairs to build model! INFO @ Mon, 07 Sep 2015 18:46:48: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:48: #2 number of paired peaks: 808 WARNING @ Mon, 07 Sep 2015 18:46:48: Fewer paired peaks (808) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 808 pairs to build model! INFO @ Mon, 07 Sep 2015 18:46:48: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:50: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:50: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:50: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:50: #2 predicted fragment length is 101 bps INFO @ Mon, 07 Sep 2015 18:46:50: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 07 Sep 2015 18:46:50: #2.2 Generate R script for model : SRX005648.20_model.r INFO @ Mon, 07 Sep 2015 18:46:50: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:50: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:50: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:50: #2 predicted fragment length is 101 bps INFO @ Mon, 07 Sep 2015 18:46:50: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 07 Sep 2015 18:46:50: #2.2 Generate R script for model : SRX005648.05_model.r INFO @ Mon, 07 Sep 2015 18:46:50: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:50: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:50: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:50: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:50: #2 predicted fragment length is 101 bps INFO @ Mon, 07 Sep 2015 18:46:50: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 07 Sep 2015 18:46:50: #2.2 Generate R script for model : SRX005648.10_model.r INFO @ Mon, 07 Sep 2015 18:46:50: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:50: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:47:02: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:47:02: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:47:02: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:47:10: #4 Write output xls file... SRX005648.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:10: #4 Write peak in narrowPeak format file... SRX005648.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:10: #4 Write summits bed file... SRX005648.20_summits.bed INFO @ Mon, 07 Sep 2015 18:47:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (178 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:47:10: #4 Write output xls file... SRX005648.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:10: #4 Write peak in narrowPeak format file... SRX005648.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:10: #4 Write summits bed file... SRX005648.10_summits.bed INFO @ Mon, 07 Sep 2015 18:47:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:47:11: #4 Write output xls file... SRX005648.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:11: #4 Write peak in narrowPeak format file... SRX005648.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:11: #4 Write summits bed file... SRX005648.05_summits.bed INFO @ Mon, 07 Sep 2015 18:47:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (772 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。