Job ID = 3001491 sra ファイルのダウンロード中... Completed: 90648K bytes transferred in 5 seconds (130231K 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 7687 0 --:--:-- 0:00:01 --:--:-- 8529 100 14953 0 14953 0 0 5073 0 --:--:-- 0:00:02 --:--:-- 5427 100 14953 0 14953 0 0 3786 0 --:--:-- 0:00:03 --:--:-- 3980 100 14953 0 14953 0 0 3020 0 --:--:-- 0:00:04 --:--:-- 3142 100 14953 0 14953 0 0 2511 0 --:--:-- 0:00:05 --:--:-- 2595 100 14953 0 14953 0 0 2150 0 --:--:-- 0:00:06 --:--:-- 0 100 14953 0 14953 0 0 1879 0 --:--:-- 0:00:07 --:--:-- 0 100 14953 0 14953 0 0 1669 0 --:--:-- 0:00:08 --:--:-- 0 100 14953 0 14953 0 0 1501 0 --:--:-- 0:00:09 --:--:-- 0 100 14953 0 14953 0 0 1364 0 --:--:-- 0:00:10 --:--:-- 0 100 14953 0 14953 0 0 1249 0 --:--:-- 0:00:11 --:--:-- 0 100 14953 0 14953 0 0 1153 0 --:--:-- 0:00:12 --:--:-- 0 100 14953 0 14953 0 0 1070 0 --:--:-- 0:00:13 --:--:-- 0 100 14953 0 14953 0 0 999 0 --:--:-- 0:00:14 --:--:-- 0 100 14953 0 14953 0 0 936 0 --:--:-- 0:00:15 --:--:-- 0 100 14953 0 14953 0 0 881 0 --:--:-- 0:00:16 --:--:-- 0 100 14953 0 14953 0 0 832 0 --:--:-- 0:00:17 --:--:-- 0 100 14953 0 14953 0 0 788 0 --:--:-- 0:00:18 --:--:-- 0 100 14953 0 14953 0 0 748 0 --:--:-- 0:00:19 --:--:-- 0 100 14953 0 14953 0 0 712 0 --:--:-- 0:00:20 --:--:-- 0 100 14953 0 14953 0 0 680 0 --:--:-- 0:00:21 --:--:-- 0 100 14953 0 14953 0 0 650 0 --:--:-- 0:00:22 --:--:-- 0 100 14953 0 14953 0 0 623 0 --:--:-- 0:00:23 --:--:-- 0 100 14953 0 14953 0 0 598 0 --:--:-- 0:00:24 --:--:-- 0 100 14953 0 14953 0 0 575 0 --:--:-- 0:00:25 --:--:-- 0 100 14953 0 14953 0 0 554 0 --:--:-- 0:00:26 --:--:-- 0 100 14953 0 14953 0 0 534 0 --:--:-- 0:00:27 --:--:-- 0 100 14953 0 14953 0 0 515 0 --:--:-- 0:00:28 --:--:-- 0 100 14953 0 14953 0 0 498 0 --:--:-- 0:00:29 --:--:-- 0 100 14953 0 14953 0 0 482 0 --:--:-- 0:00:30 --:--:-- 0 100 25083 0 25083 0 0 788 0 --:--:-- 0:00:31 --:--:-- 2102 100 34775 0 34775 0 0 1086 0 --:--:-- 0:00:31 --:--:-- 4949 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 5707229 spots for /home/okishinya/chipatlas/results/ce10/SRX005625/SRR017594.sra Written 5707229 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 5707229 reads; of these: 5707229 (100.00%) were unpaired; of these: 2139215 (37.48%) aligned 0 times 3043771 (53.33%) aligned exactly 1 time 524243 (9.19%) aligned >1 times 62.52% 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] 1142888 / 3568014 = 0.3203 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 18:46:33: # Command line: callpeak -t SRX005625.bam -f BAM -g ce -n SRX005625.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX005625.10 # format = BAM # ChIP-seq file = ['SRX005625.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 18:46:33: # Command line: callpeak -t SRX005625.bam -f BAM -g ce -n SRX005625.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX005625.05 # format = BAM # ChIP-seq file = ['SRX005625.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 18:46:33: # Command line: callpeak -t SRX005625.bam -f BAM -g ce -n SRX005625.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX005625.20 # format = BAM # ChIP-seq file = ['SRX005625.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 18:46:33: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:33: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:33: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:46:33: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:33: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:33: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:46:38: 1000000 INFO @ Mon, 07 Sep 2015 18:46:39: 1000000 INFO @ Mon, 07 Sep 2015 18:46:39: 1000000 INFO @ Mon, 07 Sep 2015 18:46:44: 2000000 INFO @ Mon, 07 Sep 2015 18:46:44: 2000000 INFO @ Mon, 07 Sep 2015 18:46:44: 2000000 INFO @ Mon, 07 Sep 2015 18:46:46: #1 tag size is determined as 27 bps INFO @ Mon, 07 Sep 2015 18:46:46: #1 tag size = 27 INFO @ Mon, 07 Sep 2015 18:46:46: #1 total tags in treatment: 2425126 INFO @ Mon, 07 Sep 2015 18:46:46: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:46:46: #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 18:46:46: #1 tags after filtering in treatment: 2425113 INFO @ Mon, 07 Sep 2015 18:46:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:46:46: #1 finished! INFO @ Mon, 07 Sep 2015 18:46:46: #2 Build Peak Model... 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: 2425126 INFO @ Mon, 07 Sep 2015 18:46:47: #1 total tags in treatment: 2425126 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: #2 number of paired peaks: 1454 INFO @ Mon, 07 Sep 2015 18:46:47: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:47: #1 tags after filtering in treatment: 2425113 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: 2425113 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: 1454 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: 1454 INFO @ Mon, 07 Sep 2015 18:46:48: start model_add_line... INFO @ Mon, 07 Sep 2015 18:46:51: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:51: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:51: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:51: #2 predicted fragment length is 112 bps INFO @ Mon, 07 Sep 2015 18:46:51: #2 alternative fragment length(s) may be 112 bps INFO @ Mon, 07 Sep 2015 18:46:51: #2.2 Generate R script for model : SRX005625.05_model.r INFO @ Mon, 07 Sep 2015 18:46:51: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:52: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:52: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:52: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:52: #2 predicted fragment length is 112 bps INFO @ Mon, 07 Sep 2015 18:46:52: #2 alternative fragment length(s) may be 112 bps INFO @ Mon, 07 Sep 2015 18:46:52: #2.2 Generate R script for model : SRX005625.20_model.r INFO @ Mon, 07 Sep 2015 18:46:52: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:46:52: start X-correlation... INFO @ Mon, 07 Sep 2015 18:46:52: end of X-cor INFO @ Mon, 07 Sep 2015 18:46:52: #2 finished! INFO @ Mon, 07 Sep 2015 18:46:52: #2 predicted fragment length is 112 bps INFO @ Mon, 07 Sep 2015 18:46:52: #2 alternative fragment length(s) may be 112 bps INFO @ Mon, 07 Sep 2015 18:46:52: #2.2 Generate R script for model : SRX005625.10_model.r INFO @ Mon, 07 Sep 2015 18:46:53: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:47:07: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:47:07: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:47:08: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:47:16: #4 Write output xls file... SRX005625.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:16: #4 Write peak in narrowPeak format file... SRX005625.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:16: #4 Write summits bed file... SRX005625.20_summits.bed INFO @ Mon, 07 Sep 2015 18:47:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:47:18: #4 Write output xls file... SRX005625.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:18: #4 Write peak in narrowPeak format file... SRX005625.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:18: #4 Write summits bed file... SRX005625.05_summits.bed INFO @ Mon, 07 Sep 2015 18:47:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1612 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:47:19: #4 Write output xls file... SRX005625.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:47:19: #4 Write peak in narrowPeak format file... SRX005625.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:47:19: #4 Write summits bed file... SRX005625.10_summits.bed INFO @ Mon, 07 Sep 2015 18:47:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (595 records, 4 fields): 214 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。