Job ID = 3001475 sra ファイルのダウンロード中... Completed: 3809769K bytes transferred in 42 seconds (726282K 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 --:--:-- --:--:-- --:--:-- 0 101 2547 0 2547 0 0 4528 0 --:--:-- --:--:-- --:--:-- 6846 100 14953 0 14953 0 0 8533 0 --:--:-- 0:00:01 --:--:-- 9572 100 14953 0 14953 0 0 5429 0 --:--:-- 0:00:02 --:--:-- 5831 100 14953 0 14953 0 0 3980 0 --:--:-- 0:00:03 --:--:-- 4193 100 14953 0 14953 0 0 3143 0 --:--:-- 0:00:04 --:--:-- 3274 100 14953 0 14953 0 0 2596 0 --:--:-- 0:00:05 --:--:-- 2387 100 14953 0 14953 0 0 2211 0 --:--:-- 0:00:06 --:--:-- 0 100 16407 0 16407 0 0 2164 0 --:--:-- 0:00:07 --:--:-- 301 100 40623 0 40623 0 0 5227 0 --:--:-- 0:00:07 --:--:-- 6393 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 15218948 spots for /home/okishinya/chipatlas/results/ce10/SRX003818/SRR015058.sra Written 15218948 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: 00:01:34 15218948 reads; of these: 15218948 (100.00%) were unpaired; of these: 11005476 (72.31%) aligned 0 times 3712089 (24.39%) aligned exactly 1 time 501383 (3.29%) aligned >1 times 27.69% overall alignment rate Time searching: 00:01:34 Overall time: 00:01:34 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] 408518 / 4213472 = 0.0970 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 18:48:11: # Command line: callpeak -t SRX003818.bam -f BAM -g ce -n SRX003818.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX003818.05 # format = BAM # ChIP-seq file = ['SRX003818.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 18:48:11: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:48:11: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:48:11: # Command line: callpeak -t SRX003818.bam -f BAM -g ce -n SRX003818.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX003818.20 # format = BAM # ChIP-seq file = ['SRX003818.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 18:48:11: # Command line: callpeak -t SRX003818.bam -f BAM -g ce -n SRX003818.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX003818.10 # format = BAM # ChIP-seq file = ['SRX003818.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 18:48:11: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:48:11: #1 read tag files... INFO @ Mon, 07 Sep 2015 18:48:11: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:48:11: #1 read treatment tags... INFO @ Mon, 07 Sep 2015 18:48:16: 1000000 INFO @ Mon, 07 Sep 2015 18:48:17: 1000000 INFO @ Mon, 07 Sep 2015 18:48:17: 1000000 INFO @ Mon, 07 Sep 2015 18:48:22: 2000000 INFO @ Mon, 07 Sep 2015 18:48:23: 2000000 INFO @ Mon, 07 Sep 2015 18:48:23: 2000000 INFO @ Mon, 07 Sep 2015 18:48:27: 3000000 INFO @ Mon, 07 Sep 2015 18:48:29: 3000000 INFO @ Mon, 07 Sep 2015 18:48:29: 3000000 INFO @ Mon, 07 Sep 2015 18:48:31: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:48:31: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:48:31: #1 total tags in treatment: 3804954 INFO @ Mon, 07 Sep 2015 18:48:31: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:48:31: #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 18:48:32: #1 tags after filtering in treatment: 3804652 INFO @ Mon, 07 Sep 2015 18:48:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:48:32: #1 finished! INFO @ Mon, 07 Sep 2015 18:48:32: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:48:33: #2 number of paired peaks: 2812 INFO @ Mon, 07 Sep 2015 18:48:33: start model_add_line... INFO @ Mon, 07 Sep 2015 18:48:35: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:48:35: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:48:35: #1 total tags in treatment: 3804954 INFO @ Mon, 07 Sep 2015 18:48:35: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:48:35: #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 18:48:35: #1 tag size is determined as 36 bps INFO @ Mon, 07 Sep 2015 18:48:35: #1 tag size = 36 INFO @ Mon, 07 Sep 2015 18:48:35: #1 total tags in treatment: 3804954 INFO @ Mon, 07 Sep 2015 18:48:35: #1 user defined the maximum tags... INFO @ Mon, 07 Sep 2015 18:48:35: #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 18:48:35: #1 tags after filtering in treatment: 3804652 INFO @ Mon, 07 Sep 2015 18:48:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:48:35: #1 finished! INFO @ Mon, 07 Sep 2015 18:48:35: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:48:35: #1 tags after filtering in treatment: 3804652 INFO @ Mon, 07 Sep 2015 18:48:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 Sep 2015 18:48:35: #1 finished! INFO @ Mon, 07 Sep 2015 18:48:35: #2 Build Peak Model... INFO @ Mon, 07 Sep 2015 18:48:36: #2 number of paired peaks: 2812 INFO @ Mon, 07 Sep 2015 18:48:36: start model_add_line... INFO @ Mon, 07 Sep 2015 18:48:36: #2 number of paired peaks: 2812 INFO @ Mon, 07 Sep 2015 18:48:36: start model_add_line... INFO @ Mon, 07 Sep 2015 18:48:43: start X-correlation... INFO @ Mon, 07 Sep 2015 18:48:43: end of X-cor INFO @ Mon, 07 Sep 2015 18:48:43: #2 finished! INFO @ Mon, 07 Sep 2015 18:48:43: #2 predicted fragment length is 88 bps INFO @ Mon, 07 Sep 2015 18:48:43: #2 alternative fragment length(s) may be 88 bps INFO @ Mon, 07 Sep 2015 18:48:43: #2.2 Generate R script for model : SRX003818.05_model.r INFO @ Mon, 07 Sep 2015 18:48:43: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:48:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:48:46: start X-correlation... INFO @ Mon, 07 Sep 2015 18:48:46: end of X-cor INFO @ Mon, 07 Sep 2015 18:48:46: #2 finished! INFO @ Mon, 07 Sep 2015 18:48:46: #2 predicted fragment length is 88 bps INFO @ Mon, 07 Sep 2015 18:48:46: #2 alternative fragment length(s) may be 88 bps INFO @ Mon, 07 Sep 2015 18:48:46: #2.2 Generate R script for model : SRX003818.20_model.r INFO @ Mon, 07 Sep 2015 18:48:46: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:48:46: start X-correlation... INFO @ Mon, 07 Sep 2015 18:48:46: end of X-cor INFO @ Mon, 07 Sep 2015 18:48:46: #2 finished! INFO @ Mon, 07 Sep 2015 18:48:46: #2 predicted fragment length is 88 bps INFO @ Mon, 07 Sep 2015 18:48:46: #2 alternative fragment length(s) may be 88 bps INFO @ Mon, 07 Sep 2015 18:48:46: #2.2 Generate R script for model : SRX003818.10_model.r INFO @ Mon, 07 Sep 2015 18:48:47: #3 Call peaks... INFO @ Mon, 07 Sep 2015 18:48:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 Sep 2015 18:49:07: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:49:10: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:49:11: #3 Call peaks for each chromosome... INFO @ Mon, 07 Sep 2015 18:49:27: #4 Write output xls file... SRX003818.20_peaks.xls INFO @ Mon, 07 Sep 2015 18:49:27: #4 Write peak in narrowPeak format file... SRX003818.20_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:49:27: #4 Write summits bed file... SRX003818.20_summits.bed INFO @ Mon, 07 Sep 2015 18:49:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1627 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:49:27: #4 Write output xls file... SRX003818.05_peaks.xls INFO @ Mon, 07 Sep 2015 18:49:27: #4 Write peak in narrowPeak format file... SRX003818.05_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:49:27: #4 Write summits bed file... SRX003818.05_summits.bed INFO @ Mon, 07 Sep 2015 18:49:27: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7870 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 07 Sep 2015 18:49:29: #4 Write output xls file... SRX003818.10_peaks.xls INFO @ Mon, 07 Sep 2015 18:49:29: #4 Write peak in narrowPeak format file... SRX003818.10_peaks.narrowPeak INFO @ Mon, 07 Sep 2015 18:49:29: #4 Write summits bed file... SRX003818.10_summits.bed INFO @ Mon, 07 Sep 2015 18:49:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3950 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。