Job ID = 9025447 sra ファイルのダウンロード中... Completed: 57445K bytes transferred in 3 seconds (120739K 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 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 21558 0 21558 0 0 2472 0 --:--:-- 0:00:08 --:--:-- 10344 100 46889 0 46889 0 0 4827 0 --:--:-- 0:00:09 --:--:-- 15223 100 46889 0 46889 0 0 4826 0 --:--:-- 0:00:09 --:--:-- 15218 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 2905382 spots for /home/okishinya/chipatlas/results/ce10/SRX1007132/SRR1993092.sra Written 2905382 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:20 2905382 reads; of these: 2905382 (100.00%) were unpaired; of these: 2602146 (89.56%) aligned 0 times 253932 (8.74%) aligned exactly 1 time 49304 (1.70%) aligned >1 times 10.44% overall alignment rate Time searching: 00:00:21 Overall time: 00:00:21 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] 21068 / 303236 = 0.0695 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 @ Sat, 03 Jun 2017 03:48:38: # Command line: callpeak -t SRX1007132.bam -f BAM -g ce -n SRX1007132.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1007132.20 # format = BAM # ChIP-seq file = ['SRX1007132.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 @ Sat, 03 Jun 2017 03:48:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 03:48:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 03:48:38: # Command line: callpeak -t SRX1007132.bam -f BAM -g ce -n SRX1007132.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1007132.05 # format = BAM # ChIP-seq file = ['SRX1007132.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 @ Sat, 03 Jun 2017 03:48:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 03:48:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 03:48:38: # Command line: callpeak -t SRX1007132.bam -f BAM -g ce -n SRX1007132.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1007132.10 # format = BAM # ChIP-seq file = ['SRX1007132.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 @ Sat, 03 Jun 2017 03:48:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 03:48:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 03:48:40: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 03:48:40: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 03:48:40: #1 total tags in treatment: 282168 INFO @ Sat, 03 Jun 2017 03:48:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 03:48:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 03:48:40: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 03:48:40: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 03:48:40: #1 total tags in treatment: 282168 INFO @ Sat, 03 Jun 2017 03:48:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 03:48:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 03:48:40: #1 tags after filtering in treatment: 282123 INFO @ Sat, 03 Jun 2017 03:48:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 03:48:40: #1 finished! INFO @ Sat, 03 Jun 2017 03:48:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 03:48:40: #1 tags after filtering in treatment: 282123 INFO @ Sat, 03 Jun 2017 03:48:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 03:48:40: #1 finished! INFO @ Sat, 03 Jun 2017 03:48:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 03:48:40: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 03:48:40: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 03:48:40: #1 total tags in treatment: 282168 INFO @ Sat, 03 Jun 2017 03:48:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 03:48:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 03:48:40: #1 tags after filtering in treatment: 282123 INFO @ Sat, 03 Jun 2017 03:48:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 03:48:40: #1 finished! INFO @ Sat, 03 Jun 2017 03:48:40: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 03:48:40: #2 number of paired peaks: 2092 INFO @ Sat, 03 Jun 2017 03:48:40: start model_add_line... INFO @ Sat, 03 Jun 2017 03:48:40: #2 number of paired peaks: 2092 INFO @ Sat, 03 Jun 2017 03:48:40: start model_add_line... INFO @ Sat, 03 Jun 2017 03:48:41: #2 number of paired peaks: 2092 INFO @ Sat, 03 Jun 2017 03:48:41: start model_add_line... INFO @ Sat, 03 Jun 2017 03:48:41: start X-correlation... INFO @ Sat, 03 Jun 2017 03:48:41: end of X-cor INFO @ Sat, 03 Jun 2017 03:48:41: #2 finished! INFO @ Sat, 03 Jun 2017 03:48:41: #2 predicted fragment length is 83 bps INFO @ Sat, 03 Jun 2017 03:48:41: #2 alternative fragment length(s) may be 83 bps INFO @ Sat, 03 Jun 2017 03:48:41: #2.2 Generate R script for model : SRX1007132.20_model.r INFO @ Sat, 03 Jun 2017 03:48:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 03:48:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 03:48:41: start X-correlation... INFO @ Sat, 03 Jun 2017 03:48:41: end of X-cor INFO @ Sat, 03 Jun 2017 03:48:41: #2 finished! INFO @ Sat, 03 Jun 2017 03:48:41: #2 predicted fragment length is 83 bps INFO @ Sat, 03 Jun 2017 03:48:41: #2 alternative fragment length(s) may be 83 bps INFO @ Sat, 03 Jun 2017 03:48:41: #2.2 Generate R script for model : SRX1007132.10_model.r INFO @ Sat, 03 Jun 2017 03:48:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 03:48:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 03:48:41: start X-correlation... INFO @ Sat, 03 Jun 2017 03:48:41: end of X-cor INFO @ Sat, 03 Jun 2017 03:48:41: #2 finished! INFO @ Sat, 03 Jun 2017 03:48:41: #2 predicted fragment length is 83 bps INFO @ Sat, 03 Jun 2017 03:48:41: #2 alternative fragment length(s) may be 83 bps INFO @ Sat, 03 Jun 2017 03:48:41: #2.2 Generate R script for model : SRX1007132.05_model.r INFO @ Sat, 03 Jun 2017 03:48:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 03:48:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 03:48:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 03:48:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 03:48:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 03:48:44: #4 Write output xls file... SRX1007132.20_peaks.xls INFO @ Sat, 03 Jun 2017 03:48:44: #4 Write peak in narrowPeak format file... SRX1007132.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 03:48:44: #4 Write summits bed file... SRX1007132.20_summits.bed INFO @ Sat, 03 Jun 2017 03:48:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 03:48:44: #4 Write output xls file... SRX1007132.10_peaks.xls INFO @ Sat, 03 Jun 2017 03:48:44: #4 Write peak in narrowPeak format file... SRX1007132.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 03:48:44: #4 Write summits bed file... SRX1007132.10_summits.bed INFO @ Sat, 03 Jun 2017 03:48:44: Done! BedGraph に変換しました。 pass1 - making usageList (6 chroms): 1 millis BigWig に変換中... pass2 - checking and writing primary data (722 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 03:48:45: #4 Write output xls file... SRX1007132.05_peaks.xls INFO @ Sat, 03 Jun 2017 03:48:45: #4 Write peak in narrowPeak format file... SRX1007132.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 03:48:45: #4 Write summits bed file... SRX1007132.05_summits.bed INFO @ Sat, 03 Jun 2017 03:48:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1679 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。