Job ID = 9025511 sra ファイルのダウンロード中... Completed: 93975K bytes transferred in 4 seconds (184298K 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 --:--:-- 0:00:06 --:--:-- 0 100 23766 0 23766 0 0 3053 0 --:--:-- 0:00:07 --:--:-- 17709 100 47294 0 47294 0 0 5710 0 --:--:-- 0:00:08 --:--:-- 25717 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 3999906 spots for /home/okishinya/chipatlas/results/ce10/SRX1388760/SRR2832476.sra Written 3999906 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: 00:01:10 3999906 reads; of these: 3999906 (100.00%) were unpaired; of these: 758783 (18.97%) aligned 0 times 2800374 (70.01%) aligned exactly 1 time 440749 (11.02%) aligned >1 times 81.03% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 257714 / 3241123 = 0.0795 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 04:12:57: # Command line: callpeak -t SRX1388760.bam -f BAM -g ce -n SRX1388760.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388760.05 # format = BAM # ChIP-seq file = ['SRX1388760.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 04:12:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:12:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:12:57: # Command line: callpeak -t SRX1388760.bam -f BAM -g ce -n SRX1388760.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388760.10 # format = BAM # ChIP-seq file = ['SRX1388760.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 04:12:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:12:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:12:57: # Command line: callpeak -t SRX1388760.bam -f BAM -g ce -n SRX1388760.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388760.20 # format = BAM # ChIP-seq file = ['SRX1388760.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 04:12:57: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:12:57: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:13:03: 1000000 INFO @ Sat, 03 Jun 2017 04:13:03: 1000000 INFO @ Sat, 03 Jun 2017 04:13:03: 1000000 INFO @ Sat, 03 Jun 2017 04:13:09: 2000000 INFO @ Sat, 03 Jun 2017 04:13:09: 2000000 INFO @ Sat, 03 Jun 2017 04:13:09: 2000000 INFO @ Sat, 03 Jun 2017 04:13:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:13:14: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:13:14: #1 total tags in treatment: 2983409 INFO @ Sat, 03 Jun 2017 04:13:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:13:14: #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 04:13:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:13:14: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:13:14: #1 total tags in treatment: 2983409 INFO @ Sat, 03 Jun 2017 04:13:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:13:14: #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 04:13:15: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:13:15: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:13:15: #1 total tags in treatment: 2983409 INFO @ Sat, 03 Jun 2017 04:13:15: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:13:15: #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 04:13:15: #1 tags after filtering in treatment: 2983036 INFO @ Sat, 03 Jun 2017 04:13:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:13:15: #1 finished! INFO @ Sat, 03 Jun 2017 04:13:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:13:15: #1 tags after filtering in treatment: 2983036 INFO @ Sat, 03 Jun 2017 04:13:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:13:15: #1 finished! INFO @ Sat, 03 Jun 2017 04:13:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:13:15: #1 tags after filtering in treatment: 2983036 INFO @ Sat, 03 Jun 2017 04:13:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:13:15: #1 finished! INFO @ Sat, 03 Jun 2017 04:13:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:13:16: #2 number of paired peaks: 2354 INFO @ Sat, 03 Jun 2017 04:13:16: start model_add_line... INFO @ Sat, 03 Jun 2017 04:13:16: #2 number of paired peaks: 2354 INFO @ Sat, 03 Jun 2017 04:13:16: start model_add_line... INFO @ Sat, 03 Jun 2017 04:13:16: #2 number of paired peaks: 2354 INFO @ Sat, 03 Jun 2017 04:13:16: start model_add_line... INFO @ Sat, 03 Jun 2017 04:13:23: start X-correlation... INFO @ Sat, 03 Jun 2017 04:13:23: end of X-cor INFO @ Sat, 03 Jun 2017 04:13:23: #2 finished! INFO @ Sat, 03 Jun 2017 04:13:23: #2 predicted fragment length is 171 bps INFO @ Sat, 03 Jun 2017 04:13:23: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 03 Jun 2017 04:13:23: #2.2 Generate R script for model : SRX1388760.05_model.r INFO @ Sat, 03 Jun 2017 04:13:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:13:23: start X-correlation... INFO @ Sat, 03 Jun 2017 04:13:23: end of X-cor INFO @ Sat, 03 Jun 2017 04:13:23: #2 finished! INFO @ Sat, 03 Jun 2017 04:13:23: #2 predicted fragment length is 171 bps INFO @ Sat, 03 Jun 2017 04:13:23: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 03 Jun 2017 04:13:23: #2.2 Generate R script for model : SRX1388760.10_model.r INFO @ Sat, 03 Jun 2017 04:13:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:13:24: start X-correlation... INFO @ Sat, 03 Jun 2017 04:13:24: end of X-cor INFO @ Sat, 03 Jun 2017 04:13:24: #2 finished! INFO @ Sat, 03 Jun 2017 04:13:24: #2 predicted fragment length is 171 bps INFO @ Sat, 03 Jun 2017 04:13:24: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 03 Jun 2017 04:13:24: #2.2 Generate R script for model : SRX1388760.20_model.r INFO @ Sat, 03 Jun 2017 04:13:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:13:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:13:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:13:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:13:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:13:56: #4 Write output xls file... SRX1388760.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:13:56: #4 Write peak in narrowPeak format file... SRX1388760.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:13:56: #4 Write summits bed file... SRX1388760.20_summits.bed INFO @ Sat, 03 Jun 2017 04:13:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (326 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:13:57: #4 Write output xls file... SRX1388760.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:13:57: #4 Write peak in narrowPeak format file... SRX1388760.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:13:57: #4 Write summits bed file... SRX1388760.10_summits.bed INFO @ Sat, 03 Jun 2017 04:13:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (986 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:13:58: #4 Write output xls file... SRX1388760.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:13:58: #4 Write peak in narrowPeak format file... SRX1388760.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:13:58: #4 Write summits bed file... SRX1388760.05_summits.bed INFO @ Sat, 03 Jun 2017 04:13:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2367 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。