Job ID = 9025648 sra ファイルのダウンロード中... Completed: 102489K bytes transferred in 4 seconds (187309K 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 23766 0 23766 0 0 2843 0 --:--:-- 0:00:08 --:--:-- 12125 100 46687 0 46687 0 0 5247 0 --:--:-- 0:00:08 --:--:-- 18682 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 4398420 spots for /home/okishinya/chipatlas/results/ce10/SRX2144174/SRR4188778.sra Written 4398420 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: 00:00:59 4398420 reads; of these: 4398420 (100.00%) were unpaired; of these: 446438 (10.15%) aligned 0 times 3470246 (78.90%) aligned exactly 1 time 481736 (10.95%) aligned >1 times 89.85% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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] 250158 / 3951982 = 0.0633 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 04:48:14: # Command line: callpeak -t SRX2144174.bam -f BAM -g ce -n SRX2144174.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144174.05 # format = BAM # ChIP-seq file = ['SRX2144174.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 04:48:14: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:48:14: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:48:14: # Command line: callpeak -t SRX2144174.bam -f BAM -g ce -n SRX2144174.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144174.10 # format = BAM # ChIP-seq file = ['SRX2144174.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 04:48:14: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:48:14: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:48:14: # Command line: callpeak -t SRX2144174.bam -f BAM -g ce -n SRX2144174.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144174.20 # format = BAM # ChIP-seq file = ['SRX2144174.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 04:48:14: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:48:14: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:48:20: 1000000 INFO @ Sat, 03 Jun 2017 04:48:20: 1000000 INFO @ Sat, 03 Jun 2017 04:48:21: 1000000 INFO @ Sat, 03 Jun 2017 04:48:26: 2000000 INFO @ Sat, 03 Jun 2017 04:48:26: 2000000 INFO @ Sat, 03 Jun 2017 04:48:27: 2000000 INFO @ Sat, 03 Jun 2017 04:48:31: 3000000 INFO @ Sat, 03 Jun 2017 04:48:33: 3000000 INFO @ Sat, 03 Jun 2017 04:48:34: 3000000 INFO @ Sat, 03 Jun 2017 04:48:35: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:48:35: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:48:35: #1 total tags in treatment: 3701824 INFO @ Sat, 03 Jun 2017 04:48:35: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:48:35: #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 04:48:36: #1 tags after filtering in treatment: 3701205 INFO @ Sat, 03 Jun 2017 04:48:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:48:36: #1 finished! INFO @ Sat, 03 Jun 2017 04:48:36: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:48:37: #2 number of paired peaks: 3506 INFO @ Sat, 03 Jun 2017 04:48:37: start model_add_line... INFO @ Sat, 03 Jun 2017 04:48:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:48:37: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:48:37: #1 total tags in treatment: 3701824 INFO @ Sat, 03 Jun 2017 04:48:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:48:37: #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 04:48:38: #1 tags after filtering in treatment: 3701205 INFO @ Sat, 03 Jun 2017 04:48:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:48:38: #1 finished! INFO @ Sat, 03 Jun 2017 04:48:38: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:48:38: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:48:38: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:48:38: #1 total tags in treatment: 3701824 INFO @ Sat, 03 Jun 2017 04:48:38: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:48:38: #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 04:48:39: #2 number of paired peaks: 3506 INFO @ Sat, 03 Jun 2017 04:48:39: start model_add_line... INFO @ Sat, 03 Jun 2017 04:48:39: #1 tags after filtering in treatment: 3701205 INFO @ Sat, 03 Jun 2017 04:48:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:48:39: #1 finished! INFO @ Sat, 03 Jun 2017 04:48:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:48:40: #2 number of paired peaks: 3506 INFO @ Sat, 03 Jun 2017 04:48:40: start model_add_line... INFO @ Sat, 03 Jun 2017 04:48:51: start X-correlation... INFO @ Sat, 03 Jun 2017 04:48:51: end of X-cor INFO @ Sat, 03 Jun 2017 04:48:51: #2 finished! INFO @ Sat, 03 Jun 2017 04:48:51: #2 predicted fragment length is 160 bps INFO @ Sat, 03 Jun 2017 04:48:51: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 03 Jun 2017 04:48:51: #2.2 Generate R script for model : SRX2144174.05_model.r INFO @ Sat, 03 Jun 2017 04:48:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:48:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:48:53: start X-correlation... INFO @ Sat, 03 Jun 2017 04:48:53: end of X-cor INFO @ Sat, 03 Jun 2017 04:48:53: #2 finished! INFO @ Sat, 03 Jun 2017 04:48:53: #2 predicted fragment length is 160 bps INFO @ Sat, 03 Jun 2017 04:48:53: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 03 Jun 2017 04:48:53: #2.2 Generate R script for model : SRX2144174.10_model.r INFO @ Sat, 03 Jun 2017 04:48:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:48:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:48:54: start X-correlation... INFO @ Sat, 03 Jun 2017 04:48:54: end of X-cor INFO @ Sat, 03 Jun 2017 04:48:54: #2 finished! INFO @ Sat, 03 Jun 2017 04:48:54: #2 predicted fragment length is 160 bps INFO @ Sat, 03 Jun 2017 04:48:54: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 03 Jun 2017 04:48:54: #2.2 Generate R script for model : SRX2144174.20_model.r INFO @ Sat, 03 Jun 2017 04:48:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:48:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:49:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:49:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:49:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:49:32: #4 Write output xls file... SRX2144174.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:49:32: #4 Write peak in narrowPeak format file... SRX2144174.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:49:32: #4 Write summits bed file... SRX2144174.05_summits.bed INFO @ Sat, 03 Jun 2017 04:49:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3193 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:49:32: #4 Write output xls file... SRX2144174.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:49:32: #4 Write peak in narrowPeak format file... SRX2144174.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:49:32: #4 Write summits bed file... SRX2144174.20_summits.bed INFO @ Sat, 03 Jun 2017 04:49:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (562 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:49:34: #4 Write output xls file... SRX2144174.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:49:34: #4 Write peak in narrowPeak format file... SRX2144174.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:49:34: #4 Write summits bed file... SRX2144174.10_summits.bed INFO @ Sat, 03 Jun 2017 04:49:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1471 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。