Job ID = 9025632 sra ファイルのダウンロード中... Completed: 653295K bytes transferred in 8 seconds (615574K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:10 --:--:-- 0 100 21557 0 21557 0 0 1884 0 --:--:-- 0:00:11 --:--:-- 4266 100 46173 0 46173 0 0 3764 0 --:--:-- 0:00:12 --:--:-- 9461 100 64593 0 64593 0 0 5195 0 --:--:-- 0:00:12 --:--:-- 15972 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 19098144 spots for /home/okishinya/chipatlas/results/ce10/SRX208774/SRR628908.sra Written 19098144 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: 00:08:06 19098144 reads; of these: 19098144 (100.00%) were unpaired; of these: 2242494 (11.74%) aligned 0 times 13282142 (69.55%) aligned exactly 1 time 3573508 (18.71%) aligned >1 times 88.26% overall alignment rate Time searching: 00:08:06 Overall time: 00:08:06 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_sort_core] merging from 8 files... [bam_rmdupse_core] 12974796 / 16855650 = 0.7698 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 04:56:43: # Command line: callpeak -t SRX208774.bam -f BAM -g ce -n SRX208774.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208774.20 # format = BAM # ChIP-seq file = ['SRX208774.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 04:56:43: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:56:43: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:56:43: # Command line: callpeak -t SRX208774.bam -f BAM -g ce -n SRX208774.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208774.05 # format = BAM # ChIP-seq file = ['SRX208774.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 04:56:43: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:56:43: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:56:43: # Command line: callpeak -t SRX208774.bam -f BAM -g ce -n SRX208774.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208774.10 # format = BAM # ChIP-seq file = ['SRX208774.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 04:56:43: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:56:43: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:56:50: 1000000 INFO @ Sat, 03 Jun 2017 04:56:50: 1000000 INFO @ Sat, 03 Jun 2017 04:56:51: 1000000 INFO @ Sat, 03 Jun 2017 04:56:58: 2000000 INFO @ Sat, 03 Jun 2017 04:56:58: 2000000 INFO @ Sat, 03 Jun 2017 04:56:59: 2000000 INFO @ Sat, 03 Jun 2017 04:57:06: 3000000 INFO @ Sat, 03 Jun 2017 04:57:06: 3000000 INFO @ Sat, 03 Jun 2017 04:57:09: 3000000 INFO @ Sat, 03 Jun 2017 04:57:13: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:57:13: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:57:13: #1 total tags in treatment: 3880854 INFO @ Sat, 03 Jun 2017 04:57:13: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:57:13: #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 04:57:13: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:57:13: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:57:13: #1 total tags in treatment: 3880854 INFO @ Sat, 03 Jun 2017 04:57:13: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:57:13: #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 04:57:14: #1 tags after filtering in treatment: 3526715 INFO @ Sat, 03 Jun 2017 04:57:14: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 03 Jun 2017 04:57:14: #1 finished! INFO @ Sat, 03 Jun 2017 04:57:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:57:14: #1 tags after filtering in treatment: 3526715 INFO @ Sat, 03 Jun 2017 04:57:14: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 03 Jun 2017 04:57:14: #1 finished! INFO @ Sat, 03 Jun 2017 04:57:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:57:15: #2 number of paired peaks: 2104 INFO @ Sat, 03 Jun 2017 04:57:15: start model_add_line... INFO @ Sat, 03 Jun 2017 04:57:15: #2 number of paired peaks: 2104 INFO @ Sat, 03 Jun 2017 04:57:15: start model_add_line... INFO @ Sat, 03 Jun 2017 04:57:16: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:57:16: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:57:16: #1 total tags in treatment: 3880854 INFO @ Sat, 03 Jun 2017 04:57:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:57:16: #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 04:57:17: #1 tags after filtering in treatment: 3526715 INFO @ Sat, 03 Jun 2017 04:57:17: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 03 Jun 2017 04:57:17: #1 finished! INFO @ Sat, 03 Jun 2017 04:57:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:57:18: #2 number of paired peaks: 2104 INFO @ Sat, 03 Jun 2017 04:57:18: start model_add_line... INFO @ Sat, 03 Jun 2017 04:57:25: start X-correlation... INFO @ Sat, 03 Jun 2017 04:57:25: end of X-cor INFO @ Sat, 03 Jun 2017 04:57:25: #2 finished! INFO @ Sat, 03 Jun 2017 04:57:25: #2 predicted fragment length is 267 bps INFO @ Sat, 03 Jun 2017 04:57:25: #2 alternative fragment length(s) may be 267 bps INFO @ Sat, 03 Jun 2017 04:57:25: #2.2 Generate R script for model : SRX208774.05_model.r INFO @ Sat, 03 Jun 2017 04:57:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:57:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:57:25: start X-correlation... INFO @ Sat, 03 Jun 2017 04:57:25: end of X-cor INFO @ Sat, 03 Jun 2017 04:57:25: #2 finished! INFO @ Sat, 03 Jun 2017 04:57:25: #2 predicted fragment length is 267 bps INFO @ Sat, 03 Jun 2017 04:57:25: #2 alternative fragment length(s) may be 267 bps INFO @ Sat, 03 Jun 2017 04:57:25: #2.2 Generate R script for model : SRX208774.20_model.r INFO @ Sat, 03 Jun 2017 04:57:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:57:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:57:28: start X-correlation... INFO @ Sat, 03 Jun 2017 04:57:28: end of X-cor INFO @ Sat, 03 Jun 2017 04:57:28: #2 finished! INFO @ Sat, 03 Jun 2017 04:57:28: #2 predicted fragment length is 267 bps INFO @ Sat, 03 Jun 2017 04:57:28: #2 alternative fragment length(s) may be 267 bps INFO @ Sat, 03 Jun 2017 04:57:28: #2.2 Generate R script for model : SRX208774.10_model.r INFO @ Sat, 03 Jun 2017 04:57:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:57:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:57:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:57:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:57:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:58:07: #4 Write output xls file... SRX208774.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:58:07: #4 Write peak in narrowPeak format file... SRX208774.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:58:07: #4 Write summits bed file... SRX208774.20_summits.bed INFO @ Sat, 03 Jun 2017 04:58:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1426 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:58:09: #4 Write output xls file... SRX208774.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:58:09: #4 Write peak in narrowPeak format file... SRX208774.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:58:09: #4 Write summits bed file... SRX208774.05_summits.bed INFO @ Sat, 03 Jun 2017 04:58:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2265 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 04:58:13: #4 Write output xls file... SRX208774.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:58:13: #4 Write peak in narrowPeak format file... SRX208774.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:58:14: #4 Write summits bed file... SRX208774.10_summits.bed INFO @ Sat, 03 Jun 2017 04:58:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1842 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。