Job ID = 9031877 sra ファイルのダウンロード中... Completed: 963545K bytes transferred in 10 seconds (743714K 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 --:--:-- 0 100 7663 0 7663 0 0 1043 0 --:--:-- 0:00:07 --:--:-- 9602 100 38318 0 38318 0 0 4596 0 --:--:-- 0:00:08 --:--:-- 21358 100 58914 0 58914 0 0 6796 0 --:--:-- 0:00:08 --:--:-- 27711 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 30181637 spots for /home/okishinya/chipatlas/results/dm3/SRX529167/SRR1265773.sra Written 30181637 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: 00:08:50 30181637 reads; of these: 30181637 (100.00%) were unpaired; of these: 701254 (2.32%) aligned 0 times 24664802 (81.72%) aligned exactly 1 time 4815581 (15.96%) aligned >1 times 97.68% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 11935318 / 29480383 = 0.4049 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 22:04:42: # Command line: callpeak -t SRX529167.bam -f BAM -g dm -n SRX529167.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX529167.20 # format = BAM # ChIP-seq file = ['SRX529167.bam'] # control file = None # effective genome size = 1.20e+08 # 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 22:04:42: #1 read tag files... INFO @ Sat, 03 Jun 2017 22:04:42: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 22:04:42: # Command line: callpeak -t SRX529167.bam -f BAM -g dm -n SRX529167.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX529167.10 # format = BAM # ChIP-seq file = ['SRX529167.bam'] # control file = None # effective genome size = 1.20e+08 # 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 22:04:42: #1 read tag files... INFO @ Sat, 03 Jun 2017 22:04:42: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 22:04:42: # Command line: callpeak -t SRX529167.bam -f BAM -g dm -n SRX529167.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX529167.05 # format = BAM # ChIP-seq file = ['SRX529167.bam'] # control file = None # effective genome size = 1.20e+08 # 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 22:04:42: #1 read tag files... INFO @ Sat, 03 Jun 2017 22:04:42: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 22:04:48: 1000000 INFO @ Sat, 03 Jun 2017 22:04:48: 1000000 INFO @ Sat, 03 Jun 2017 22:04:48: 1000000 INFO @ Sat, 03 Jun 2017 22:04:55: 2000000 INFO @ Sat, 03 Jun 2017 22:04:55: 2000000 INFO @ Sat, 03 Jun 2017 22:04:55: 2000000 INFO @ Sat, 03 Jun 2017 22:05:01: 3000000 INFO @ Sat, 03 Jun 2017 22:05:01: 3000000 INFO @ Sat, 03 Jun 2017 22:05:01: 3000000 INFO @ Sat, 03 Jun 2017 22:05:07: 4000000 INFO @ Sat, 03 Jun 2017 22:05:07: 4000000 INFO @ Sat, 03 Jun 2017 22:05:07: 4000000 INFO @ Sat, 03 Jun 2017 22:05:13: 5000000 INFO @ Sat, 03 Jun 2017 22:05:13: 5000000 INFO @ Sat, 03 Jun 2017 22:05:13: 5000000 INFO @ Sat, 03 Jun 2017 22:05:19: 6000000 INFO @ Sat, 03 Jun 2017 22:05:19: 6000000 INFO @ Sat, 03 Jun 2017 22:05:19: 6000000 INFO @ Sat, 03 Jun 2017 22:05:25: 7000000 INFO @ Sat, 03 Jun 2017 22:05:25: 7000000 INFO @ Sat, 03 Jun 2017 22:05:25: 7000000 INFO @ Sat, 03 Jun 2017 22:05:32: 8000000 INFO @ Sat, 03 Jun 2017 22:05:32: 8000000 INFO @ Sat, 03 Jun 2017 22:05:32: 8000000 INFO @ Sat, 03 Jun 2017 22:05:38: 9000000 INFO @ Sat, 03 Jun 2017 22:05:38: 9000000 INFO @ Sat, 03 Jun 2017 22:05:38: 9000000 INFO @ Sat, 03 Jun 2017 22:05:44: 10000000 INFO @ Sat, 03 Jun 2017 22:05:44: 10000000 INFO @ Sat, 03 Jun 2017 22:05:44: 10000000 INFO @ Sat, 03 Jun 2017 22:05:50: 11000000 INFO @ Sat, 03 Jun 2017 22:05:50: 11000000 INFO @ Sat, 03 Jun 2017 22:05:50: 11000000 INFO @ Sat, 03 Jun 2017 22:05:56: 12000000 INFO @ Sat, 03 Jun 2017 22:05:56: 12000000 INFO @ Sat, 03 Jun 2017 22:05:56: 12000000 INFO @ Sat, 03 Jun 2017 22:06:02: 13000000 INFO @ Sat, 03 Jun 2017 22:06:02: 13000000 INFO @ Sat, 03 Jun 2017 22:06:02: 13000000 INFO @ Sat, 03 Jun 2017 22:06:09: 14000000 INFO @ Sat, 03 Jun 2017 22:06:09: 14000000 INFO @ Sat, 03 Jun 2017 22:06:09: 14000000 INFO @ Sat, 03 Jun 2017 22:06:15: 15000000 INFO @ Sat, 03 Jun 2017 22:06:15: 15000000 INFO @ Sat, 03 Jun 2017 22:06:15: 15000000 INFO @ Sat, 03 Jun 2017 22:06:21: 16000000 INFO @ Sat, 03 Jun 2017 22:06:21: 16000000 INFO @ Sat, 03 Jun 2017 22:06:21: 16000000 INFO @ Sat, 03 Jun 2017 22:06:27: 17000000 INFO @ Sat, 03 Jun 2017 22:06:27: 17000000 INFO @ Sat, 03 Jun 2017 22:06:27: 17000000 INFO @ Sat, 03 Jun 2017 22:06:31: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 22:06:31: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 22:06:31: #1 total tags in treatment: 17545065 INFO @ Sat, 03 Jun 2017 22:06:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 22:06:31: #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 22:06:31: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 22:06:31: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 22:06:31: #1 total tags in treatment: 17545065 INFO @ Sat, 03 Jun 2017 22:06:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 22:06:31: #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 22:06:31: #1 tag size is determined as 49 bps INFO @ Sat, 03 Jun 2017 22:06:31: #1 tag size = 49 INFO @ Sat, 03 Jun 2017 22:06:31: #1 total tags in treatment: 17545065 INFO @ Sat, 03 Jun 2017 22:06:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 22:06:31: #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 22:06:34: #1 tags after filtering in treatment: 17537380 INFO @ Sat, 03 Jun 2017 22:06:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 22:06:34: #1 finished! INFO @ Sat, 03 Jun 2017 22:06:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 22:06:34: #1 tags after filtering in treatment: 17537380 INFO @ Sat, 03 Jun 2017 22:06:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 22:06:34: #1 finished! INFO @ Sat, 03 Jun 2017 22:06:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 22:06:34: #1 tags after filtering in treatment: 17537380 INFO @ Sat, 03 Jun 2017 22:06:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 22:06:34: #1 finished! INFO @ Sat, 03 Jun 2017 22:06:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 22:06:38: #2 number of paired peaks: 5953 INFO @ Sat, 03 Jun 2017 22:06:38: start model_add_line... INFO @ Sat, 03 Jun 2017 22:06:38: #2 number of paired peaks: 5953 INFO @ Sat, 03 Jun 2017 22:06:38: start model_add_line... INFO @ Sat, 03 Jun 2017 22:06:38: #2 number of paired peaks: 5953 INFO @ Sat, 03 Jun 2017 22:06:38: start model_add_line... INFO @ Sat, 03 Jun 2017 22:07:37: start X-correlation... INFO @ Sat, 03 Jun 2017 22:07:37: end of X-cor INFO @ Sat, 03 Jun 2017 22:07:37: #2 finished! INFO @ Sat, 03 Jun 2017 22:07:37: #2 predicted fragment length is 195 bps INFO @ Sat, 03 Jun 2017 22:07:37: #2 alternative fragment length(s) may be 4,195 bps INFO @ Sat, 03 Jun 2017 22:07:37: #2.2 Generate R script for model : SRX529167.10_model.r INFO @ Sat, 03 Jun 2017 22:07:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 22:07:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 22:07:38: start X-correlation... INFO @ Sat, 03 Jun 2017 22:07:38: end of X-cor INFO @ Sat, 03 Jun 2017 22:07:38: #2 finished! INFO @ Sat, 03 Jun 2017 22:07:38: #2 predicted fragment length is 195 bps INFO @ Sat, 03 Jun 2017 22:07:38: #2 alternative fragment length(s) may be 4,195 bps INFO @ Sat, 03 Jun 2017 22:07:38: #2.2 Generate R script for model : SRX529167.05_model.r INFO @ Sat, 03 Jun 2017 22:07:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 22:07:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 22:07:39: start X-correlation... INFO @ Sat, 03 Jun 2017 22:07:39: end of X-cor INFO @ Sat, 03 Jun 2017 22:07:39: #2 finished! INFO @ Sat, 03 Jun 2017 22:07:39: #2 predicted fragment length is 195 bps INFO @ Sat, 03 Jun 2017 22:07:39: #2 alternative fragment length(s) may be 4,195 bps INFO @ Sat, 03 Jun 2017 22:07:39: #2.2 Generate R script for model : SRX529167.20_model.r INFO @ Sat, 03 Jun 2017 22:07:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 22:07:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 22:09:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 22:09:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 22:09:19: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 22:10:20: #4 Write output xls file... SRX529167.20_peaks.xls INFO @ Sat, 03 Jun 2017 22:10:20: #4 Write peak in narrowPeak format file... SRX529167.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 22:10:20: #4 Write summits bed file... SRX529167.20_summits.bed INFO @ Sat, 03 Jun 2017 22:10:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4663 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 22:10:34: #4 Write output xls file... SRX529167.10_peaks.xls INFO @ Sat, 03 Jun 2017 22:10:34: #4 Write peak in narrowPeak format file... SRX529167.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 22:10:34: #4 Write summits bed file... SRX529167.10_summits.bed INFO @ Sat, 03 Jun 2017 22:10:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9282 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 22:10:50: #4 Write output xls file... SRX529167.05_peaks.xls INFO @ Sat, 03 Jun 2017 22:10:50: #4 Write peak in narrowPeak format file... SRX529167.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 22:10:51: #4 Write summits bed file... SRX529167.05_summits.bed INFO @ Sat, 03 Jun 2017 22:10:51: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13729 records, 4 fields): 18 millis CompletedMACS2peakCalling