Job ID = 9029527 sra ファイルのダウンロード中... Completed: 142719K bytes transferred in 4 seconds (255081K 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 --:--:-- 0 101 5455 0 5455 0 0 756 0 --:--:-- 0:00:07 --:--:-- 8536 100 27350 0 27350 0 0 3332 0 --:--:-- 0:00:08 --:--:-- 16727 100 70466 0 70466 0 0 7797 0 --:--:-- 0:00:09 --:--:-- 28598 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 5631272 spots for /home/okishinya/chipatlas/results/dm3/SRX1816636/SRR3620837.sra Written 5631272 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: 00:01:37 5631272 reads; of these: 5631272 (100.00%) were unpaired; of these: 1351170 (23.99%) aligned 0 times 3766868 (66.89%) aligned exactly 1 time 513234 (9.11%) aligned >1 times 76.01% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 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_rmdupse_core] 3875762 / 4280102 = 0.9055 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 14:04:13: # Command line: callpeak -t SRX1816636.bam -f BAM -g dm -n SRX1816636.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1816636.20 # format = BAM # ChIP-seq file = ['SRX1816636.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 14:04:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:04:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:04:13: # Command line: callpeak -t SRX1816636.bam -f BAM -g dm -n SRX1816636.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1816636.05 # format = BAM # ChIP-seq file = ['SRX1816636.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 14:04:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:04:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:04:13: # Command line: callpeak -t SRX1816636.bam -f BAM -g dm -n SRX1816636.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1816636.10 # format = BAM # ChIP-seq file = ['SRX1816636.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 14:04:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:04:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:04:16: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:04:16: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:04:16: #1 total tags in treatment: 404340 INFO @ Sat, 03 Jun 2017 14:04:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:04:16: #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 14:04:17: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:04:17: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:04:17: #1 total tags in treatment: 404340 INFO @ Sat, 03 Jun 2017 14:04:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:04:17: #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 14:04:17: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:04:17: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:04:17: #1 total tags in treatment: 404340 INFO @ Sat, 03 Jun 2017 14:04:17: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:04:17: #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 14:04:17: #1 tags after filtering in treatment: 404000 INFO @ Sat, 03 Jun 2017 14:04:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:04:17: #1 finished! INFO @ Sat, 03 Jun 2017 14:04:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:04:17: #1 tags after filtering in treatment: 404000 INFO @ Sat, 03 Jun 2017 14:04:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:04:17: #1 finished! INFO @ Sat, 03 Jun 2017 14:04:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:04:17: #1 tags after filtering in treatment: 404000 INFO @ Sat, 03 Jun 2017 14:04:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:04:17: #1 finished! INFO @ Sat, 03 Jun 2017 14:04:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:04:17: #2 number of paired peaks: 3257 INFO @ Sat, 03 Jun 2017 14:04:17: start model_add_line... INFO @ Sat, 03 Jun 2017 14:04:17: #2 number of paired peaks: 3257 INFO @ Sat, 03 Jun 2017 14:04:17: start model_add_line... INFO @ Sat, 03 Jun 2017 14:04:17: #2 number of paired peaks: 3257 INFO @ Sat, 03 Jun 2017 14:04:17: start model_add_line... INFO @ Sat, 03 Jun 2017 14:04:18: start X-correlation... INFO @ Sat, 03 Jun 2017 14:04:18: end of X-cor INFO @ Sat, 03 Jun 2017 14:04:18: #2 finished! INFO @ Sat, 03 Jun 2017 14:04:18: #2 predicted fragment length is 177 bps INFO @ Sat, 03 Jun 2017 14:04:18: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 03 Jun 2017 14:04:18: #2.2 Generate R script for model : SRX1816636.10_model.r INFO @ Sat, 03 Jun 2017 14:04:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:04:19: start X-correlation... INFO @ Sat, 03 Jun 2017 14:04:19: end of X-cor INFO @ Sat, 03 Jun 2017 14:04:19: #2 finished! INFO @ Sat, 03 Jun 2017 14:04:19: #2 predicted fragment length is 177 bps INFO @ Sat, 03 Jun 2017 14:04:19: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 03 Jun 2017 14:04:19: #2.2 Generate R script for model : SRX1816636.05_model.r INFO @ Sat, 03 Jun 2017 14:04:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:04:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:04:19: start X-correlation... INFO @ Sat, 03 Jun 2017 14:04:19: end of X-cor INFO @ Sat, 03 Jun 2017 14:04:19: #2 finished! INFO @ Sat, 03 Jun 2017 14:04:19: #2 predicted fragment length is 177 bps INFO @ Sat, 03 Jun 2017 14:04:19: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 03 Jun 2017 14:04:19: #2.2 Generate R script for model : SRX1816636.20_model.r INFO @ Sat, 03 Jun 2017 14:04:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:04:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:04:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:04:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:04:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 14:04:24: #4 Write output xls file... SRX1816636.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:24: #4 Write peak in narrowPeak format file... SRX1816636.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:24: #4 Write summits bed file... SRX1816636.10_summits.bed INFO @ Sat, 03 Jun 2017 14:04:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1523 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:24: #4 Write output xls file... SRX1816636.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:24: #4 Write peak in narrowPeak format file... SRX1816636.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:24: #4 Write summits bed file... SRX1816636.05_summits.bed INFO @ Sat, 03 Jun 2017 14:04:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2231 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:25: #4 Write output xls file... SRX1816636.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:25: #4 Write peak in narrowPeak format file... SRX1816636.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:25: #4 Write summits bed file... SRX1816636.20_summits.bed INFO @ Sat, 03 Jun 2017 14:04:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (690 records, 4 fields): 3 millis CompletedMACS2peakCalling