Job ID = 9028939 sra ファイルのダウンロード中... Completed: 222437K bytes transferred in 5 seconds (325515K 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 14324 0 14324 0 0 1793 0 --:--:-- 0:00:07 --:--:-- 10626 100 62318 0 62318 0 0 6937 0 --:--:-- 0:00:08 --:--:-- 26586 100 64566 0 64566 0 0 7187 0 --:--:-- 0:00:08 --:--:-- 27533 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 5610477 spots for /home/okishinya/chipatlas/results/dm3/SRX1038032/SRR2039661.sra Written 5610477 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:17 5610477 reads; of these: 5610477 (100.00%) were unpaired; of these: 3704165 (66.02%) aligned 0 times 1393313 (24.83%) aligned exactly 1 time 512999 (9.14%) aligned >1 times 33.98% overall alignment rate Time searching: 00:01:18 Overall time: 00:01:18 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] 664400 / 1906312 = 0.3485 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 12:27:20: # Command line: callpeak -t SRX1038032.bam -f BAM -g dm -n SRX1038032.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1038032.05 # format = BAM # ChIP-seq file = ['SRX1038032.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 12:27:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:20: # Command line: callpeak -t SRX1038032.bam -f BAM -g dm -n SRX1038032.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1038032.20 # format = BAM # ChIP-seq file = ['SRX1038032.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 12:27:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:20: # Command line: callpeak -t SRX1038032.bam -f BAM -g dm -n SRX1038032.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1038032.10 # format = BAM # ChIP-seq file = ['SRX1038032.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 12:27:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:27: 1000000 INFO @ Sat, 03 Jun 2017 12:27:27: 1000000 INFO @ Sat, 03 Jun 2017 12:27:27: 1000000 INFO @ Sat, 03 Jun 2017 12:27:29: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 12:27:29: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 12:27:29: #1 total tags in treatment: 1241912 INFO @ Sat, 03 Jun 2017 12:27:29: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:27:29: #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 12:27:29: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 12:27:29: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 12:27:29: #1 total tags in treatment: 1241912 INFO @ Sat, 03 Jun 2017 12:27:29: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:27:29: #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 12:27:29: #1 tags after filtering in treatment: 1241153 INFO @ Sat, 03 Jun 2017 12:27:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:27:29: #1 finished! INFO @ Sat, 03 Jun 2017 12:27:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:27:29: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 12:27:29: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 12:27:29: #1 total tags in treatment: 1241912 INFO @ Sat, 03 Jun 2017 12:27:29: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:27:29: #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 12:27:29: #1 tags after filtering in treatment: 1241153 INFO @ Sat, 03 Jun 2017 12:27:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:27:29: #1 finished! INFO @ Sat, 03 Jun 2017 12:27:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:27:29: #1 tags after filtering in treatment: 1241153 INFO @ Sat, 03 Jun 2017 12:27:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:27:29: #1 finished! INFO @ Sat, 03 Jun 2017 12:27:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:27:30: #2 number of paired peaks: 4582 INFO @ Sat, 03 Jun 2017 12:27:30: start model_add_line... INFO @ Sat, 03 Jun 2017 12:27:30: #2 number of paired peaks: 4582 INFO @ Sat, 03 Jun 2017 12:27:30: start model_add_line... INFO @ Sat, 03 Jun 2017 12:27:30: #2 number of paired peaks: 4582 INFO @ Sat, 03 Jun 2017 12:27:30: start model_add_line... INFO @ Sat, 03 Jun 2017 12:27:36: start X-correlation... INFO @ Sat, 03 Jun 2017 12:27:36: end of X-cor INFO @ Sat, 03 Jun 2017 12:27:36: #2 finished! INFO @ Sat, 03 Jun 2017 12:27:36: #2 predicted fragment length is 131 bps INFO @ Sat, 03 Jun 2017 12:27:36: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 03 Jun 2017 12:27:36: #2.2 Generate R script for model : SRX1038032.20_model.r INFO @ Sat, 03 Jun 2017 12:27:36: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:27:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:27:37: start X-correlation... INFO @ Sat, 03 Jun 2017 12:27:37: end of X-cor INFO @ Sat, 03 Jun 2017 12:27:37: #2 finished! INFO @ Sat, 03 Jun 2017 12:27:37: #2 predicted fragment length is 131 bps INFO @ Sat, 03 Jun 2017 12:27:37: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 03 Jun 2017 12:27:37: #2.2 Generate R script for model : SRX1038032.05_model.r INFO @ Sat, 03 Jun 2017 12:27:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:27:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:27:37: start X-correlation... INFO @ Sat, 03 Jun 2017 12:27:37: end of X-cor INFO @ Sat, 03 Jun 2017 12:27:37: #2 finished! INFO @ Sat, 03 Jun 2017 12:27:37: #2 predicted fragment length is 131 bps INFO @ Sat, 03 Jun 2017 12:27:37: #2 alternative fragment length(s) may be 131 bps INFO @ Sat, 03 Jun 2017 12:27:37: #2.2 Generate R script for model : SRX1038032.10_model.r INFO @ Sat, 03 Jun 2017 12:27:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:27:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:27:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:27:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:27:46: #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 12:27:51: #4 Write output xls file... SRX1038032.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:27:51: #4 Write peak in narrowPeak format file... SRX1038032.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:27:51: #4 Write summits bed file... SRX1038032.20_summits.bed INFO @ Sat, 03 Jun 2017 12:27:51: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (793 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:27:51: #4 Write output xls file... SRX1038032.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:27:51: #4 Write peak in narrowPeak format file... SRX1038032.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:27:52: #4 Write summits bed file... SRX1038032.05_summits.bed INFO @ Sat, 03 Jun 2017 12:27:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1804 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:27:52: #4 Write output xls file... SRX1038032.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:27:52: #4 Write peak in narrowPeak format file... SRX1038032.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:27:52: #4 Write summits bed file... SRX1038032.10_summits.bed INFO @ Sat, 03 Jun 2017 12:27:52: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1151 records, 4 fields): 3 millis CompletedMACS2peakCalling