Job ID = 9033154 sra ファイルのダウンロード中... Completed: 580548K bytes transferred in 7 seconds (604330K 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 1077 0 --:--:-- 0:00:07 --:--:-- 10369 100 30317 0 30317 0 0 3738 0 --:--:-- 0:00:08 --:--:-- 17473 100 86317 0 86317 0 0 9478 0 --:--:-- 0:00:09 --:--:-- 31606 100 92005 0 92005 0 0 10102 0 --:--:-- 0:00:09 --:--:-- 33676 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 23459756 spots for /home/okishinya/chipatlas/results/dm3/SRX914962/SRR1873272.sra Written 23459756 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: 00:00:01 Multiseed full-index search: 00:02:43 23459756 reads; of these: 23459756 (100.00%) were unpaired; of these: 17244844 (73.51%) aligned 0 times 5609049 (23.91%) aligned exactly 1 time 605863 (2.58%) aligned >1 times 26.49% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 5011527 / 6214912 = 0.8064 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 @ Sun, 04 Jun 2017 00:09:47: # Command line: callpeak -t SRX914962.bam -f BAM -g dm -n SRX914962.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX914962.05 # format = BAM # ChIP-seq file = ['SRX914962.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 @ Sun, 04 Jun 2017 00:09:47: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:09:47: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:09:47: # Command line: callpeak -t SRX914962.bam -f BAM -g dm -n SRX914962.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX914962.10 # format = BAM # ChIP-seq file = ['SRX914962.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 @ Sun, 04 Jun 2017 00:09:47: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:09:47: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:09:47: # Command line: callpeak -t SRX914962.bam -f BAM -g dm -n SRX914962.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX914962.20 # format = BAM # ChIP-seq file = ['SRX914962.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 @ Sun, 04 Jun 2017 00:09:47: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:09:47: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:09:55: 1000000 INFO @ Sun, 04 Jun 2017 00:09:55: 1000000 INFO @ Sun, 04 Jun 2017 00:09:55: 1000000 INFO @ Sun, 04 Jun 2017 00:09:56: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:09:56: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:09:56: #1 total tags in treatment: 1203385 INFO @ Sun, 04 Jun 2017 00:09:56: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:09:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:09:56: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:09:56: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:09:56: #1 total tags in treatment: 1203385 INFO @ Sun, 04 Jun 2017 00:09:56: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:09:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:09:56: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:09:56: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:09:56: #1 total tags in treatment: 1203385 INFO @ Sun, 04 Jun 2017 00:09:56: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:09:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:09:57: #1 tags after filtering in treatment: 1203226 INFO @ Sun, 04 Jun 2017 00:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:09:57: #1 finished! INFO @ Sun, 04 Jun 2017 00:09:57: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:09:57: #1 tags after filtering in treatment: 1203226 INFO @ Sun, 04 Jun 2017 00:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:09:57: #1 finished! INFO @ Sun, 04 Jun 2017 00:09:57: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:09:57: #1 tags after filtering in treatment: 1203226 INFO @ Sun, 04 Jun 2017 00:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:09:57: #1 finished! INFO @ Sun, 04 Jun 2017 00:09:57: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:09:57: #2 number of paired peaks: 1037 INFO @ Sun, 04 Jun 2017 00:09:57: start model_add_line... INFO @ Sun, 04 Jun 2017 00:09:57: #2 number of paired peaks: 1037 INFO @ Sun, 04 Jun 2017 00:09:57: start model_add_line... INFO @ Sun, 04 Jun 2017 00:09:57: #2 number of paired peaks: 1037 INFO @ Sun, 04 Jun 2017 00:09:57: start model_add_line... INFO @ Sun, 04 Jun 2017 00:09:58: start X-correlation... INFO @ Sun, 04 Jun 2017 00:09:58: end of X-cor INFO @ Sun, 04 Jun 2017 00:09:58: #2 finished! INFO @ Sun, 04 Jun 2017 00:09:58: #2 predicted fragment length is 144 bps INFO @ Sun, 04 Jun 2017 00:09:58: #2 alternative fragment length(s) may be 144,185 bps INFO @ Sun, 04 Jun 2017 00:09:58: #2.2 Generate R script for model : SRX914962.20_model.r INFO @ Sun, 04 Jun 2017 00:09:58: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:09:58: start X-correlation... INFO @ Sun, 04 Jun 2017 00:09:58: end of X-cor INFO @ Sun, 04 Jun 2017 00:09:58: #2 finished! INFO @ Sun, 04 Jun 2017 00:09:58: #2 predicted fragment length is 144 bps INFO @ Sun, 04 Jun 2017 00:09:58: #2 alternative fragment length(s) may be 144,185 bps INFO @ Sun, 04 Jun 2017 00:09:58: #2.2 Generate R script for model : SRX914962.05_model.r INFO @ Sun, 04 Jun 2017 00:09:58: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:09:58: start X-correlation... INFO @ Sun, 04 Jun 2017 00:09:58: end of X-cor INFO @ Sun, 04 Jun 2017 00:09:58: #2 finished! INFO @ Sun, 04 Jun 2017 00:09:58: #2 predicted fragment length is 144 bps INFO @ Sun, 04 Jun 2017 00:09:58: #2 alternative fragment length(s) may be 144,185 bps INFO @ Sun, 04 Jun 2017 00:09:58: #2.2 Generate R script for model : SRX914962.10_model.r INFO @ Sun, 04 Jun 2017 00:09:58: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:10:06: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:10:06: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:10:07: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:10:11: #4 Write output xls file... SRX914962.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:10:11: #4 Write peak in narrowPeak format file... SRX914962.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:10:11: #4 Write summits bed file... SRX914962.20_summits.bed INFO @ Sun, 04 Jun 2017 00:10:11: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (28 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:10:11: #4 Write output xls file... SRX914962.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:10:11: #4 Write peak in narrowPeak format file... SRX914962.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:10:11: #4 Write summits bed file... SRX914962.05_summits.bed INFO @ Sun, 04 Jun 2017 00:10:11: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (238 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:10:12: #4 Write output xls file... SRX914962.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:10:12: #4 Write peak in narrowPeak format file... SRX914962.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:10:12: #4 Write summits bed file... SRX914962.10_summits.bed INFO @ Sun, 04 Jun 2017 00:10:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (79 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。