Job ID = 9025507 sra ファイルのダウンロード中... Completed: 94141K bytes transferred in 3 seconds (203389K 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 1048 0 --:--:-- 0:00:07 --:--:-- 8600 100 30318 0 30318 0 0 3724 0 --:--:-- 0:00:08 --:--:-- 17616 100 45848 0 45848 0 0 5411 0 --:--:-- 0:00:08 --:--:-- 22353 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 4071852 spots for /home/okishinya/chipatlas/results/ce10/SRX1388756/SRR2832472.sra Written 4071852 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: 00:01:01 4071852 reads; of these: 4071852 (100.00%) were unpaired; of these: 137818 (3.38%) aligned 0 times 3466798 (85.14%) aligned exactly 1 time 467236 (11.47%) aligned >1 times 96.62% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 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_rmdupse_core] 321251 / 3934034 = 0.0817 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 04:11:25: # Command line: callpeak -t SRX1388756.bam -f BAM -g ce -n SRX1388756.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388756.10 # format = BAM # ChIP-seq file = ['SRX1388756.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 04:11:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:11:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:11:26: # Command line: callpeak -t SRX1388756.bam -f BAM -g ce -n SRX1388756.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388756.05 # format = BAM # ChIP-seq file = ['SRX1388756.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 04:11:26: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:11:26: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:11:26: # Command line: callpeak -t SRX1388756.bam -f BAM -g ce -n SRX1388756.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388756.20 # format = BAM # ChIP-seq file = ['SRX1388756.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 04:11:26: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:11:26: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:11:31: 1000000 INFO @ Sat, 03 Jun 2017 04:11:32: 1000000 INFO @ Sat, 03 Jun 2017 04:11:32: 1000000 INFO @ Sat, 03 Jun 2017 04:11:37: 2000000 INFO @ Sat, 03 Jun 2017 04:11:39: 2000000 INFO @ Sat, 03 Jun 2017 04:11:39: 2000000 INFO @ Sat, 03 Jun 2017 04:11:43: 3000000 INFO @ Sat, 03 Jun 2017 04:11:46: 3000000 INFO @ Sat, 03 Jun 2017 04:11:46: 3000000 INFO @ Sat, 03 Jun 2017 04:11:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:11:47: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:11:47: #1 total tags in treatment: 3612783 INFO @ Sat, 03 Jun 2017 04:11:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:11:47: #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 04:11:47: #1 tags after filtering in treatment: 3612261 INFO @ Sat, 03 Jun 2017 04:11:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:11:47: #1 finished! INFO @ Sat, 03 Jun 2017 04:11:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:11:48: #2 number of paired peaks: 3729 INFO @ Sat, 03 Jun 2017 04:11:48: start model_add_line... INFO @ Sat, 03 Jun 2017 04:11:50: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:11:50: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:11:50: #1 total tags in treatment: 3612783 INFO @ Sat, 03 Jun 2017 04:11:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:11:50: #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 04:11:50: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:11:50: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:11:50: #1 total tags in treatment: 3612783 INFO @ Sat, 03 Jun 2017 04:11:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:11:50: #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 04:11:51: #1 tags after filtering in treatment: 3612261 INFO @ Sat, 03 Jun 2017 04:11:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:11:51: #1 finished! INFO @ Sat, 03 Jun 2017 04:11:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:11:51: #1 tags after filtering in treatment: 3612261 INFO @ Sat, 03 Jun 2017 04:11:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:11:51: #1 finished! INFO @ Sat, 03 Jun 2017 04:11:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:11:52: #2 number of paired peaks: 3729 INFO @ Sat, 03 Jun 2017 04:11:52: start model_add_line... INFO @ Sat, 03 Jun 2017 04:11:52: #2 number of paired peaks: 3729 INFO @ Sat, 03 Jun 2017 04:11:52: start model_add_line... INFO @ Sat, 03 Jun 2017 04:12:03: start X-correlation... INFO @ Sat, 03 Jun 2017 04:12:03: end of X-cor INFO @ Sat, 03 Jun 2017 04:12:03: #2 finished! INFO @ Sat, 03 Jun 2017 04:12:03: #2 predicted fragment length is 180 bps INFO @ Sat, 03 Jun 2017 04:12:03: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 03 Jun 2017 04:12:03: #2.2 Generate R script for model : SRX1388756.10_model.r INFO @ Sat, 03 Jun 2017 04:12:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:12:07: start X-correlation... INFO @ Sat, 03 Jun 2017 04:12:07: start X-correlation... INFO @ Sat, 03 Jun 2017 04:12:07: end of X-cor INFO @ Sat, 03 Jun 2017 04:12:07: #2 finished! INFO @ Sat, 03 Jun 2017 04:12:07: #2 predicted fragment length is 180 bps INFO @ Sat, 03 Jun 2017 04:12:07: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 03 Jun 2017 04:12:07: #2.2 Generate R script for model : SRX1388756.20_model.r INFO @ Sat, 03 Jun 2017 04:12:07: end of X-cor INFO @ Sat, 03 Jun 2017 04:12:07: #2 finished! INFO @ Sat, 03 Jun 2017 04:12:07: #2 predicted fragment length is 180 bps INFO @ Sat, 03 Jun 2017 04:12:07: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 03 Jun 2017 04:12:07: #2.2 Generate R script for model : SRX1388756.05_model.r INFO @ Sat, 03 Jun 2017 04:12:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:12:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:12:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:12:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:12:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:12:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:12:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:12:43: #4 Write output xls file... SRX1388756.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:12:43: #4 Write peak in narrowPeak format file... SRX1388756.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:12:43: #4 Write summits bed file... SRX1388756.10_summits.bed INFO @ Sat, 03 Jun 2017 04:12:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1531 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:12:47: #4 Write output xls file... SRX1388756.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:12:47: #4 Write peak in narrowPeak format file... SRX1388756.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:12:47: #4 Write summits bed file... SRX1388756.20_summits.bed INFO @ Sat, 03 Jun 2017 04:12:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (560 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:12:50: #4 Write output xls file... SRX1388756.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:12:50: #4 Write peak in narrowPeak format file... SRX1388756.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:12:50: #4 Write summits bed file... SRX1388756.05_summits.bed INFO @ Sat, 03 Jun 2017 04:12:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2982 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。