Job ID = 9036393 sra ファイルのダウンロード中... Completed: 223323K bytes transferred in 6 seconds (295470K 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 0 734 0 --:--:-- 0:00:07 --:--:-- 7020 100 38317 0 38317 0 0 4549 0 --:--:-- 0:00:08 --:--:-- 21599 100 65478 0 65478 0 0 7478 0 --:--:-- 0:00:08 --:--:-- 31091 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 6552081 spots for /home/okishinya/chipatlas/results/sacCer3/SRX211372/SRR636623.sra Written 6552081 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: 00:00:37 6552081 reads; of these: 6552081 (100.00%) were unpaired; of these: 5599569 (85.46%) aligned 0 times 757548 (11.56%) aligned exactly 1 time 194964 (2.98%) aligned >1 times 14.54% overall alignment rate Time searching: 00:00:37 Overall time: 00:00:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 430324 / 952512 = 0.4518 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 03:03:56: # Command line: callpeak -t SRX211372.bam -f BAM -g 12100000 -n SRX211372.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX211372.05 # format = BAM # ChIP-seq file = ['SRX211372.bam'] # control file = None # effective genome size = 1.21e+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 @ Sun, 04 Jun 2017 03:03:56: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:03:56: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:03:56: # Command line: callpeak -t SRX211372.bam -f BAM -g 12100000 -n SRX211372.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX211372.10 # format = BAM # ChIP-seq file = ['SRX211372.bam'] # control file = None # effective genome size = 1.21e+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 @ Sun, 04 Jun 2017 03:03:56: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:03:56: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:03:56: # Command line: callpeak -t SRX211372.bam -f BAM -g 12100000 -n SRX211372.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX211372.20 # format = BAM # ChIP-seq file = ['SRX211372.bam'] # control file = None # effective genome size = 1.21e+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 @ Sun, 04 Jun 2017 03:03:56: #1 read tag files... INFO @ Sun, 04 Jun 2017 03:03:56: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 03:03:59: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:03:59: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:03:59: #1 total tags in treatment: 522188 INFO @ Sun, 04 Jun 2017 03:03:59: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:03:59: #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 03:03:59: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:03:59: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:03:59: #1 total tags in treatment: 522188 INFO @ Sun, 04 Jun 2017 03:03:59: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:03:59: #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 03:03:59: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 03:03:59: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 03:03:59: #1 total tags in treatment: 522188 INFO @ Sun, 04 Jun 2017 03:03:59: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 03:03:59: #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 03:03:59: #1 tags after filtering in treatment: 520078 INFO @ Sun, 04 Jun 2017 03:03:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:03:59: #1 finished! INFO @ Sun, 04 Jun 2017 03:03:59: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:03:59: #1 tags after filtering in treatment: 520078 INFO @ Sun, 04 Jun 2017 03:03:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:03:59: #1 finished! INFO @ Sun, 04 Jun 2017 03:03:59: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:03:59: #1 tags after filtering in treatment: 520078 INFO @ Sun, 04 Jun 2017 03:03:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 03:03:59: #1 finished! INFO @ Sun, 04 Jun 2017 03:03:59: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 03:03:59: #2 number of paired peaks: 177 WARNING @ Sun, 04 Jun 2017 03:03:59: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sun, 04 Jun 2017 03:03:59: start model_add_line... INFO @ Sun, 04 Jun 2017 03:03:59: #2 number of paired peaks: 177 WARNING @ Sun, 04 Jun 2017 03:03:59: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sun, 04 Jun 2017 03:03:59: start model_add_line... INFO @ Sun, 04 Jun 2017 03:03:59: #2 number of paired peaks: 177 WARNING @ Sun, 04 Jun 2017 03:03:59: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sun, 04 Jun 2017 03:03:59: start model_add_line... INFO @ Sun, 04 Jun 2017 03:04:01: start X-correlation... INFO @ Sun, 04 Jun 2017 03:04:01: end of X-cor INFO @ Sun, 04 Jun 2017 03:04:01: #2 finished! INFO @ Sun, 04 Jun 2017 03:04:01: #2 predicted fragment length is 110 bps INFO @ Sun, 04 Jun 2017 03:04:01: #2 alternative fragment length(s) may be 0,35,59,87,110,129,202,236,281,336,378,430,452,467,515,540,575 bps INFO @ Sun, 04 Jun 2017 03:04:01: #2.2 Generate R script for model : SRX211372.20_model.r INFO @ Sun, 04 Jun 2017 03:04:01: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:04:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:04:01: start X-correlation... INFO @ Sun, 04 Jun 2017 03:04:01: end of X-cor INFO @ Sun, 04 Jun 2017 03:04:01: #2 finished! INFO @ Sun, 04 Jun 2017 03:04:01: #2 predicted fragment length is 110 bps INFO @ Sun, 04 Jun 2017 03:04:01: #2 alternative fragment length(s) may be 0,35,59,87,110,129,202,236,281,336,378,430,452,467,515,540,575 bps INFO @ Sun, 04 Jun 2017 03:04:01: #2.2 Generate R script for model : SRX211372.10_model.r INFO @ Sun, 04 Jun 2017 03:04:01: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:04:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:04:01: start X-correlation... INFO @ Sun, 04 Jun 2017 03:04:01: end of X-cor INFO @ Sun, 04 Jun 2017 03:04:01: #2 finished! INFO @ Sun, 04 Jun 2017 03:04:01: #2 predicted fragment length is 110 bps INFO @ Sun, 04 Jun 2017 03:04:01: #2 alternative fragment length(s) may be 0,35,59,87,110,129,202,236,281,336,378,430,452,467,515,540,575 bps INFO @ Sun, 04 Jun 2017 03:04:01: #2.2 Generate R script for model : SRX211372.05_model.r INFO @ Sun, 04 Jun 2017 03:04:01: #3 Call peaks... INFO @ Sun, 04 Jun 2017 03:04:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 03:04:04: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:04:04: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:04:05: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 03:04:06: #4 Write output xls file... SRX211372.20_peaks.xls INFO @ Sun, 04 Jun 2017 03:04:06: #4 Write peak in narrowPeak format file... SRX211372.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:04:06: #4 Write output xls file... SRX211372.10_peaks.xls INFO @ Sun, 04 Jun 2017 03:04:06: #4 Write summits bed file... SRX211372.20_summits.bed INFO @ Sun, 04 Jun 2017 03:04:06: #4 Write peak in narrowPeak format file... SRX211372.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:04:06: Done! INFO @ Sun, 04 Jun 2017 03:04:06: #4 Write summits bed file... SRX211372.10_summits.bed INFO @ Sun, 04 Jun 2017 03:04:06: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 03:04:07: #4 Write output xls file... SRX211372.05_peaks.xls INFO @ Sun, 04 Jun 2017 03:04:07: #4 Write peak in narrowPeak format file... SRX211372.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 03:04:07: #4 Write summits bed file... SRX211372.05_summits.bed INFO @ Sun, 04 Jun 2017 03:04:07: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (21 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。