Job ID = 9035939 sra ファイルのダウンロード中... Completed: 148533K bytes transferred in 4 seconds (262119K 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 6903 0 6903 0 0 974 0 --:--:-- 0:00:07 --:--:-- 9482 100 30318 0 30318 0 0 3752 0 --:--:-- 0:00:08 --:--:-- 17596 100 70318 0 70318 0 0 7747 0 --:--:-- 0:00:09 --:--:-- 25871 100 72988 0 72988 0 0 8041 0 --:--:-- 0:00:09 --:--:-- 26843 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 6829517 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1142471/SRR2155466.sra Written 6829517 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: 00:01:23 6829517 reads; of these: 6829517 (100.00%) were unpaired; of these: 2466412 (36.11%) aligned 0 times 3143898 (46.03%) aligned exactly 1 time 1219207 (17.85%) aligned >1 times 63.89% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 1848171 / 4363105 = 0.4236 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 01:58:09: # Command line: callpeak -t SRX1142471.bam -f BAM -g 12100000 -n SRX1142471.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1142471.05 # format = BAM # ChIP-seq file = ['SRX1142471.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 01:58:09: #1 read tag files... INFO @ Sun, 04 Jun 2017 01:58:09: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 01:58:09: # Command line: callpeak -t SRX1142471.bam -f BAM -g 12100000 -n SRX1142471.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1142471.10 # format = BAM # ChIP-seq file = ['SRX1142471.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 01:58:09: #1 read tag files... INFO @ Sun, 04 Jun 2017 01:58:09: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 01:58:09: # Command line: callpeak -t SRX1142471.bam -f BAM -g 12100000 -n SRX1142471.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1142471.20 # format = BAM # ChIP-seq file = ['SRX1142471.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 01:58:09: #1 read tag files... INFO @ Sun, 04 Jun 2017 01:58:09: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 01:58:14: 1000000 INFO @ Sun, 04 Jun 2017 01:58:14: 1000000 INFO @ Sun, 04 Jun 2017 01:58:14: 1000000 INFO @ Sun, 04 Jun 2017 01:58:19: 2000000 INFO @ Sun, 04 Jun 2017 01:58:19: 2000000 INFO @ Sun, 04 Jun 2017 01:58:19: 2000000 INFO @ Sun, 04 Jun 2017 01:58:22: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 01:58:22: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 01:58:22: #1 total tags in treatment: 2514934 INFO @ Sun, 04 Jun 2017 01:58:22: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 01:58:22: #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 01:58:22: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 01:58:22: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 01:58:22: #1 total tags in treatment: 2514934 INFO @ Sun, 04 Jun 2017 01:58:22: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 01:58:22: #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 01:58:22: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 01:58:22: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 01:58:22: #1 total tags in treatment: 2514934 INFO @ Sun, 04 Jun 2017 01:58:22: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 01:58:22: #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 01:58:22: #1 tags after filtering in treatment: 2513996 INFO @ Sun, 04 Jun 2017 01:58:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 01:58:22: #1 finished! INFO @ Sun, 04 Jun 2017 01:58:22: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 01:58:22: #1 tags after filtering in treatment: 2513996 INFO @ Sun, 04 Jun 2017 01:58:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 01:58:22: #1 finished! INFO @ Sun, 04 Jun 2017 01:58:22: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 01:58:23: #1 tags after filtering in treatment: 2513996 INFO @ Sun, 04 Jun 2017 01:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 01:58:23: #1 finished! INFO @ Sun, 04 Jun 2017 01:58:23: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 01:58:23: #2 number of paired peaks: 101 WARNING @ Sun, 04 Jun 2017 01:58:23: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sun, 04 Jun 2017 01:58:23: start model_add_line... INFO @ Sun, 04 Jun 2017 01:58:23: #2 number of paired peaks: 101 WARNING @ Sun, 04 Jun 2017 01:58:23: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sun, 04 Jun 2017 01:58:23: start model_add_line... INFO @ Sun, 04 Jun 2017 01:58:23: #2 number of paired peaks: 101 WARNING @ Sun, 04 Jun 2017 01:58:23: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sun, 04 Jun 2017 01:58:23: start model_add_line... INFO @ Sun, 04 Jun 2017 01:58:24: start X-correlation... INFO @ Sun, 04 Jun 2017 01:58:25: end of X-cor INFO @ Sun, 04 Jun 2017 01:58:25: #2 finished! INFO @ Sun, 04 Jun 2017 01:58:25: #2 predicted fragment length is 127 bps INFO @ Sun, 04 Jun 2017 01:58:25: #2 alternative fragment length(s) may be 3,97,127 bps INFO @ Sun, 04 Jun 2017 01:58:25: #2.2 Generate R script for model : SRX1142471.10_model.r INFO @ Sun, 04 Jun 2017 01:58:25: #3 Call peaks... INFO @ Sun, 04 Jun 2017 01:58:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 01:58:25: start X-correlation... INFO @ Sun, 04 Jun 2017 01:58:25: end of X-cor INFO @ Sun, 04 Jun 2017 01:58:25: #2 finished! INFO @ Sun, 04 Jun 2017 01:58:25: #2 predicted fragment length is 127 bps INFO @ Sun, 04 Jun 2017 01:58:25: #2 alternative fragment length(s) may be 3,97,127 bps INFO @ Sun, 04 Jun 2017 01:58:25: #2.2 Generate R script for model : SRX1142471.20_model.r INFO @ Sun, 04 Jun 2017 01:58:25: #3 Call peaks... INFO @ Sun, 04 Jun 2017 01:58:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 01:58:25: start X-correlation... INFO @ Sun, 04 Jun 2017 01:58:25: end of X-cor INFO @ Sun, 04 Jun 2017 01:58:25: #2 finished! INFO @ Sun, 04 Jun 2017 01:58:25: #2 predicted fragment length is 127 bps INFO @ Sun, 04 Jun 2017 01:58:25: #2 alternative fragment length(s) may be 3,97,127 bps INFO @ Sun, 04 Jun 2017 01:58:25: #2.2 Generate R script for model : SRX1142471.05_model.r INFO @ Sun, 04 Jun 2017 01:58:25: #3 Call peaks... INFO @ Sun, 04 Jun 2017 01:58:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 01:58:38: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 01:58:38: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 01:58:38: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 01:58:47: #4 Write output xls file... SRX1142471.10_peaks.xls INFO @ Sun, 04 Jun 2017 01:58:47: #4 Write peak in narrowPeak format file... SRX1142471.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 01:58:47: #4 Write summits bed file... SRX1142471.10_summits.bed INFO @ Sun, 04 Jun 2017 01:58:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (394 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 01:58:47: #4 Write output xls file... SRX1142471.20_peaks.xls INFO @ Sun, 04 Jun 2017 01:58:47: #4 Write peak in narrowPeak format file... SRX1142471.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 01:58:47: #4 Write summits bed file... SRX1142471.20_summits.bed INFO @ Sun, 04 Jun 2017 01:58:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 01:58:47: #4 Write output xls file... SRX1142471.05_peaks.xls INFO @ Sun, 04 Jun 2017 01:58:47: #4 Write peak in narrowPeak format file... SRX1142471.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 01:58:47: #4 Write summits bed file... SRX1142471.05_summits.bed INFO @ Sun, 04 Jun 2017 01:58:47: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (671 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。