Job ID = 11245008 sra ファイルのダウンロード中... Completed: 265229K bytes transferred in 7 seconds (280288K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Read 4775680 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554723/SRR7696396.sra Written 4775680 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554723/SRR7696396.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:02:46 4775680 reads; of these: 4775680 (100.00%) were paired; of these: 2391798 (50.08%) aligned concordantly 0 times 1996792 (41.81%) aligned concordantly exactly 1 time 387090 (8.11%) aligned concordantly >1 times ---- 2391798 pairs aligned concordantly 0 times; of these: 37256 (1.56%) aligned discordantly 1 time ---- 2354542 pairs aligned 0 times concordantly or discordantly; of these: 4709084 mates make up the pairs; of these: 4632985 (98.38%) aligned 0 times 47432 (1.01%) aligned exactly 1 time 28667 (0.61%) aligned >1 times 51.49% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 228415 / 2413697 = 0.0946 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 @ Tue, 09 Oct 2018 23:10:00: # Command line: callpeak -t SRX4554723.bam -f BAM -g 12100000 -n SRX4554723.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554723.05 # format = BAM # ChIP-seq file = ['SRX4554723.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 # Paired-End mode is off INFO @ Tue, 09 Oct 2018 23:10:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:10:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:10:00: # Command line: callpeak -t SRX4554723.bam -f BAM -g 12100000 -n SRX4554723.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554723.20 # format = BAM # ChIP-seq file = ['SRX4554723.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 # Paired-End mode is off INFO @ Tue, 09 Oct 2018 23:10:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:10:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:10:00: # Command line: callpeak -t SRX4554723.bam -f BAM -g 12100000 -n SRX4554723.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554723.10 # format = BAM # ChIP-seq file = ['SRX4554723.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 # Paired-End mode is off INFO @ Tue, 09 Oct 2018 23:10:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:10:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:10:06: 1000000 INFO @ Tue, 09 Oct 2018 23:10:06: 1000000 INFO @ Tue, 09 Oct 2018 23:10:07: 1000000 INFO @ Tue, 09 Oct 2018 23:10:13: 2000000 INFO @ Tue, 09 Oct 2018 23:10:13: 2000000 INFO @ Tue, 09 Oct 2018 23:10:14: 2000000 INFO @ Tue, 09 Oct 2018 23:10:20: 3000000 INFO @ Tue, 09 Oct 2018 23:10:20: 3000000 INFO @ Tue, 09 Oct 2018 23:10:22: 3000000 INFO @ Tue, 09 Oct 2018 23:10:27: 4000000 INFO @ Tue, 09 Oct 2018 23:10:27: 4000000 INFO @ Tue, 09 Oct 2018 23:10:29: 4000000 INFO @ Tue, 09 Oct 2018 23:10:30: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:10:30: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:10:30: #1 total tags in treatment: 2156977 INFO @ Tue, 09 Oct 2018 23:10:30: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:10:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:10:30: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:10:30: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:10:30: #1 total tags in treatment: 2156977 INFO @ Tue, 09 Oct 2018 23:10:30: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:10:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:10:30: #1 tags after filtering in treatment: 988776 INFO @ Tue, 09 Oct 2018 23:10:30: #1 Redundant rate of treatment: 0.54 INFO @ Tue, 09 Oct 2018 23:10:30: #1 finished! INFO @ Tue, 09 Oct 2018 23:10:30: #1 tags after filtering in treatment: 988776 INFO @ Tue, 09 Oct 2018 23:10:30: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:10:30: #1 Redundant rate of treatment: 0.54 INFO @ Tue, 09 Oct 2018 23:10:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:10:30: #1 finished! INFO @ Tue, 09 Oct 2018 23:10:30: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:10:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:10:30: #2 number of paired peaks: 912 WARNING @ Tue, 09 Oct 2018 23:10:30: Fewer paired peaks (912) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 912 pairs to build model! INFO @ Tue, 09 Oct 2018 23:10:30: start model_add_line... INFO @ Tue, 09 Oct 2018 23:10:30: #2 number of paired peaks: 912 WARNING @ Tue, 09 Oct 2018 23:10:30: Fewer paired peaks (912) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 912 pairs to build model! INFO @ Tue, 09 Oct 2018 23:10:30: start model_add_line... INFO @ Tue, 09 Oct 2018 23:10:30: start X-correlation... INFO @ Tue, 09 Oct 2018 23:10:30: start X-correlation... INFO @ Tue, 09 Oct 2018 23:10:30: end of X-cor INFO @ Tue, 09 Oct 2018 23:10:30: end of X-cor INFO @ Tue, 09 Oct 2018 23:10:30: #2 finished! INFO @ Tue, 09 Oct 2018 23:10:30: #2 finished! INFO @ Tue, 09 Oct 2018 23:10:30: #2 predicted fragment length is 151 bps INFO @ Tue, 09 Oct 2018 23:10:30: #2 predicted fragment length is 151 bps INFO @ Tue, 09 Oct 2018 23:10:30: #2 alternative fragment length(s) may be 0,127,151,225,252,270,288,462 bps INFO @ Tue, 09 Oct 2018 23:10:30: #2 alternative fragment length(s) may be 0,127,151,225,252,270,288,462 bps INFO @ Tue, 09 Oct 2018 23:10:30: #2.2 Generate R script for model : SRX4554723.05_model.r INFO @ Tue, 09 Oct 2018 23:10:30: #2.2 Generate R script for model : SRX4554723.20_model.r INFO @ Tue, 09 Oct 2018 23:10:30: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:10:30: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:10:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:10:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:10:32: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:10:32: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:10:32: #1 total tags in treatment: 2156977 INFO @ Tue, 09 Oct 2018 23:10:32: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:10:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:10:32: #1 tags after filtering in treatment: 988776 INFO @ Tue, 09 Oct 2018 23:10:32: #1 Redundant rate of treatment: 0.54 INFO @ Tue, 09 Oct 2018 23:10:32: #1 finished! INFO @ Tue, 09 Oct 2018 23:10:32: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:10:33: #2 number of paired peaks: 912 WARNING @ Tue, 09 Oct 2018 23:10:33: Fewer paired peaks (912) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 912 pairs to build model! INFO @ Tue, 09 Oct 2018 23:10:33: start model_add_line... INFO @ Tue, 09 Oct 2018 23:10:33: start X-correlation... INFO @ Tue, 09 Oct 2018 23:10:33: end of X-cor INFO @ Tue, 09 Oct 2018 23:10:33: #2 finished! INFO @ Tue, 09 Oct 2018 23:10:33: #2 predicted fragment length is 151 bps INFO @ Tue, 09 Oct 2018 23:10:33: #2 alternative fragment length(s) may be 0,127,151,225,252,270,288,462 bps INFO @ Tue, 09 Oct 2018 23:10:33: #2.2 Generate R script for model : SRX4554723.10_model.r INFO @ Tue, 09 Oct 2018 23:10:33: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:10:35: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:10:35: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:10:36: #4 Write output xls file... SRX4554723.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:10:36: #4 Write peak in narrowPeak format file... SRX4554723.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:10:36: #4 Write summits bed file... SRX4554723.20_summits.bed INFO @ Tue, 09 Oct 2018 23:10:36: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (133 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:10:36: #4 Write output xls file... SRX4554723.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:10:36: #4 Write peak in narrowPeak format file... SRX4554723.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:10:36: #4 Write summits bed file... SRX4554723.05_summits.bed INFO @ Tue, 09 Oct 2018 23:10:36: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (550 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:10:38: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:10:39: #4 Write output xls file... SRX4554723.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:10:39: #4 Write peak in narrowPeak format file... SRX4554723.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:10:39: #4 Write summits bed file... SRX4554723.10_summits.bed INFO @ Tue, 09 Oct 2018 23:10:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (405 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。