Job ID = 11244976 sra ファイルのダウンロード中... Completed: 163376K bytes transferred in 5 seconds (237896K 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 5158150 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554689/SRR7696362.sra Written 5158150 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554689/SRR7696362.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: 00:03:01 5158150 reads; of these: 5158150 (100.00%) were paired; of these: 3838835 (74.42%) aligned concordantly 0 times 969532 (18.80%) aligned concordantly exactly 1 time 349783 (6.78%) aligned concordantly >1 times ---- 3838835 pairs aligned concordantly 0 times; of these: 736 (0.02%) aligned discordantly 1 time ---- 3838099 pairs aligned 0 times concordantly or discordantly; of these: 7676198 mates make up the pairs; of these: 5110170 (66.57%) aligned 0 times 1947949 (25.38%) aligned exactly 1 time 618079 (8.05%) aligned >1 times 50.47% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 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] 252087 / 1319510 = 0.1910 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 23:01:34: # Command line: callpeak -t SRX4554689.bam -f BAM -g 12100000 -n SRX4554689.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554689.10 # format = BAM # ChIP-seq file = ['SRX4554689.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 23:01:34: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:01:34: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:01:34: # Command line: callpeak -t SRX4554689.bam -f BAM -g 12100000 -n SRX4554689.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554689.20 # format = BAM # ChIP-seq file = ['SRX4554689.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 23:01:34: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:01:34: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:01:34: # Command line: callpeak -t SRX4554689.bam -f BAM -g 12100000 -n SRX4554689.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554689.05 # format = BAM # ChIP-seq file = ['SRX4554689.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 23:01:34: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:01:34: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:01:40: 1000000 INFO @ Tue, 09 Oct 2018 23:01:40: 1000000 INFO @ Tue, 09 Oct 2018 23:01:40: 1000000 INFO @ Tue, 09 Oct 2018 23:01:46: 2000000 INFO @ Tue, 09 Oct 2018 23:01:46: 2000000 INFO @ Tue, 09 Oct 2018 23:01:47: 2000000 INFO @ Tue, 09 Oct 2018 23:01:52: 3000000 INFO @ Tue, 09 Oct 2018 23:01:52: 3000000 INFO @ Tue, 09 Oct 2018 23:01:53: 3000000 INFO @ Tue, 09 Oct 2018 23:01:58: 4000000 INFO @ Tue, 09 Oct 2018 23:01:58: 4000000 INFO @ Tue, 09 Oct 2018 23:01:59: 4000000 INFO @ Tue, 09 Oct 2018 23:02:02: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:02:02: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:02:02: #1 total tags in treatment: 1067234 INFO @ Tue, 09 Oct 2018 23:02:02: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:02:02: #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 23:02:02: #1 tags after filtering in treatment: 647452 INFO @ Tue, 09 Oct 2018 23:02:02: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 09 Oct 2018 23:02:02: #1 finished! INFO @ Tue, 09 Oct 2018 23:02:02: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:02:02: #2 number of paired peaks: 545 WARNING @ Tue, 09 Oct 2018 23:02:02: Fewer paired peaks (545) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 545 pairs to build model! INFO @ Tue, 09 Oct 2018 23:02:02: start model_add_line... INFO @ Tue, 09 Oct 2018 23:02:02: start X-correlation... INFO @ Tue, 09 Oct 2018 23:02:02: end of X-cor INFO @ Tue, 09 Oct 2018 23:02:02: #2 finished! INFO @ Tue, 09 Oct 2018 23:02:02: #2 predicted fragment length is 256 bps INFO @ Tue, 09 Oct 2018 23:02:02: #2 alternative fragment length(s) may be 1,222,256,281,572,592 bps INFO @ Tue, 09 Oct 2018 23:02:02: #2.2 Generate R script for model : SRX4554689.10_model.r INFO @ Tue, 09 Oct 2018 23:02:02: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:02:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:02:02: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:02:02: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:02:02: #1 total tags in treatment: 1067234 INFO @ Tue, 09 Oct 2018 23:02:02: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:02:02: #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 23:02:02: #1 tags after filtering in treatment: 647452 INFO @ Tue, 09 Oct 2018 23:02:02: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 09 Oct 2018 23:02:02: #1 finished! INFO @ Tue, 09 Oct 2018 23:02:02: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:02:03: #2 number of paired peaks: 545 WARNING @ Tue, 09 Oct 2018 23:02:03: Fewer paired peaks (545) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 545 pairs to build model! INFO @ Tue, 09 Oct 2018 23:02:03: start model_add_line... INFO @ Tue, 09 Oct 2018 23:02:03: start X-correlation... INFO @ Tue, 09 Oct 2018 23:02:03: end of X-cor INFO @ Tue, 09 Oct 2018 23:02:03: #2 finished! INFO @ Tue, 09 Oct 2018 23:02:03: #2 predicted fragment length is 256 bps INFO @ Tue, 09 Oct 2018 23:02:03: #2 alternative fragment length(s) may be 1,222,256,281,572,592 bps INFO @ Tue, 09 Oct 2018 23:02:03: #2.2 Generate R script for model : SRX4554689.20_model.r INFO @ Tue, 09 Oct 2018 23:02:03: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:02:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:02:03: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:02:03: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:02:03: #1 total tags in treatment: 1067234 INFO @ Tue, 09 Oct 2018 23:02:03: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:02:03: #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 23:02:03: #1 tags after filtering in treatment: 647452 INFO @ Tue, 09 Oct 2018 23:02:03: #1 Redundant rate of treatment: 0.39 INFO @ Tue, 09 Oct 2018 23:02:03: #1 finished! INFO @ Tue, 09 Oct 2018 23:02:03: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:02:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:02:03: #2 number of paired peaks: 545 WARNING @ Tue, 09 Oct 2018 23:02:03: Fewer paired peaks (545) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 545 pairs to build model! INFO @ Tue, 09 Oct 2018 23:02:03: start model_add_line... INFO @ Tue, 09 Oct 2018 23:02:03: start X-correlation... INFO @ Tue, 09 Oct 2018 23:02:03: end of X-cor INFO @ Tue, 09 Oct 2018 23:02:03: #2 finished! INFO @ Tue, 09 Oct 2018 23:02:03: #2 predicted fragment length is 256 bps INFO @ Tue, 09 Oct 2018 23:02:03: #2 alternative fragment length(s) may be 1,222,256,281,572,592 bps INFO @ Tue, 09 Oct 2018 23:02:03: #2.2 Generate R script for model : SRX4554689.05_model.r INFO @ Tue, 09 Oct 2018 23:02:03: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:02:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:02:06: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:02:06: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:02:07: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:02:07: #4 Write output xls file... SRX4554689.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:02:07: #4 Write peak in narrowPeak format file... SRX4554689.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:02:07: #4 Write summits bed file... SRX4554689.10_summits.bed INFO @ Tue, 09 Oct 2018 23:02:07: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis INFO @ Tue, 09 Oct 2018 23:02:07: #4 Write output xls file... SRX4554689.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:02:07: #4 Write peak in narrowPeak format file... SRX4554689.20_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:02:07: #4 Write summits bed file... SRX4554689.20_summits.bed INFO @ Tue, 09 Oct 2018 23:02:07: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:02:08: #4 Write output xls file... SRX4554689.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:02:08: #4 Write peak in narrowPeak format file... SRX4554689.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:02:08: #4 Write summits bed file... SRX4554689.05_summits.bed INFO @ Tue, 09 Oct 2018 23:02:08: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。