Job ID = 11244999 sra ファイルのダウンロード中... Completed: 235097K bytes transferred in 6 seconds (290666K 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 6918453 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554712/SRR7696385.sra Written 6918453 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554712/SRR7696385.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: 00:03:37 6918453 reads; of these: 6918453 (100.00%) were paired; of these: 4199252 (60.70%) aligned concordantly 0 times 1508802 (21.81%) aligned concordantly exactly 1 time 1210399 (17.50%) aligned concordantly >1 times ---- 4199252 pairs aligned concordantly 0 times; of these: 1198 (0.03%) aligned discordantly 1 time ---- 4198054 pairs aligned 0 times concordantly or discordantly; of these: 8396108 mates make up the pairs; of these: 6317529 (75.24%) aligned 0 times 1232457 (14.68%) aligned exactly 1 time 846122 (10.08%) aligned >1 times 54.34% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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_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] 814116 / 2720061 = 0.2993 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 23:09:18: # Command line: callpeak -t SRX4554712.bam -f BAM -g 12100000 -n SRX4554712.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554712.05 # format = BAM # ChIP-seq file = ['SRX4554712.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 23:09:18: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:09:18: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:09:18: # Command line: callpeak -t SRX4554712.bam -f BAM -g 12100000 -n SRX4554712.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554712.20 # format = BAM # ChIP-seq file = ['SRX4554712.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 23:09:18: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:09:18: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:09:18: # Command line: callpeak -t SRX4554712.bam -f BAM -g 12100000 -n SRX4554712.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554712.10 # format = BAM # ChIP-seq file = ['SRX4554712.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 23:09:18: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:09:18: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:09:24: 1000000 INFO @ Tue, 09 Oct 2018 23:09:24: 1000000 INFO @ Tue, 09 Oct 2018 23:09:24: 1000000 INFO @ Tue, 09 Oct 2018 23:09:29: 2000000 INFO @ Tue, 09 Oct 2018 23:09:30: 2000000 INFO @ Tue, 09 Oct 2018 23:09:30: 2000000 INFO @ Tue, 09 Oct 2018 23:09:35: 3000000 INFO @ Tue, 09 Oct 2018 23:09:37: 3000000 INFO @ Tue, 09 Oct 2018 23:09:37: 3000000 INFO @ Tue, 09 Oct 2018 23:09:40: 4000000 INFO @ Tue, 09 Oct 2018 23:09:42: 4000000 INFO @ Tue, 09 Oct 2018 23:09:42: 4000000 INFO @ Tue, 09 Oct 2018 23:09:45: 5000000 INFO @ Tue, 09 Oct 2018 23:09:48: 5000000 INFO @ Tue, 09 Oct 2018 23:09:48: 5000000 INFO @ Tue, 09 Oct 2018 23:09:50: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:09:50: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:09:50: #1 total tags in treatment: 1905100 INFO @ Tue, 09 Oct 2018 23:09:50: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:09:50: #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 23:09:50: #1 tags after filtering in treatment: 1001055 INFO @ Tue, 09 Oct 2018 23:09:50: #1 Redundant rate of treatment: 0.47 INFO @ Tue, 09 Oct 2018 23:09:50: #1 finished! INFO @ Tue, 09 Oct 2018 23:09:50: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:09:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:09:50: #2 number of paired peaks: 130 WARNING @ Tue, 09 Oct 2018 23:09:50: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Tue, 09 Oct 2018 23:09:50: start model_add_line... INFO @ Tue, 09 Oct 2018 23:09:50: start X-correlation... INFO @ Tue, 09 Oct 2018 23:09:50: end of X-cor INFO @ Tue, 09 Oct 2018 23:09:50: #2 finished! INFO @ Tue, 09 Oct 2018 23:09:50: #2 predicted fragment length is 176 bps INFO @ Tue, 09 Oct 2018 23:09:50: #2 alternative fragment length(s) may be 1,136,156,176,200,219,232,320,353,454,507,553,565 bps INFO @ Tue, 09 Oct 2018 23:09:50: #2.2 Generate R script for model : SRX4554712.10_model.r INFO @ Tue, 09 Oct 2018 23:09:50: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:09:53: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:09:53: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:09:53: #1 total tags in treatment: 1905100 INFO @ Tue, 09 Oct 2018 23:09:53: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:09:53: #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 23:09:53: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:09:53: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:09:53: #1 total tags in treatment: 1905100 INFO @ Tue, 09 Oct 2018 23:09:53: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:09:53: #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 23:09:53: #1 tags after filtering in treatment: 1001055 INFO @ Tue, 09 Oct 2018 23:09:53: #1 Redundant rate of treatment: 0.47 INFO @ Tue, 09 Oct 2018 23:09:53: #1 finished! INFO @ Tue, 09 Oct 2018 23:09:53: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:09:53: #1 tags after filtering in treatment: 1001055 INFO @ Tue, 09 Oct 2018 23:09:53: #1 Redundant rate of treatment: 0.47 INFO @ Tue, 09 Oct 2018 23:09:53: #1 finished! INFO @ Tue, 09 Oct 2018 23:09:53: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:09:54: #2 number of paired peaks: 130 INFO @ Tue, 09 Oct 2018 23:09:54: #2 number of paired peaks: 130 WARNING @ Tue, 09 Oct 2018 23:09:54: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! WARNING @ Tue, 09 Oct 2018 23:09:54: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Tue, 09 Oct 2018 23:09:54: start model_add_line... INFO @ Tue, 09 Oct 2018 23:09:54: start model_add_line... INFO @ Tue, 09 Oct 2018 23:09:54: start X-correlation... INFO @ Tue, 09 Oct 2018 23:09:54: start X-correlation... INFO @ Tue, 09 Oct 2018 23:09:54: end of X-cor INFO @ Tue, 09 Oct 2018 23:09:54: end of X-cor INFO @ Tue, 09 Oct 2018 23:09:54: #2 finished! INFO @ Tue, 09 Oct 2018 23:09:54: #2 finished! INFO @ Tue, 09 Oct 2018 23:09:54: #2 predicted fragment length is 176 bps INFO @ Tue, 09 Oct 2018 23:09:54: #2 predicted fragment length is 176 bps INFO @ Tue, 09 Oct 2018 23:09:54: #2 alternative fragment length(s) may be 1,136,156,176,200,219,232,320,353,454,507,553,565 bps INFO @ Tue, 09 Oct 2018 23:09:54: #2 alternative fragment length(s) may be 1,136,156,176,200,219,232,320,353,454,507,553,565 bps INFO @ Tue, 09 Oct 2018 23:09:54: #2.2 Generate R script for model : SRX4554712.05_model.r INFO @ Tue, 09 Oct 2018 23:09:54: #2.2 Generate R script for model : SRX4554712.20_model.r INFO @ Tue, 09 Oct 2018 23:09:54: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:09:54: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:09:54: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:09:55: #4 Write output xls file... SRX4554712.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:09:55: #4 Write peak in narrowPeak format file... SRX4554712.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:09:55: #4 Write summits bed file... SRX4554712.10_summits.bed INFO @ Tue, 09 Oct 2018 23:09:55: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (26 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:09:58: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:09:58: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:09:59: #4 Write output xls file... SRX4554712.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:09:59: #4 Write peak in narrowPeak format file... SRX4554712.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:09:59: #4 Write summits bed file... SRX4554712.20_summits.bed INFO @ Tue, 09 Oct 2018 23:09:59: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:09:59: #4 Write output xls file... SRX4554712.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:09:59: #4 Write peak in narrowPeak format file... SRX4554712.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:09:59: #4 Write summits bed file... SRX4554712.05_summits.bed INFO @ Tue, 09 Oct 2018 23:09:59: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (123 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。