Job ID = 11245034 sra ファイルのダウンロード中... Completed: 167074K bytes transferred in 5 seconds (252057K 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 3395259 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554747/SRR7696420.sra Written 3395259 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554747/SRR7696420.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: 00:02:04 3395259 reads; of these: 3395259 (100.00%) were paired; of these: 1145267 (33.73%) aligned concordantly 0 times 1942642 (57.22%) aligned concordantly exactly 1 time 307350 (9.05%) aligned concordantly >1 times ---- 1145267 pairs aligned concordantly 0 times; of these: 12139 (1.06%) aligned discordantly 1 time ---- 1133128 pairs aligned 0 times concordantly or discordantly; of these: 2266256 mates make up the pairs; of these: 2220225 (97.97%) aligned 0 times 34974 (1.54%) aligned exactly 1 time 11057 (0.49%) aligned >1 times 67.30% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 281023 / 2258485 = 0.1244 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 23:14:20: # Command line: callpeak -t SRX4554747.bam -f BAM -g 12100000 -n SRX4554747.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554747.20 # format = BAM # ChIP-seq file = ['SRX4554747.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 23:14:20: # Command line: callpeak -t SRX4554747.bam -f BAM -g 12100000 -n SRX4554747.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554747.05 # format = BAM # ChIP-seq file = ['SRX4554747.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 23:14:20: # Command line: callpeak -t SRX4554747.bam -f BAM -g 12100000 -n SRX4554747.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554747.10 # format = BAM # ChIP-seq file = ['SRX4554747.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 23:14:20: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:14:20: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:14:20: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:14:20: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:14:20: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:14:20: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:14:26: 1000000 INFO @ Tue, 09 Oct 2018 23:14:27: 1000000 INFO @ Tue, 09 Oct 2018 23:14:27: 1000000 INFO @ Tue, 09 Oct 2018 23:14:33: 2000000 INFO @ Tue, 09 Oct 2018 23:14:34: 2000000 INFO @ Tue, 09 Oct 2018 23:14:34: 2000000 INFO @ Tue, 09 Oct 2018 23:14:40: 3000000 INFO @ Tue, 09 Oct 2018 23:14:41: 3000000 INFO @ Tue, 09 Oct 2018 23:14:41: 3000000 INFO @ Tue, 09 Oct 2018 23:14:48: 4000000 INFO @ Tue, 09 Oct 2018 23:14:48: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:14:48: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:14:48: #1 total tags in treatment: 1969625 INFO @ Tue, 09 Oct 2018 23:14:48: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:14:48: #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 23:14:48: #1 tags after filtering in treatment: 1548560 INFO @ Tue, 09 Oct 2018 23:14:48: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:14:48: #1 finished! INFO @ Tue, 09 Oct 2018 23:14:48: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:14:48: #2 number of paired peaks: 106 WARNING @ Tue, 09 Oct 2018 23:14:48: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 09 Oct 2018 23:14:48: start model_add_line... INFO @ Tue, 09 Oct 2018 23:14:48: start X-correlation... INFO @ Tue, 09 Oct 2018 23:14:48: end of X-cor INFO @ Tue, 09 Oct 2018 23:14:48: #2 finished! INFO @ Tue, 09 Oct 2018 23:14:48: #2 predicted fragment length is 122 bps INFO @ Tue, 09 Oct 2018 23:14:48: #2 alternative fragment length(s) may be 18,38,73,106,122,150,193,209,240,328,361,467,485,507,549,589 bps INFO @ Tue, 09 Oct 2018 23:14:48: #2.2 Generate R script for model : SRX4554747.10_model.r INFO @ Tue, 09 Oct 2018 23:14:48: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:14:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:14:48: 4000000 INFO @ Tue, 09 Oct 2018 23:14:48: 4000000 INFO @ Tue, 09 Oct 2018 23:14:48: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:14:48: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:14:48: #1 total tags in treatment: 1969625 INFO @ Tue, 09 Oct 2018 23:14:48: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:14:48: #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 23:14:48: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:14:48: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:14:48: #1 total tags in treatment: 1969625 INFO @ Tue, 09 Oct 2018 23:14:48: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:14:48: #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 23:14:48: #1 tags after filtering in treatment: 1548560 INFO @ Tue, 09 Oct 2018 23:14:48: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:14:48: #1 finished! INFO @ Tue, 09 Oct 2018 23:14:48: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:14:48: #1 tags after filtering in treatment: 1548560 INFO @ Tue, 09 Oct 2018 23:14:48: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 09 Oct 2018 23:14:48: #1 finished! INFO @ Tue, 09 Oct 2018 23:14:48: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:14:49: #2 number of paired peaks: 106 WARNING @ Tue, 09 Oct 2018 23:14:49: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 09 Oct 2018 23:14:49: start model_add_line... INFO @ Tue, 09 Oct 2018 23:14:49: #2 number of paired peaks: 106 WARNING @ Tue, 09 Oct 2018 23:14:49: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 09 Oct 2018 23:14:49: start model_add_line... INFO @ Tue, 09 Oct 2018 23:14:49: start X-correlation... INFO @ Tue, 09 Oct 2018 23:14:49: start X-correlation... INFO @ Tue, 09 Oct 2018 23:14:49: end of X-cor INFO @ Tue, 09 Oct 2018 23:14:49: end of X-cor INFO @ Tue, 09 Oct 2018 23:14:49: #2 finished! INFO @ Tue, 09 Oct 2018 23:14:49: #2 finished! INFO @ Tue, 09 Oct 2018 23:14:49: #2 predicted fragment length is 122 bps INFO @ Tue, 09 Oct 2018 23:14:49: #2 predicted fragment length is 122 bps INFO @ Tue, 09 Oct 2018 23:14:49: #2 alternative fragment length(s) may be 18,38,73,106,122,150,193,209,240,328,361,467,485,507,549,589 bps INFO @ Tue, 09 Oct 2018 23:14:49: #2 alternative fragment length(s) may be 18,38,73,106,122,150,193,209,240,328,361,467,485,507,549,589 bps INFO @ Tue, 09 Oct 2018 23:14:49: #2.2 Generate R script for model : SRX4554747.20_model.r INFO @ Tue, 09 Oct 2018 23:14:49: #2.2 Generate R script for model : SRX4554747.05_model.r INFO @ Tue, 09 Oct 2018 23:14:49: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:14:49: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:14:53: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:14:53: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:14:53: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:14:54: #4 Write output xls file... SRX4554747.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:14:54: #4 Write peak in narrowPeak format file... SRX4554747.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:14:54: #4 Write summits bed file... SRX4554747.10_summits.bed INFO @ Tue, 09 Oct 2018 23:14:54: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:14:55: #4 Write output xls file... SRX4554747.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:14:55: #4 Write peak in narrowPeak format file... SRX4554747.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:14:55: #4 Write summits bed file... SRX4554747.05_summits.bed INFO @ Tue, 09 Oct 2018 23:14:55: #4 Write output xls file... SRX4554747.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:14:55: #4 Write peak in narrowPeak format file... SRX4554747.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:14:55: Done! INFO @ Tue, 09 Oct 2018 23:14:55: #4 Write summits bed file... SRX4554747.20_summits.bed INFO @ Tue, 09 Oct 2018 23:14:55: Done! pass1 - making usageList (4 chroms): 1 millis pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。