Job ID = 11245058 sra ファイルのダウンロード中... Completed: 275018K bytes transferred in 9 seconds (243818K 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 8110630 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554769/SRR7696441.sra Written 8110630 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554769/SRR7696441.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: 00:03:23 8110630 reads; of these: 8110630 (100.00%) were paired; of these: 5570622 (68.68%) aligned concordantly 0 times 2233626 (27.54%) aligned concordantly exactly 1 time 306382 (3.78%) aligned concordantly >1 times ---- 5570622 pairs aligned concordantly 0 times; of these: 3120 (0.06%) aligned discordantly 1 time ---- 5567502 pairs aligned 0 times concordantly or discordantly; of these: 11135004 mates make up the pairs; of these: 8468524 (76.05%) aligned 0 times 2371323 (21.30%) aligned exactly 1 time 295157 (2.65%) aligned >1 times 47.79% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:24 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] 348379 / 2542798 = 0.1370 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 23:21:18: # Command line: callpeak -t SRX4554769.bam -f BAM -g 12100000 -n SRX4554769.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554769.10 # format = BAM # ChIP-seq file = ['SRX4554769.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 23:21:18: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:21:18: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:21:18: # Command line: callpeak -t SRX4554769.bam -f BAM -g 12100000 -n SRX4554769.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554769.05 # format = BAM # ChIP-seq file = ['SRX4554769.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 23:21:18: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:21:18: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:21:18: # Command line: callpeak -t SRX4554769.bam -f BAM -g 12100000 -n SRX4554769.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554769.20 # format = BAM # ChIP-seq file = ['SRX4554769.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 23:21:18: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:21:18: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:21:24: 1000000 INFO @ Tue, 09 Oct 2018 23:21:24: 1000000 INFO @ Tue, 09 Oct 2018 23:21:25: 1000000 INFO @ Tue, 09 Oct 2018 23:21:30: 2000000 INFO @ Tue, 09 Oct 2018 23:21:31: 2000000 INFO @ Tue, 09 Oct 2018 23:21:31: 2000000 INFO @ Tue, 09 Oct 2018 23:21:35: 3000000 INFO @ Tue, 09 Oct 2018 23:21:37: 3000000 INFO @ Tue, 09 Oct 2018 23:21:37: 3000000 INFO @ Tue, 09 Oct 2018 23:21:41: 4000000 INFO @ Tue, 09 Oct 2018 23:21:43: 4000000 INFO @ Tue, 09 Oct 2018 23:21:43: 4000000 INFO @ Tue, 09 Oct 2018 23:21:47: 5000000 INFO @ Tue, 09 Oct 2018 23:21:49: 5000000 INFO @ Tue, 09 Oct 2018 23:21:49: 5000000 INFO @ Tue, 09 Oct 2018 23:21:53: 6000000 INFO @ Tue, 09 Oct 2018 23:21:56: 6000000 INFO @ Tue, 09 Oct 2018 23:21:56: 6000000 INFO @ Tue, 09 Oct 2018 23:21:59: 7000000 INFO @ Tue, 09 Oct 2018 23:22:00: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:22:00: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:22:00: #1 total tags in treatment: 2191654 INFO @ Tue, 09 Oct 2018 23:22:00: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:22:00: #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 23:22:00: #1 tags after filtering in treatment: 1232703 INFO @ Tue, 09 Oct 2018 23:22:00: #1 Redundant rate of treatment: 0.44 INFO @ Tue, 09 Oct 2018 23:22:00: #1 finished! INFO @ Tue, 09 Oct 2018 23:22:00: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:22:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:22:00: #2 number of paired peaks: 122 WARNING @ Tue, 09 Oct 2018 23:22:00: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 09 Oct 2018 23:22:00: start model_add_line... INFO @ Tue, 09 Oct 2018 23:22:00: start X-correlation... INFO @ Tue, 09 Oct 2018 23:22:00: end of X-cor INFO @ Tue, 09 Oct 2018 23:22:00: #2 finished! INFO @ Tue, 09 Oct 2018 23:22:00: #2 predicted fragment length is 182 bps INFO @ Tue, 09 Oct 2018 23:22:00: #2 alternative fragment length(s) may be 3,182,271,288 bps INFO @ Tue, 09 Oct 2018 23:22:00: #2.2 Generate R script for model : SRX4554769.10_model.r INFO @ Tue, 09 Oct 2018 23:22:00: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:22:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:22:02: 7000000 INFO @ Tue, 09 Oct 2018 23:22:02: 7000000 INFO @ Tue, 09 Oct 2018 23:22:03: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:22:03: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:22:03: #1 total tags in treatment: 2191654 INFO @ Tue, 09 Oct 2018 23:22:03: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:22:03: #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 23:22:03: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:22:03: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:22:03: #1 total tags in treatment: 2191654 INFO @ Tue, 09 Oct 2018 23:22:03: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:22:03: #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 23:22:03: #1 tags after filtering in treatment: 1232703 INFO @ Tue, 09 Oct 2018 23:22:03: #1 Redundant rate of treatment: 0.44 INFO @ Tue, 09 Oct 2018 23:22:03: #1 finished! INFO @ Tue, 09 Oct 2018 23:22:03: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:22:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:22:03: #1 tags after filtering in treatment: 1232703 INFO @ Tue, 09 Oct 2018 23:22:03: #1 Redundant rate of treatment: 0.44 INFO @ Tue, 09 Oct 2018 23:22:03: #1 finished! INFO @ Tue, 09 Oct 2018 23:22:03: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:22:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:22:03: #2 number of paired peaks: 122 WARNING @ Tue, 09 Oct 2018 23:22:03: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 09 Oct 2018 23:22:03: start model_add_line... INFO @ Tue, 09 Oct 2018 23:22:03: start X-correlation... INFO @ Tue, 09 Oct 2018 23:22:03: #2 number of paired peaks: 122 WARNING @ Tue, 09 Oct 2018 23:22:03: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 09 Oct 2018 23:22:03: start model_add_line... INFO @ Tue, 09 Oct 2018 23:22:03: end of X-cor INFO @ Tue, 09 Oct 2018 23:22:03: #2 finished! INFO @ Tue, 09 Oct 2018 23:22:03: #2 predicted fragment length is 182 bps INFO @ Tue, 09 Oct 2018 23:22:03: #2 alternative fragment length(s) may be 3,182,271,288 bps INFO @ Tue, 09 Oct 2018 23:22:03: #2.2 Generate R script for model : SRX4554769.05_model.r INFO @ Tue, 09 Oct 2018 23:22:03: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:22:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:22:03: start X-correlation... INFO @ Tue, 09 Oct 2018 23:22:03: end of X-cor INFO @ Tue, 09 Oct 2018 23:22:03: #2 finished! INFO @ Tue, 09 Oct 2018 23:22:03: #2 predicted fragment length is 182 bps INFO @ Tue, 09 Oct 2018 23:22:03: #2 alternative fragment length(s) may be 3,182,271,288 bps INFO @ Tue, 09 Oct 2018 23:22:03: #2.2 Generate R script for model : SRX4554769.20_model.r INFO @ Tue, 09 Oct 2018 23:22:03: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:22:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:22:06: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:22:07: #4 Write output xls file... SRX4554769.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:22:07: #4 Write peak in narrowPeak format file... SRX4554769.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:22:07: #4 Write summits bed file... SRX4554769.10_summits.bed INFO @ Tue, 09 Oct 2018 23:22:07: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (258 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:22:08: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:22:09: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:22:10: #4 Write output xls file... SRX4554769.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:22:10: #4 Write peak in narrowPeak format file... SRX4554769.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:22:10: #4 Write summits bed file... SRX4554769.05_summits.bed INFO @ Tue, 09 Oct 2018 23:22:10: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (738 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:22:10: #4 Write output xls file... SRX4554769.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:22:10: #4 Write peak in narrowPeak format file... SRX4554769.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:22:10: #4 Write summits bed file... SRX4554769.20_summits.bed INFO @ Tue, 09 Oct 2018 23:22:10: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (42 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。