Job ID = 11244941 sra ファイルのダウンロード中... Completed: 132961K bytes transferred in 5 seconds (208532K 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 4600947 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554674/SRR7696347.sra Written 4600947 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554674/SRR7696347.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: 00:00:43 4600947 reads; of these: 4600947 (100.00%) were paired; of these: 4392966 (95.48%) aligned concordantly 0 times 173605 (3.77%) aligned concordantly exactly 1 time 34376 (0.75%) aligned concordantly >1 times ---- 4392966 pairs aligned concordantly 0 times; of these: 3178 (0.07%) aligned discordantly 1 time ---- 4389788 pairs aligned 0 times concordantly or discordantly; of these: 8779576 mates make up the pairs; of these: 8439437 (96.13%) aligned 0 times 281802 (3.21%) aligned exactly 1 time 58337 (0.66%) aligned >1 times 8.29% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 26921 / 211070 = 0.1275 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 22:54:07: # Command line: callpeak -t SRX4554674.bam -f BAM -g 12100000 -n SRX4554674.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554674.20 # format = BAM # ChIP-seq file = ['SRX4554674.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 22:54:07: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:54:07: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:54:07: # Command line: callpeak -t SRX4554674.bam -f BAM -g 12100000 -n SRX4554674.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554674.10 # format = BAM # ChIP-seq file = ['SRX4554674.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 22:54:07: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:54:07: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:54:07: # Command line: callpeak -t SRX4554674.bam -f BAM -g 12100000 -n SRX4554674.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554674.05 # format = BAM # ChIP-seq file = ['SRX4554674.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 22:54:07: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:54:07: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:54:11: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:54:11: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:54:11: #1 total tags in treatment: 181253 INFO @ Tue, 09 Oct 2018 22:54:11: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:54:11: #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 22:54:11: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:54:11: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:54:11: #1 total tags in treatment: 181253 INFO @ Tue, 09 Oct 2018 22:54:11: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:54:11: #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 22:54:11: #1 tags after filtering in treatment: 159791 INFO @ Tue, 09 Oct 2018 22:54:11: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 09 Oct 2018 22:54:11: #1 finished! INFO @ Tue, 09 Oct 2018 22:54:11: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:54:11: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:54:11: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:54:11: #1 total tags in treatment: 181253 INFO @ Tue, 09 Oct 2018 22:54:11: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:54:11: #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 22:54:11: #1 tags after filtering in treatment: 159791 INFO @ Tue, 09 Oct 2018 22:54:11: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 09 Oct 2018 22:54:11: #1 finished! INFO @ Tue, 09 Oct 2018 22:54:11: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:54:11: #1 tags after filtering in treatment: 159791 INFO @ Tue, 09 Oct 2018 22:54:11: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 09 Oct 2018 22:54:11: #1 finished! INFO @ Tue, 09 Oct 2018 22:54:11: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:54:11: #2 number of paired peaks: 360 WARNING @ Tue, 09 Oct 2018 22:54:11: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 09 Oct 2018 22:54:11: start model_add_line... INFO @ Tue, 09 Oct 2018 22:54:11: start X-correlation... INFO @ Tue, 09 Oct 2018 22:54:11: #2 number of paired peaks: 360 WARNING @ Tue, 09 Oct 2018 22:54:11: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 09 Oct 2018 22:54:11: start model_add_line... INFO @ Tue, 09 Oct 2018 22:54:11: end of X-cor INFO @ Tue, 09 Oct 2018 22:54:11: #2 finished! INFO @ Tue, 09 Oct 2018 22:54:11: #2 predicted fragment length is 177 bps INFO @ Tue, 09 Oct 2018 22:54:11: #2 alternative fragment length(s) may be 71,104,124,146,177,215,304,540,590 bps INFO @ Tue, 09 Oct 2018 22:54:11: #2.2 Generate R script for model : SRX4554674.20_model.r INFO @ Tue, 09 Oct 2018 22:54:11: start X-correlation... INFO @ Tue, 09 Oct 2018 22:54:11: end of X-cor INFO @ Tue, 09 Oct 2018 22:54:11: #2 finished! INFO @ Tue, 09 Oct 2018 22:54:11: #2 predicted fragment length is 177 bps INFO @ Tue, 09 Oct 2018 22:54:11: #2 alternative fragment length(s) may be 71,104,124,146,177,215,304,540,590 bps INFO @ Tue, 09 Oct 2018 22:54:11: #2.2 Generate R script for model : SRX4554674.10_model.r INFO @ Tue, 09 Oct 2018 22:54:11: #2 number of paired peaks: 360 WARNING @ Tue, 09 Oct 2018 22:54:11: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 09 Oct 2018 22:54:11: start model_add_line... INFO @ Tue, 09 Oct 2018 22:54:11: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:54:11: start X-correlation... INFO @ Tue, 09 Oct 2018 22:54:11: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:54:11: end of X-cor INFO @ Tue, 09 Oct 2018 22:54:11: #2 finished! INFO @ Tue, 09 Oct 2018 22:54:11: #2 predicted fragment length is 177 bps INFO @ Tue, 09 Oct 2018 22:54:11: #2 alternative fragment length(s) may be 71,104,124,146,177,215,304,540,590 bps INFO @ Tue, 09 Oct 2018 22:54:11: #2.2 Generate R script for model : SRX4554674.05_model.r INFO @ Tue, 09 Oct 2018 22:54:11: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:54:11: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:54:11: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:54:11: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:54:11: #4 Write output xls file... SRX4554674.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:54:11: #4 Write peak in narrowPeak format file... SRX4554674.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:54:11: #4 Write output xls file... SRX4554674.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:54:11: #4 Write summits bed file... SRX4554674.10_summits.bed INFO @ Tue, 09 Oct 2018 22:54:11: Done! INFO @ Tue, 09 Oct 2018 22:54:11: #4 Write peak in narrowPeak format file... SRX4554674.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:54:11: #4 Write summits bed file... SRX4554674.05_summits.bed INFO @ Tue, 09 Oct 2018 22:54:11: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (193 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 0 millis INFO @ Tue, 09 Oct 2018 22:54:12: #4 Write output xls file... SRX4554674.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:54:12: #4 Write peak in narrowPeak format file... SRX4554674.20_peaks.narrowPeak pass2 - checking and writing primary data (356 records, 4 fields): 3 millis INFO @ Tue, 09 Oct 2018 22:54:12: #4 Write summits bed file... SRX4554674.20_summits.bed INFO @ Tue, 09 Oct 2018 22:54:12: Done! CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (31 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。