Job ID = 11244932 sra ファイルのダウンロード中... Completed: 209479K bytes transferred in 6 seconds (265110K 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 6370862 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554669/SRR7696342.sra Written 6370862 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554669/SRR7696342.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: 00:02:00 6370862 reads; of these: 6370862 (100.00%) were paired; of these: 4402730 (69.11%) aligned concordantly 0 times 1430977 (22.46%) aligned concordantly exactly 1 time 537155 (8.43%) aligned concordantly >1 times ---- 4402730 pairs aligned concordantly 0 times; of these: 46855 (1.06%) aligned discordantly 1 time ---- 4355875 pairs aligned 0 times concordantly or discordantly; of these: 8711750 mates make up the pairs; of these: 8614177 (98.88%) aligned 0 times 44678 (0.51%) aligned exactly 1 time 52895 (0.61%) aligned >1 times 32.39% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 57587 / 2004962 = 0.0287 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 22:55:20: # Command line: callpeak -t SRX4554669.bam -f BAM -g 12100000 -n SRX4554669.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554669.10 # format = BAM # ChIP-seq file = ['SRX4554669.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 22:55:20: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:55:20: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:55:20: # Command line: callpeak -t SRX4554669.bam -f BAM -g 12100000 -n SRX4554669.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554669.05 # format = BAM # ChIP-seq file = ['SRX4554669.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 22:55:20: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:55:20: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:55:20: # Command line: callpeak -t SRX4554669.bam -f BAM -g 12100000 -n SRX4554669.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554669.20 # format = BAM # ChIP-seq file = ['SRX4554669.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 22:55:20: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:55:20: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:55:26: 1000000 INFO @ Tue, 09 Oct 2018 22:55:26: 1000000 INFO @ Tue, 09 Oct 2018 22:55:26: 1000000 INFO @ Tue, 09 Oct 2018 22:55:32: 2000000 INFO @ Tue, 09 Oct 2018 22:55:33: 2000000 INFO @ Tue, 09 Oct 2018 22:55:33: 2000000 INFO @ Tue, 09 Oct 2018 22:55:38: 3000000 INFO @ Tue, 09 Oct 2018 22:55:39: 3000000 INFO @ Tue, 09 Oct 2018 22:55:39: 3000000 INFO @ Tue, 09 Oct 2018 22:55:43: 4000000 INFO @ Tue, 09 Oct 2018 22:55:44: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:55:44: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:55:44: #1 total tags in treatment: 1911325 INFO @ Tue, 09 Oct 2018 22:55:44: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:55:44: #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 22:55:44: #1 tags after filtering in treatment: 1413715 INFO @ Tue, 09 Oct 2018 22:55:44: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 09 Oct 2018 22:55:44: #1 finished! INFO @ Tue, 09 Oct 2018 22:55:44: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:55:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:55:44: #2 number of paired peaks: 313 WARNING @ Tue, 09 Oct 2018 22:55:44: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 09 Oct 2018 22:55:44: start model_add_line... INFO @ Tue, 09 Oct 2018 22:55:44: start X-correlation... INFO @ Tue, 09 Oct 2018 22:55:44: end of X-cor INFO @ Tue, 09 Oct 2018 22:55:44: #2 finished! INFO @ Tue, 09 Oct 2018 22:55:44: #2 predicted fragment length is 121 bps INFO @ Tue, 09 Oct 2018 22:55:44: #2 alternative fragment length(s) may be 1,63,93,121,546,575,597 bps INFO @ Tue, 09 Oct 2018 22:55:44: #2.2 Generate R script for model : SRX4554669.10_model.r INFO @ Tue, 09 Oct 2018 22:55:44: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:55:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:55:45: 4000000 INFO @ Tue, 09 Oct 2018 22:55:45: 4000000 INFO @ Tue, 09 Oct 2018 22:55:45: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:55:45: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:55:45: #1 total tags in treatment: 1911325 INFO @ Tue, 09 Oct 2018 22:55:45: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:55:45: #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 22:55:45: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:55:45: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:55:45: #1 total tags in treatment: 1911325 INFO @ Tue, 09 Oct 2018 22:55:45: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:55:45: #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 22:55:45: #1 tags after filtering in treatment: 1413715 INFO @ Tue, 09 Oct 2018 22:55:45: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 09 Oct 2018 22:55:45: #1 finished! INFO @ Tue, 09 Oct 2018 22:55:45: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:55:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:55:45: #1 tags after filtering in treatment: 1413715 INFO @ Tue, 09 Oct 2018 22:55:45: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 09 Oct 2018 22:55:45: #1 finished! INFO @ Tue, 09 Oct 2018 22:55:45: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:55:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:55:46: #2 number of paired peaks: 313 WARNING @ Tue, 09 Oct 2018 22:55:46: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 09 Oct 2018 22:55:46: start model_add_line... INFO @ Tue, 09 Oct 2018 22:55:46: #2 number of paired peaks: 313 WARNING @ Tue, 09 Oct 2018 22:55:46: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Tue, 09 Oct 2018 22:55:46: start model_add_line... INFO @ Tue, 09 Oct 2018 22:55:46: start X-correlation... INFO @ Tue, 09 Oct 2018 22:55:46: start X-correlation... INFO @ Tue, 09 Oct 2018 22:55:46: end of X-cor INFO @ Tue, 09 Oct 2018 22:55:46: end of X-cor INFO @ Tue, 09 Oct 2018 22:55:46: #2 finished! INFO @ Tue, 09 Oct 2018 22:55:46: #2 finished! INFO @ Tue, 09 Oct 2018 22:55:46: #2 predicted fragment length is 121 bps INFO @ Tue, 09 Oct 2018 22:55:46: #2 predicted fragment length is 121 bps INFO @ Tue, 09 Oct 2018 22:55:46: #2 alternative fragment length(s) may be 1,63,93,121,546,575,597 bps INFO @ Tue, 09 Oct 2018 22:55:46: #2 alternative fragment length(s) may be 1,63,93,121,546,575,597 bps INFO @ Tue, 09 Oct 2018 22:55:46: #2.2 Generate R script for model : SRX4554669.05_model.r INFO @ Tue, 09 Oct 2018 22:55:46: #2.2 Generate R script for model : SRX4554669.20_model.r INFO @ Tue, 09 Oct 2018 22:55:46: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:55:46: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:55:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:55:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:55:49: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:55:50: #4 Write output xls file... SRX4554669.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:55:50: #4 Write peak in narrowPeak format file... SRX4554669.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:55:50: #4 Write summits bed file... SRX4554669.10_summits.bed INFO @ Tue, 09 Oct 2018 22:55:50: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (125 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:55:50: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:55:50: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:55:52: #4 Write output xls file... SRX4554669.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:55:52: #4 Write peak in narrowPeak format file... SRX4554669.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:55:52: #4 Write summits bed file... SRX4554669.20_summits.bed INFO @ Tue, 09 Oct 2018 22:55:52: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:55:52: #4 Write output xls file... SRX4554669.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:55:52: #4 Write peak in narrowPeak format file... SRX4554669.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:55:52: #4 Write summits bed file... SRX4554669.05_summits.bed INFO @ Tue, 09 Oct 2018 22:55:52: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (476 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。