Job ID = 11245043 sra ファイルのダウンロード中... Completed: 437108K bytes transferred in 19 seconds (184738K 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 6876901 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554754/SRR7696427.sra Written 6876901 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554754/SRR7696427.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: 00:03:22 6876901 reads; of these: 6876901 (100.00%) were paired; of these: 4536123 (65.96%) aligned concordantly 0 times 1972117 (28.68%) aligned concordantly exactly 1 time 368661 (5.36%) aligned concordantly >1 times ---- 4536123 pairs aligned concordantly 0 times; of these: 12270 (0.27%) aligned discordantly 1 time ---- 4523853 pairs aligned 0 times concordantly or discordantly; of these: 9047706 mates make up the pairs; of these: 8969224 (99.13%) aligned 0 times 41496 (0.46%) aligned exactly 1 time 36986 (0.41%) aligned >1 times 34.79% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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] 1214848 / 2350665 = 0.5168 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 23:17:52: # Command line: callpeak -t SRX4554754.bam -f BAM -g 12100000 -n SRX4554754.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554754.05 # format = BAM # ChIP-seq file = ['SRX4554754.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 23:17:52: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:17:52: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:17:52: # Command line: callpeak -t SRX4554754.bam -f BAM -g 12100000 -n SRX4554754.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554754.20 # format = BAM # ChIP-seq file = ['SRX4554754.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 23:17:52: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:17:52: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:17:52: # Command line: callpeak -t SRX4554754.bam -f BAM -g 12100000 -n SRX4554754.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554754.10 # format = BAM # ChIP-seq file = ['SRX4554754.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 23:17:52: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:17:52: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:00: 1000000 INFO @ Tue, 09 Oct 2018 23:18:00: 1000000 INFO @ Tue, 09 Oct 2018 23:18:01: 1000000 INFO @ Tue, 09 Oct 2018 23:18:08: 2000000 INFO @ Tue, 09 Oct 2018 23:18:08: 2000000 INFO @ Tue, 09 Oct 2018 23:18:11: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:18:11: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:18:11: #1 total tags in treatment: 1129696 INFO @ Tue, 09 Oct 2018 23:18:11: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:11: #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 23:18:11: #1 tags after filtering in treatment: 752628 INFO @ Tue, 09 Oct 2018 23:18:11: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 09 Oct 2018 23:18:11: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:11: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:11: 2000000 INFO @ Tue, 09 Oct 2018 23:18:11: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:18:11: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:18:11: #1 total tags in treatment: 1129696 INFO @ Tue, 09 Oct 2018 23:18:11: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:11: #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 23:18:11: #1 tags after filtering in treatment: 752628 INFO @ Tue, 09 Oct 2018 23:18:11: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 09 Oct 2018 23:18:11: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:11: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:11: #2 number of paired peaks: 972 WARNING @ Tue, 09 Oct 2018 23:18:11: Fewer paired peaks (972) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 972 pairs to build model! INFO @ Tue, 09 Oct 2018 23:18:11: start model_add_line... INFO @ Tue, 09 Oct 2018 23:18:11: start X-correlation... INFO @ Tue, 09 Oct 2018 23:18:11: end of X-cor INFO @ Tue, 09 Oct 2018 23:18:11: #2 finished! INFO @ Tue, 09 Oct 2018 23:18:11: #2 predicted fragment length is 203 bps INFO @ Tue, 09 Oct 2018 23:18:11: #2 alternative fragment length(s) may be 2,164,171,203,223,248,296,591 bps INFO @ Tue, 09 Oct 2018 23:18:11: #2.2 Generate R script for model : SRX4554754.05_model.r INFO @ Tue, 09 Oct 2018 23:18:11: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:18:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:18:11: #2 number of paired peaks: 972 WARNING @ Tue, 09 Oct 2018 23:18:11: Fewer paired peaks (972) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 972 pairs to build model! INFO @ Tue, 09 Oct 2018 23:18:11: start model_add_line... INFO @ Tue, 09 Oct 2018 23:18:11: start X-correlation... INFO @ Tue, 09 Oct 2018 23:18:11: end of X-cor INFO @ Tue, 09 Oct 2018 23:18:11: #2 finished! INFO @ Tue, 09 Oct 2018 23:18:11: #2 predicted fragment length is 203 bps INFO @ Tue, 09 Oct 2018 23:18:11: #2 alternative fragment length(s) may be 2,164,171,203,223,248,296,591 bps INFO @ Tue, 09 Oct 2018 23:18:11: #2.2 Generate R script for model : SRX4554754.20_model.r INFO @ Tue, 09 Oct 2018 23:18:11: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:18:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:18:14: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:18:14: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:18:14: #1 total tags in treatment: 1129696 INFO @ Tue, 09 Oct 2018 23:18:14: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:14: #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 23:18:14: #1 tags after filtering in treatment: 752628 INFO @ Tue, 09 Oct 2018 23:18:14: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 09 Oct 2018 23:18:14: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:14: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:14: #2 number of paired peaks: 972 WARNING @ Tue, 09 Oct 2018 23:18:14: Fewer paired peaks (972) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 972 pairs to build model! INFO @ Tue, 09 Oct 2018 23:18:14: start model_add_line... INFO @ Tue, 09 Oct 2018 23:18:14: start X-correlation... INFO @ Tue, 09 Oct 2018 23:18:14: end of X-cor INFO @ Tue, 09 Oct 2018 23:18:14: #2 finished! INFO @ Tue, 09 Oct 2018 23:18:14: #2 predicted fragment length is 203 bps INFO @ Tue, 09 Oct 2018 23:18:14: #2 alternative fragment length(s) may be 2,164,171,203,223,248,296,591 bps INFO @ Tue, 09 Oct 2018 23:18:14: #2.2 Generate R script for model : SRX4554754.10_model.r INFO @ Tue, 09 Oct 2018 23:18:14: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:18:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:18:16: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:18:16: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:18:17: #4 Write output xls file... SRX4554754.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:18:17: #4 Write peak in narrowPeak format file... SRX4554754.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:18:17: #4 Write summits bed file... SRX4554754.05_summits.bed INFO @ Tue, 09 Oct 2018 23:18:17: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:18:17: #4 Write output xls file... SRX4554754.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:18:17: #4 Write peak in narrowPeak format file... SRX4554754.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:18:17: #4 Write summits bed file... SRX4554754.20_summits.bed INFO @ Tue, 09 Oct 2018 23:18:17: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:18:19: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:18:20: #4 Write output xls file... SRX4554754.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:18:20: #4 Write peak in narrowPeak format file... SRX4554754.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:18:20: #4 Write summits bed file... SRX4554754.10_summits.bed INFO @ Tue, 09 Oct 2018 23:18:20: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (350 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。