Job ID = 11193150 sra ファイルのダウンロード中... Completed: 202388K bytes transferred in 5 seconds (296216K 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 5351013 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337742/SRR7467861.sra Written 5351013 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337742/SRR7467861.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: 00:02:25 5351013 reads; of these: 5351013 (100.00%) were paired; of these: 4632713 (86.58%) aligned concordantly 0 times 635900 (11.88%) aligned concordantly exactly 1 time 82400 (1.54%) aligned concordantly >1 times ---- 4632713 pairs aligned concordantly 0 times; of these: 269025 (5.81%) aligned discordantly 1 time ---- 4363688 pairs aligned 0 times concordantly or discordantly; of these: 8727376 mates make up the pairs; of these: 7207955 (82.59%) aligned 0 times 1318072 (15.10%) aligned exactly 1 time 201349 (2.31%) aligned >1 times 32.65% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 461585 / 927968 = 0.4974 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 @ Sat, 15 Sep 2018 11:04:44: # Command line: callpeak -t SRX4337742.bam -f BAM -g 12100000 -n SRX4337742.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337742.10 # format = BAM # ChIP-seq file = ['SRX4337742.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 @ Sat, 15 Sep 2018 11:04:44: # Command line: callpeak -t SRX4337742.bam -f BAM -g 12100000 -n SRX4337742.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337742.05 # format = BAM # ChIP-seq file = ['SRX4337742.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 @ Sat, 15 Sep 2018 11:04:44: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:04:44: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:04:44: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:04:44: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:04:44: # Command line: callpeak -t SRX4337742.bam -f BAM -g 12100000 -n SRX4337742.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337742.20 # format = BAM # ChIP-seq file = ['SRX4337742.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 @ Sat, 15 Sep 2018 11:04:44: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:04:44: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:04:51: 1000000 INFO @ Sat, 15 Sep 2018 11:04:53: 1000000 INFO @ Sat, 15 Sep 2018 11:04:53: 1000000 INFO @ Sat, 15 Sep 2018 11:04:59: 2000000 INFO @ Sat, 15 Sep 2018 11:05:02: 2000000 INFO @ Sat, 15 Sep 2018 11:05:02: 2000000 INFO @ Sat, 15 Sep 2018 11:05:03: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:05:03: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:05:03: #1 total tags in treatment: 344937 INFO @ Sat, 15 Sep 2018 11:05:03: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:05:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:05:03: #1 tags after filtering in treatment: 323073 INFO @ Sat, 15 Sep 2018 11:05:03: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 15 Sep 2018 11:05:03: #1 finished! INFO @ Sat, 15 Sep 2018 11:05:03: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:05:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:05:04: #2 number of paired peaks: 199 WARNING @ Sat, 15 Sep 2018 11:05:04: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Sat, 15 Sep 2018 11:05:04: start model_add_line... INFO @ Sat, 15 Sep 2018 11:05:04: start X-correlation... INFO @ Sat, 15 Sep 2018 11:05:04: end of X-cor INFO @ Sat, 15 Sep 2018 11:05:04: #2 finished! INFO @ Sat, 15 Sep 2018 11:05:04: #2 predicted fragment length is 179 bps INFO @ Sat, 15 Sep 2018 11:05:04: #2 alternative fragment length(s) may be 97,150,179 bps INFO @ Sat, 15 Sep 2018 11:05:04: #2.2 Generate R script for model : SRX4337742.05_model.r INFO @ Sat, 15 Sep 2018 11:05:04: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:05:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:05:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:05:05: #4 Write output xls file... SRX4337742.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:05:05: #4 Write peak in narrowPeak format file... SRX4337742.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:05:05: #4 Write summits bed file... SRX4337742.05_summits.bed INFO @ Sat, 15 Sep 2018 11:05:05: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (348 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:05:07: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:05:07: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:05:07: #1 total tags in treatment: 344937 INFO @ Sat, 15 Sep 2018 11:05:07: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:05:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:05:07: #1 tags after filtering in treatment: 323073 INFO @ Sat, 15 Sep 2018 11:05:07: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 15 Sep 2018 11:05:07: #1 finished! INFO @ Sat, 15 Sep 2018 11:05:07: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:05:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:05:07: #2 number of paired peaks: 199 WARNING @ Sat, 15 Sep 2018 11:05:07: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Sat, 15 Sep 2018 11:05:07: start model_add_line... INFO @ Sat, 15 Sep 2018 11:05:07: start X-correlation... INFO @ Sat, 15 Sep 2018 11:05:07: end of X-cor INFO @ Sat, 15 Sep 2018 11:05:07: #2 finished! INFO @ Sat, 15 Sep 2018 11:05:07: #2 predicted fragment length is 179 bps INFO @ Sat, 15 Sep 2018 11:05:07: #2 alternative fragment length(s) may be 97,150,179 bps INFO @ Sat, 15 Sep 2018 11:05:07: #2.2 Generate R script for model : SRX4337742.10_model.r INFO @ Sat, 15 Sep 2018 11:05:07: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:05:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:05:07: #1 tag size is determined as 44 bps INFO @ Sat, 15 Sep 2018 11:05:07: #1 tag size = 44 INFO @ Sat, 15 Sep 2018 11:05:07: #1 total tags in treatment: 344937 INFO @ Sat, 15 Sep 2018 11:05:07: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:05:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:05:07: #1 tags after filtering in treatment: 323073 INFO @ Sat, 15 Sep 2018 11:05:07: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 15 Sep 2018 11:05:07: #1 finished! INFO @ Sat, 15 Sep 2018 11:05:07: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:05:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:05:07: #2 number of paired peaks: 199 WARNING @ Sat, 15 Sep 2018 11:05:07: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Sat, 15 Sep 2018 11:05:07: start model_add_line... INFO @ Sat, 15 Sep 2018 11:05:07: start X-correlation... INFO @ Sat, 15 Sep 2018 11:05:07: end of X-cor INFO @ Sat, 15 Sep 2018 11:05:07: #2 finished! INFO @ Sat, 15 Sep 2018 11:05:07: #2 predicted fragment length is 179 bps INFO @ Sat, 15 Sep 2018 11:05:07: #2 alternative fragment length(s) may be 97,150,179 bps INFO @ Sat, 15 Sep 2018 11:05:07: #2.2 Generate R script for model : SRX4337742.20_model.r INFO @ Sat, 15 Sep 2018 11:05:07: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:05:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:05:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:05:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:05:08: #4 Write output xls file... SRX4337742.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:05:09: #4 Write peak in narrowPeak format file... SRX4337742.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:05:09: #4 Write summits bed file... SRX4337742.10_summits.bed INFO @ Sat, 15 Sep 2018 11:05:09: Done! INFO @ Sat, 15 Sep 2018 11:05:09: #4 Write output xls file... SRX4337742.20_peaks.xls pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 4 millis INFO @ Sat, 15 Sep 2018 11:05:09: #4 Write peak in narrowPeak format file... SRX4337742.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:05:09: #4 Write summits bed file... SRX4337742.20_summits.bed CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:05:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (52 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。