Job ID = 11192656 sra ファイルのダウンロード中... Completed: 17208K bytes transferred in 2 seconds (47822K 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 554225 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924777/SRR3824808.sra Written 554225 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1924777/SRR3824808.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: 00:00:20 554225 reads; of these: 554225 (100.00%) were paired; of these: 197169 (35.58%) aligned concordantly 0 times 336919 (60.79%) aligned concordantly exactly 1 time 20137 (3.63%) aligned concordantly >1 times ---- 197169 pairs aligned concordantly 0 times; of these: 50323 (25.52%) aligned discordantly 1 time ---- 146846 pairs aligned 0 times concordantly or discordantly; of these: 293692 mates make up the pairs; of these: 152463 (51.91%) aligned 0 times 126252 (42.99%) aligned exactly 1 time 14977 (5.10%) aligned >1 times 86.25% overall alignment rate Time searching: 00:00:20 Overall time: 00:00:20 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 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] 170531 / 372081 = 0.4583 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 09:42:55: # Command line: callpeak -t SRX1924777.bam -f BAM -g 12100000 -n SRX1924777.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1924777.20 # format = BAM # ChIP-seq file = ['SRX1924777.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 09:42:55: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:42:55: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:42:55: # Command line: callpeak -t SRX1924777.bam -f BAM -g 12100000 -n SRX1924777.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1924777.05 # format = BAM # ChIP-seq file = ['SRX1924777.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 09:42:55: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:42:55: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:42:55: # Command line: callpeak -t SRX1924777.bam -f BAM -g 12100000 -n SRX1924777.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1924777.10 # format = BAM # ChIP-seq file = ['SRX1924777.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 09:42:55: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:42:55: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:42:58: #1 tag size is determined as 35 bps INFO @ Sat, 15 Sep 2018 09:42:58: #1 tag size = 35 INFO @ Sat, 15 Sep 2018 09:42:58: #1 total tags in treatment: 191655 INFO @ Sat, 15 Sep 2018 09:42:58: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:42:58: #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 09:42:58: #1 tags after filtering in treatment: 183790 INFO @ Sat, 15 Sep 2018 09:42:58: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 09:42:58: #1 finished! INFO @ Sat, 15 Sep 2018 09:42:58: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:42:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:42:58: #1 tag size is determined as 35 bps INFO @ Sat, 15 Sep 2018 09:42:58: #1 tag size = 35 INFO @ Sat, 15 Sep 2018 09:42:58: #1 total tags in treatment: 191655 INFO @ Sat, 15 Sep 2018 09:42:58: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:42:58: #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 09:42:58: #2 number of paired peaks: 139 WARNING @ Sat, 15 Sep 2018 09:42:58: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 15 Sep 2018 09:42:58: start model_add_line... INFO @ Sat, 15 Sep 2018 09:42:58: start X-correlation... INFO @ Sat, 15 Sep 2018 09:42:58: #1 tags after filtering in treatment: 183790 INFO @ Sat, 15 Sep 2018 09:42:58: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 09:42:58: #1 finished! INFO @ Sat, 15 Sep 2018 09:42:58: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:42:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:42:58: end of X-cor INFO @ Sat, 15 Sep 2018 09:42:58: #2 finished! INFO @ Sat, 15 Sep 2018 09:42:58: #2 predicted fragment length is 209 bps INFO @ Sat, 15 Sep 2018 09:42:58: #2 alternative fragment length(s) may be 68,138,171,209,233,273,349,531 bps INFO @ Sat, 15 Sep 2018 09:42:58: #2.2 Generate R script for model : SRX1924777.20_model.r INFO @ Sat, 15 Sep 2018 09:42:58: #1 tag size is determined as 35 bps INFO @ Sat, 15 Sep 2018 09:42:58: #1 tag size = 35 INFO @ Sat, 15 Sep 2018 09:42:58: #1 total tags in treatment: 191655 INFO @ Sat, 15 Sep 2018 09:42:58: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:42:58: #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 09:42:58: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:42:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:42:58: #1 tags after filtering in treatment: 183790 INFO @ Sat, 15 Sep 2018 09:42:58: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 09:42:58: #1 finished! INFO @ Sat, 15 Sep 2018 09:42:58: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:42:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:42:58: #2 number of paired peaks: 139 WARNING @ Sat, 15 Sep 2018 09:42:58: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 15 Sep 2018 09:42:58: start model_add_line... INFO @ Sat, 15 Sep 2018 09:42:58: start X-correlation... INFO @ Sat, 15 Sep 2018 09:42:58: end of X-cor INFO @ Sat, 15 Sep 2018 09:42:58: #2 finished! INFO @ Sat, 15 Sep 2018 09:42:58: #2 predicted fragment length is 209 bps INFO @ Sat, 15 Sep 2018 09:42:58: #2 alternative fragment length(s) may be 68,138,171,209,233,273,349,531 bps INFO @ Sat, 15 Sep 2018 09:42:58: #2.2 Generate R script for model : SRX1924777.05_model.r INFO @ Sat, 15 Sep 2018 09:42:58: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:42:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:42:58: #2 number of paired peaks: 139 WARNING @ Sat, 15 Sep 2018 09:42:58: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 15 Sep 2018 09:42:58: start model_add_line... INFO @ Sat, 15 Sep 2018 09:42:58: start X-correlation... INFO @ Sat, 15 Sep 2018 09:42:58: end of X-cor INFO @ Sat, 15 Sep 2018 09:42:58: #2 finished! INFO @ Sat, 15 Sep 2018 09:42:58: #2 predicted fragment length is 209 bps INFO @ Sat, 15 Sep 2018 09:42:58: #2 alternative fragment length(s) may be 68,138,171,209,233,273,349,531 bps INFO @ Sat, 15 Sep 2018 09:42:58: #2.2 Generate R script for model : SRX1924777.10_model.r INFO @ Sat, 15 Sep 2018 09:42:58: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:42:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:42:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:42:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:42:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:42:59: #4 Write output xls file... SRX1924777.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:42:59: #4 Write peak in narrowPeak format file... SRX1924777.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:42:59: #4 Write summits bed file... SRX1924777.20_summits.bed INFO @ Sat, 15 Sep 2018 09:42:59: Done! INFO @ Sat, 15 Sep 2018 09:42:59: #4 Write output xls file... SRX1924777.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:42:59: #4 Write peak in narrowPeak format file... SRX1924777.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:42:59: #4 Write summits bed file... SRX1924777.10_summits.bed INFO @ Sat, 15 Sep 2018 09:42:59: Done! INFO @ Sat, 15 Sep 2018 09:42:59: #4 Write output xls file... SRX1924777.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:42:59: #4 Write peak in narrowPeak format file... SRX1924777.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:42:59: #4 Write summits bed file... SRX1924777.05_summits.bed INFO @ Sat, 15 Sep 2018 09:42:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (277 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。