Job ID = 11244811 sra ファイルのダウンロード中... Completed: 325180K bytes transferred in 10 seconds (244065K 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 3325176 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3659045/SRR6682739.sra Written 3325176 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3659045/SRR6682739.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: 00:04:40 3325176 reads; of these: 3325176 (100.00%) were paired; of these: 143277 (4.31%) aligned concordantly 0 times 2900930 (87.24%) aligned concordantly exactly 1 time 280969 (8.45%) aligned concordantly >1 times ---- 143277 pairs aligned concordantly 0 times; of these: 78865 (55.04%) aligned discordantly 1 time ---- 64412 pairs aligned 0 times concordantly or discordantly; of these: 128824 mates make up the pairs; of these: 59208 (45.96%) aligned 0 times 46600 (36.17%) aligned exactly 1 time 23016 (17.87%) aligned >1 times 99.11% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 79400 / 3240931 = 0.0245 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 21:58:46: # Command line: callpeak -t SRX3659045.bam -f BAM -g 12100000 -n SRX3659045.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3659045.10 # format = BAM # ChIP-seq file = ['SRX3659045.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 21:58:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 21:58:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 21:58:46: # Command line: callpeak -t SRX3659045.bam -f BAM -g 12100000 -n SRX3659045.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3659045.05 # format = BAM # ChIP-seq file = ['SRX3659045.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 21:58:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 21:58:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 21:58:46: # Command line: callpeak -t SRX3659045.bam -f BAM -g 12100000 -n SRX3659045.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3659045.20 # format = BAM # ChIP-seq file = ['SRX3659045.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 21:58:46: #1 read tag files... INFO @ Tue, 09 Oct 2018 21:58:46: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 21:58:55: 1000000 INFO @ Tue, 09 Oct 2018 21:58:55: 1000000 INFO @ Tue, 09 Oct 2018 21:58:55: 1000000 INFO @ Tue, 09 Oct 2018 21:59:04: 2000000 INFO @ Tue, 09 Oct 2018 21:59:05: 2000000 INFO @ Tue, 09 Oct 2018 21:59:05: 2000000 INFO @ Tue, 09 Oct 2018 21:59:12: 3000000 INFO @ Tue, 09 Oct 2018 21:59:15: 3000000 INFO @ Tue, 09 Oct 2018 21:59:15: 3000000 INFO @ Tue, 09 Oct 2018 21:59:21: 4000000 INFO @ Tue, 09 Oct 2018 21:59:25: 4000000 INFO @ Tue, 09 Oct 2018 21:59:25: 4000000 INFO @ Tue, 09 Oct 2018 21:59:30: 5000000 INFO @ Tue, 09 Oct 2018 21:59:35: 5000000 INFO @ Tue, 09 Oct 2018 21:59:35: 5000000 INFO @ Tue, 09 Oct 2018 21:59:38: 6000000 INFO @ Tue, 09 Oct 2018 21:59:42: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 21:59:42: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 21:59:42: #1 total tags in treatment: 3103157 INFO @ Tue, 09 Oct 2018 21:59:42: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 21:59:42: #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 21:59:42: #1 tags after filtering in treatment: 2485784 INFO @ Tue, 09 Oct 2018 21:59:42: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 21:59:42: #1 finished! INFO @ Tue, 09 Oct 2018 21:59:42: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 21:59:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 21:59:42: #2 number of paired peaks: 186 WARNING @ Tue, 09 Oct 2018 21:59:42: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 09 Oct 2018 21:59:42: start model_add_line... INFO @ Tue, 09 Oct 2018 21:59:42: start X-correlation... INFO @ Tue, 09 Oct 2018 21:59:42: end of X-cor INFO @ Tue, 09 Oct 2018 21:59:42: #2 finished! INFO @ Tue, 09 Oct 2018 21:59:42: #2 predicted fragment length is 211 bps INFO @ Tue, 09 Oct 2018 21:59:42: #2 alternative fragment length(s) may be 0,211,225,591 bps INFO @ Tue, 09 Oct 2018 21:59:42: #2.2 Generate R script for model : SRX3659045.10_model.r INFO @ Tue, 09 Oct 2018 21:59:42: #3 Call peaks... INFO @ Tue, 09 Oct 2018 21:59:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 21:59:45: 6000000 INFO @ Tue, 09 Oct 2018 21:59:45: 6000000 INFO @ Tue, 09 Oct 2018 21:59:48: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 21:59:50: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 21:59:50: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 21:59:50: #1 total tags in treatment: 3103157 INFO @ Tue, 09 Oct 2018 21:59:50: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 21:59:50: #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 21:59:50: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 21:59:50: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 21:59:50: #1 total tags in treatment: 3103157 INFO @ Tue, 09 Oct 2018 21:59:50: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 21:59:50: #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 21:59:50: #1 tags after filtering in treatment: 2485784 INFO @ Tue, 09 Oct 2018 21:59:50: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 21:59:50: #1 finished! INFO @ Tue, 09 Oct 2018 21:59:50: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 21:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 21:59:50: #1 tags after filtering in treatment: 2485784 INFO @ Tue, 09 Oct 2018 21:59:50: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 21:59:50: #1 finished! INFO @ Tue, 09 Oct 2018 21:59:50: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 21:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 21:59:50: #2 number of paired peaks: 186 WARNING @ Tue, 09 Oct 2018 21:59:50: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 09 Oct 2018 21:59:50: start model_add_line... INFO @ Tue, 09 Oct 2018 21:59:50: start X-correlation... INFO @ Tue, 09 Oct 2018 21:59:50: end of X-cor INFO @ Tue, 09 Oct 2018 21:59:50: #2 finished! INFO @ Tue, 09 Oct 2018 21:59:50: #2 predicted fragment length is 211 bps INFO @ Tue, 09 Oct 2018 21:59:50: #2 alternative fragment length(s) may be 0,211,225,591 bps INFO @ Tue, 09 Oct 2018 21:59:50: #2.2 Generate R script for model : SRX3659045.05_model.r INFO @ Tue, 09 Oct 2018 21:59:50: #2 number of paired peaks: 186 WARNING @ Tue, 09 Oct 2018 21:59:50: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 09 Oct 2018 21:59:50: start model_add_line... INFO @ Tue, 09 Oct 2018 21:59:50: #3 Call peaks... INFO @ Tue, 09 Oct 2018 21:59:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 21:59:50: start X-correlation... INFO @ Tue, 09 Oct 2018 21:59:50: end of X-cor INFO @ Tue, 09 Oct 2018 21:59:50: #2 finished! INFO @ Tue, 09 Oct 2018 21:59:50: #2 predicted fragment length is 211 bps INFO @ Tue, 09 Oct 2018 21:59:50: #2 alternative fragment length(s) may be 0,211,225,591 bps INFO @ Tue, 09 Oct 2018 21:59:50: #2.2 Generate R script for model : SRX3659045.20_model.r INFO @ Tue, 09 Oct 2018 21:59:50: #3 Call peaks... INFO @ Tue, 09 Oct 2018 21:59:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 21:59:50: #4 Write output xls file... SRX3659045.10_peaks.xls INFO @ Tue, 09 Oct 2018 21:59:50: #4 Write peak in narrowPeak format file... SRX3659045.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 21:59:50: #4 Write summits bed file... SRX3659045.10_summits.bed INFO @ Tue, 09 Oct 2018 21:59:50: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (15 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 21:59:56: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 21:59:56: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 21:59:58: #4 Write output xls file... SRX3659045.20_peaks.xls INFO @ Tue, 09 Oct 2018 21:59:58: #4 Write peak in narrowPeak format file... SRX3659045.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 21:59:58: #4 Write summits bed file... SRX3659045.20_summits.bed INFO @ Tue, 09 Oct 2018 21:59:58: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 21:59:58: #4 Write output xls file... SRX3659045.05_peaks.xls INFO @ Tue, 09 Oct 2018 21:59:58: #4 Write peak in narrowPeak format file... SRX3659045.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 21:59:58: #4 Write summits bed file... SRX3659045.05_summits.bed INFO @ Tue, 09 Oct 2018 21:59:58: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (17 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。