Job ID = 11245066 sra ファイルのダウンロード中... Completed: 182449K bytes transferred in 6 seconds (225925K 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 5331464 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554778/SRR7696450.sra Written 5331464 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554778/SRR7696450.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: 00:02:12 5331464 reads; of these: 5331464 (100.00%) were paired; of these: 3989842 (74.84%) aligned concordantly 0 times 1194541 (22.41%) aligned concordantly exactly 1 time 147081 (2.76%) aligned concordantly >1 times ---- 3989842 pairs aligned concordantly 0 times; of these: 1233 (0.03%) aligned discordantly 1 time ---- 3988609 pairs aligned 0 times concordantly or discordantly; of these: 7977218 mates make up the pairs; of these: 6349141 (79.59%) aligned 0 times 1449131 (18.17%) aligned exactly 1 time 178946 (2.24%) aligned >1 times 40.46% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 157688 / 1342499 = 0.1175 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 23:21:11: # Command line: callpeak -t SRX4554778.bam -f BAM -g 12100000 -n SRX4554778.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554778.10 # format = BAM # ChIP-seq file = ['SRX4554778.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 23:21:11: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:21:11: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:21:11: # Command line: callpeak -t SRX4554778.bam -f BAM -g 12100000 -n SRX4554778.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554778.20 # format = BAM # ChIP-seq file = ['SRX4554778.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 23:21:11: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:21:11: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:21:11: # Command line: callpeak -t SRX4554778.bam -f BAM -g 12100000 -n SRX4554778.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554778.05 # format = BAM # ChIP-seq file = ['SRX4554778.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 23:21:11: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:21:11: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:21:17: 1000000 INFO @ Tue, 09 Oct 2018 23:21:17: 1000000 INFO @ Tue, 09 Oct 2018 23:21:17: 1000000 INFO @ Tue, 09 Oct 2018 23:21:22: 2000000 INFO @ Tue, 09 Oct 2018 23:21:23: 2000000 INFO @ Tue, 09 Oct 2018 23:21:23: 2000000 INFO @ Tue, 09 Oct 2018 23:21:27: 3000000 INFO @ Tue, 09 Oct 2018 23:21:29: 3000000 INFO @ Tue, 09 Oct 2018 23:21:29: 3000000 INFO @ Tue, 09 Oct 2018 23:21:33: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:21:33: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:21:33: #1 total tags in treatment: 1183956 INFO @ Tue, 09 Oct 2018 23:21:33: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:21:33: #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 23:21:33: #1 tags after filtering in treatment: 630241 INFO @ Tue, 09 Oct 2018 23:21:33: #1 Redundant rate of treatment: 0.47 INFO @ Tue, 09 Oct 2018 23:21:33: #1 finished! INFO @ Tue, 09 Oct 2018 23:21:33: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:21:33: #2 number of paired peaks: 929 WARNING @ Tue, 09 Oct 2018 23:21:33: Fewer paired peaks (929) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 929 pairs to build model! INFO @ Tue, 09 Oct 2018 23:21:33: start model_add_line... INFO @ Tue, 09 Oct 2018 23:21:33: start X-correlation... INFO @ Tue, 09 Oct 2018 23:21:33: end of X-cor INFO @ Tue, 09 Oct 2018 23:21:33: #2 finished! INFO @ Tue, 09 Oct 2018 23:21:33: #2 predicted fragment length is 214 bps INFO @ Tue, 09 Oct 2018 23:21:33: #2 alternative fragment length(s) may be 1,214,238 bps INFO @ Tue, 09 Oct 2018 23:21:33: #2.2 Generate R script for model : SRX4554778.20_model.r INFO @ Tue, 09 Oct 2018 23:21:33: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:21:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:21:34: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:21:34: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:21:34: #1 total tags in treatment: 1183956 INFO @ Tue, 09 Oct 2018 23:21:34: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:21:34: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:21:34: #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 23:21:34: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:21:34: #1 total tags in treatment: 1183956 INFO @ Tue, 09 Oct 2018 23:21:34: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:21:34: #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 23:21:34: #1 tags after filtering in treatment: 630241 INFO @ Tue, 09 Oct 2018 23:21:34: #1 Redundant rate of treatment: 0.47 INFO @ Tue, 09 Oct 2018 23:21:34: #1 finished! INFO @ Tue, 09 Oct 2018 23:21:34: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:21:34: #1 tags after filtering in treatment: 630241 INFO @ Tue, 09 Oct 2018 23:21:34: #1 Redundant rate of treatment: 0.47 INFO @ Tue, 09 Oct 2018 23:21:34: #1 finished! INFO @ Tue, 09 Oct 2018 23:21:34: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:21:34: #2 number of paired peaks: 929 WARNING @ Tue, 09 Oct 2018 23:21:34: Fewer paired peaks (929) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 929 pairs to build model! INFO @ Tue, 09 Oct 2018 23:21:34: start model_add_line... INFO @ Tue, 09 Oct 2018 23:21:34: #2 number of paired peaks: 929 WARNING @ Tue, 09 Oct 2018 23:21:34: Fewer paired peaks (929) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 929 pairs to build model! INFO @ Tue, 09 Oct 2018 23:21:34: start model_add_line... INFO @ Tue, 09 Oct 2018 23:21:34: start X-correlation... INFO @ Tue, 09 Oct 2018 23:21:34: start X-correlation... INFO @ Tue, 09 Oct 2018 23:21:34: end of X-cor INFO @ Tue, 09 Oct 2018 23:21:34: #2 finished! INFO @ Tue, 09 Oct 2018 23:21:34: end of X-cor INFO @ Tue, 09 Oct 2018 23:21:34: #2 predicted fragment length is 214 bps INFO @ Tue, 09 Oct 2018 23:21:34: #2 finished! INFO @ Tue, 09 Oct 2018 23:21:34: #2 alternative fragment length(s) may be 1,214,238 bps INFO @ Tue, 09 Oct 2018 23:21:34: #2 predicted fragment length is 214 bps INFO @ Tue, 09 Oct 2018 23:21:34: #2.2 Generate R script for model : SRX4554778.10_model.r INFO @ Tue, 09 Oct 2018 23:21:34: #2 alternative fragment length(s) may be 1,214,238 bps INFO @ Tue, 09 Oct 2018 23:21:34: #2.2 Generate R script for model : SRX4554778.05_model.r INFO @ Tue, 09 Oct 2018 23:21:34: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:21:34: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:21:37: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:21:37: #4 Write output xls file... SRX4554778.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:21:37: #4 Write peak in narrowPeak format file... SRX4554778.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:21:37: #4 Write summits bed file... SRX4554778.20_summits.bed INFO @ Tue, 09 Oct 2018 23:21:37: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (322 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:21:38: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:21:38: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:21:39: #4 Write output xls file... SRX4554778.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:21:39: #4 Write peak in narrowPeak format file... SRX4554778.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:21:39: #4 Write summits bed file... SRX4554778.10_summits.bed INFO @ Tue, 09 Oct 2018 23:21:39: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (437 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:21:39: #4 Write output xls file... SRX4554778.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:21:39: #4 Write peak in narrowPeak format file... SRX4554778.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:21:39: #4 Write summits bed file... SRX4554778.05_summits.bed INFO @ Tue, 09 Oct 2018 23:21:39: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (529 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。