Job ID = 11193135 sra ファイルのダウンロード中... Completed: 109823K bytes transferred in 4 seconds (187281K 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 3410158 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337727/SRR7467876.sra Written 3410158 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337727/SRR7467876.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: 00:00:34 3410158 reads; of these: 3410158 (100.00%) were paired; of these: 3381157 (99.15%) aligned concordantly 0 times 24217 (0.71%) aligned concordantly exactly 1 time 4784 (0.14%) aligned concordantly >1 times ---- 3381157 pairs aligned concordantly 0 times; of these: 90090 (2.66%) aligned discordantly 1 time ---- 3291067 pairs aligned 0 times concordantly or discordantly; of these: 6582134 mates make up the pairs; of these: 6134857 (93.20%) aligned 0 times 379078 (5.76%) aligned exactly 1 time 68199 (1.04%) aligned >1 times 10.05% overall alignment rate Time searching: 00:00:34 Overall time: 00:00:35 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] 68041 / 117751 = 0.5778 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 11:00:01: # Command line: callpeak -t SRX4337727.bam -f BAM -g 12100000 -n SRX4337727.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337727.10 # format = BAM # ChIP-seq file = ['SRX4337727.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 11:00:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:00:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:00:01: # Command line: callpeak -t SRX4337727.bam -f BAM -g 12100000 -n SRX4337727.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337727.20 # format = BAM # ChIP-seq file = ['SRX4337727.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 11:00:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:00:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:00:01: # Command line: callpeak -t SRX4337727.bam -f BAM -g 12100000 -n SRX4337727.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337727.05 # format = BAM # ChIP-seq file = ['SRX4337727.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 11:00:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:00:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:00:04: #1 tag size is determined as 42 bps INFO @ Sat, 15 Sep 2018 11:00:04: #1 tag size = 42 INFO @ Sat, 15 Sep 2018 11:00:04: #1 total tags in treatment: 17580 INFO @ Sat, 15 Sep 2018 11:00:04: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:00:04: #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 11:00:04: #1 tags after filtering in treatment: 16959 INFO @ Sat, 15 Sep 2018 11:00:04: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 11:00:04: #1 finished! INFO @ Sat, 15 Sep 2018 11:00:04: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:00:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:00:04: #2 number of paired peaks: 200 WARNING @ Sat, 15 Sep 2018 11:00:04: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sat, 15 Sep 2018 11:00:04: start model_add_line... INFO @ Sat, 15 Sep 2018 11:00:04: start X-correlation... INFO @ Sat, 15 Sep 2018 11:00:04: end of X-cor INFO @ Sat, 15 Sep 2018 11:00:04: #2 finished! INFO @ Sat, 15 Sep 2018 11:00:04: #2 predicted fragment length is 206 bps INFO @ Sat, 15 Sep 2018 11:00:04: #2 alternative fragment length(s) may be 56,113,143,164,185,206,236,267,388,418,439,514,537,580 bps INFO @ Sat, 15 Sep 2018 11:00:04: #2.2 Generate R script for model : SRX4337727.10_model.r INFO @ Sat, 15 Sep 2018 11:00:04: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:00:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:00:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:00:04: #4 Write output xls file... SRX4337727.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:00:04: #4 Write peak in narrowPeak format file... SRX4337727.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:00:04: #4 Write summits bed file... SRX4337727.10_summits.bed INFO @ Sat, 15 Sep 2018 11:00:04: Done! INFO @ Sat, 15 Sep 2018 11:00:04: #1 tag size is determined as 42 bps INFO @ Sat, 15 Sep 2018 11:00:04: #1 tag size = 42 INFO @ Sat, 15 Sep 2018 11:00:04: #1 total tags in treatment: 17580 INFO @ Sat, 15 Sep 2018 11:00:04: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:00:04: #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 11:00:04: #1 tags after filtering in treatment: 16959 INFO @ Sat, 15 Sep 2018 11:00:04: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 11:00:04: #1 finished! INFO @ Sat, 15 Sep 2018 11:00:04: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:00:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:00:04: #1 tag size is determined as 42 bps INFO @ Sat, 15 Sep 2018 11:00:04: #1 tag size = 42 INFO @ Sat, 15 Sep 2018 11:00:04: #1 total tags in treatment: 17580 INFO @ Sat, 15 Sep 2018 11:00:04: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:00:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (1 chroms): 1 millis INFO @ Sat, 15 Sep 2018 11:00:04: #1 tags after filtering in treatment: 16959 INFO @ Sat, 15 Sep 2018 11:00:04: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 11:00:04: #1 finished! INFO @ Sat, 15 Sep 2018 11:00:04: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:00:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:00:04: #2 number of paired peaks: 200 WARNING @ Sat, 15 Sep 2018 11:00:04: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sat, 15 Sep 2018 11:00:04: start model_add_line... INFO @ Sat, 15 Sep 2018 11:00:04: start X-correlation... INFO @ Sat, 15 Sep 2018 11:00:04: end of X-cor INFO @ Sat, 15 Sep 2018 11:00:04: #2 finished! INFO @ Sat, 15 Sep 2018 11:00:04: #2 predicted fragment length is 206 bps INFO @ Sat, 15 Sep 2018 11:00:04: #2 alternative fragment length(s) may be 56,113,143,164,185,206,236,267,388,418,439,514,537,580 bps INFO @ Sat, 15 Sep 2018 11:00:04: #2.2 Generate R script for model : SRX4337727.20_model.r INFO @ Sat, 15 Sep 2018 11:00:04: #2 number of paired peaks: 200 WARNING @ Sat, 15 Sep 2018 11:00:04: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sat, 15 Sep 2018 11:00:04: start model_add_line... INFO @ Sat, 15 Sep 2018 11:00:04: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:00:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:00:04: start X-correlation... pass2 - checking and writing primary data (1 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:00:04: end of X-cor INFO @ Sat, 15 Sep 2018 11:00:04: #2 finished! INFO @ Sat, 15 Sep 2018 11:00:04: #2 predicted fragment length is 206 bps INFO @ Sat, 15 Sep 2018 11:00:04: #2 alternative fragment length(s) may be 56,113,143,164,185,206,236,267,388,418,439,514,537,580 bps INFO @ Sat, 15 Sep 2018 11:00:04: #2.2 Generate R script for model : SRX4337727.05_model.r INFO @ Sat, 15 Sep 2018 11:00:04: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:00:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:00:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:00:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:00:04: #4 Write output xls file... SRX4337727.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:00:04: #4 Write peak in narrowPeak format file... SRX4337727.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:00:04: #4 Write summits bed file... SRX4337727.20_summits.bed INFO @ Sat, 15 Sep 2018 11:00:04: Done! INFO @ Sat, 15 Sep 2018 11:00:04: #4 Write output xls file... SRX4337727.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:00:04: #4 Write peak in narrowPeak format file... SRX4337727.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:00:04: #4 Write summits bed file... SRX4337727.05_summits.bed INFO @ Sat, 15 Sep 2018 11:00:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。