Job ID = 11192877 sra ファイルのダウンロード中... Completed: 1299332K bytes transferred in 47 seconds (225918K 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 10578053 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2767197/SRR5483853.sra Written 10578053 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2767197/SRR5483853.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: 00:16:39 10578053 reads; of these: 10578053 (100.00%) were paired; of these: 760876 (7.19%) aligned concordantly 0 times 8229578 (77.80%) aligned concordantly exactly 1 time 1587599 (15.01%) aligned concordantly >1 times ---- 760876 pairs aligned concordantly 0 times; of these: 53074 (6.98%) aligned discordantly 1 time ---- 707802 pairs aligned 0 times concordantly or discordantly; of these: 1415604 mates make up the pairs; of these: 1098283 (77.58%) aligned 0 times 234972 (16.60%) aligned exactly 1 time 82349 (5.82%) aligned >1 times 94.81% overall alignment rate Time searching: 00:16:39 Overall time: 00:16:39 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_sort_core] merging from 16 files... [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] 9296728 / 9394370 = 0.9896 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 10:36:23: # Command line: callpeak -t SRX2767197.bam -f BAM -g 12100000 -n SRX2767197.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2767197.10 # format = BAM # ChIP-seq file = ['SRX2767197.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 10:36:23: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:36:23: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:36:23: # Command line: callpeak -t SRX2767197.bam -f BAM -g 12100000 -n SRX2767197.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2767197.20 # format = BAM # ChIP-seq file = ['SRX2767197.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 10:36:23: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:36:23: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:36:23: # Command line: callpeak -t SRX2767197.bam -f BAM -g 12100000 -n SRX2767197.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2767197.05 # format = BAM # ChIP-seq file = ['SRX2767197.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 10:36:23: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:36:23: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:36:30: 1000000 INFO @ Sat, 15 Sep 2018 10:36:31: 1000000 INFO @ Sat, 15 Sep 2018 10:36:31: 1000000 INFO @ Sat, 15 Sep 2018 10:36:34: #1 tag size is determined as 136 bps INFO @ Sat, 15 Sep 2018 10:36:34: #1 tag size = 136 INFO @ Sat, 15 Sep 2018 10:36:34: #1 total tags in treatment: 559982 INFO @ Sat, 15 Sep 2018 10:36:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:36:34: #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 10:36:34: #1 tags after filtering in treatment: 107312 INFO @ Sat, 15 Sep 2018 10:36:34: #1 Redundant rate of treatment: 0.81 INFO @ Sat, 15 Sep 2018 10:36:34: #1 finished! INFO @ Sat, 15 Sep 2018 10:36:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:36:34: #2 number of paired peaks: 268 WARNING @ Sat, 15 Sep 2018 10:36:34: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Sat, 15 Sep 2018 10:36:34: start model_add_line... INFO @ Sat, 15 Sep 2018 10:36:34: start X-correlation... INFO @ Sat, 15 Sep 2018 10:36:34: end of X-cor INFO @ Sat, 15 Sep 2018 10:36:34: #2 finished! INFO @ Sat, 15 Sep 2018 10:36:34: #2 predicted fragment length is 165 bps INFO @ Sat, 15 Sep 2018 10:36:34: #2 alternative fragment length(s) may be 4,8,67,105,165,187,246,271,304,522,578 bps INFO @ Sat, 15 Sep 2018 10:36:34: #2.2 Generate R script for model : SRX2767197.05_model.r WARNING @ Sat, 15 Sep 2018 10:36:34: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:36:34: #2 You may need to consider one of the other alternative d(s): 4,8,67,105,165,187,246,271,304,522,578 WARNING @ Sat, 15 Sep 2018 10:36:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 10:36:34: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:36:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:36:34: #1 tag size is determined as 136 bps INFO @ Sat, 15 Sep 2018 10:36:34: #1 tag size = 136 INFO @ Sat, 15 Sep 2018 10:36:34: #1 total tags in treatment: 559982 INFO @ Sat, 15 Sep 2018 10:36:34: #1 tag size is determined as 136 bps INFO @ Sat, 15 Sep 2018 10:36:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:36:34: #1 tag size = 136 INFO @ Sat, 15 Sep 2018 10:36:34: #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 10:36:34: #1 total tags in treatment: 559982 INFO @ Sat, 15 Sep 2018 10:36:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:36:34: #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 10:36:34: #1 tags after filtering in treatment: 107312 INFO @ Sat, 15 Sep 2018 10:36:34: #1 Redundant rate of treatment: 0.81 INFO @ Sat, 15 Sep 2018 10:36:34: #1 finished! INFO @ Sat, 15 Sep 2018 10:36:34: #1 tags after filtering in treatment: 107312 INFO @ Sat, 15 Sep 2018 10:36:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:36:34: #1 Redundant rate of treatment: 0.81 INFO @ Sat, 15 Sep 2018 10:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:36:34: #1 finished! INFO @ Sat, 15 Sep 2018 10:36:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:36:34: #2 number of paired peaks: 268 WARNING @ Sat, 15 Sep 2018 10:36:34: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Sat, 15 Sep 2018 10:36:34: start model_add_line... INFO @ Sat, 15 Sep 2018 10:36:34: #2 number of paired peaks: 268 WARNING @ Sat, 15 Sep 2018 10:36:34: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Sat, 15 Sep 2018 10:36:34: start model_add_line... INFO @ Sat, 15 Sep 2018 10:36:34: start X-correlation... INFO @ Sat, 15 Sep 2018 10:36:34: start X-correlation... INFO @ Sat, 15 Sep 2018 10:36:34: end of X-cor INFO @ Sat, 15 Sep 2018 10:36:34: #2 finished! INFO @ Sat, 15 Sep 2018 10:36:34: #2 predicted fragment length is 165 bps INFO @ Sat, 15 Sep 2018 10:36:34: #2 alternative fragment length(s) may be 4,8,67,105,165,187,246,271,304,522,578 bps INFO @ Sat, 15 Sep 2018 10:36:34: #2.2 Generate R script for model : SRX2767197.20_model.r INFO @ Sat, 15 Sep 2018 10:36:34: end of X-cor INFO @ Sat, 15 Sep 2018 10:36:34: #2 finished! INFO @ Sat, 15 Sep 2018 10:36:34: #2 predicted fragment length is 165 bps INFO @ Sat, 15 Sep 2018 10:36:34: #2 alternative fragment length(s) may be 4,8,67,105,165,187,246,271,304,522,578 bps INFO @ Sat, 15 Sep 2018 10:36:34: #2.2 Generate R script for model : SRX2767197.10_model.r WARNING @ Sat, 15 Sep 2018 10:36:34: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:36:34: #2 You may need to consider one of the other alternative d(s): 4,8,67,105,165,187,246,271,304,522,578 WARNING @ Sat, 15 Sep 2018 10:36:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 10:36:34: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:36:34: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 15 Sep 2018 10:36:34: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:36:34: #2 You may need to consider one of the other alternative d(s): 4,8,67,105,165,187,246,271,304,522,578 WARNING @ Sat, 15 Sep 2018 10:36:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 10:36:34: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:36:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:36:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:36:34: #4 Write output xls file... SRX2767197.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:36:34: #4 Write peak in narrowPeak format file... SRX2767197.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:36:34: #4 Write summits bed file... SRX2767197.05_summits.bed INFO @ Sat, 15 Sep 2018 10:36:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:36:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:36:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:36:34: #4 Write output xls file... SRX2767197.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:36:34: #4 Write peak in narrowPeak format file... SRX2767197.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:36:34: #4 Write output xls file... SRX2767197.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:36:34: #4 Write peak in narrowPeak format file... SRX2767197.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:36:34: #4 Write summits bed file... SRX2767197.10_summits.bed INFO @ Sat, 15 Sep 2018 10:36:34: #4 Write summits bed file... SRX2767197.20_summits.bed INFO @ Sat, 15 Sep 2018 10:36:34: Done! INFO @ Sat, 15 Sep 2018 10:36:34: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (10 records, 4 fields): 2 millis pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields)CompletedMACS2peakCalling : 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。