Job ID = 11192869 sra ファイルのダウンロード中... Completed: 609450K bytes transferred in 8 seconds (589166K 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 8897416 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2252393/SRR4432884.sra Written 8897416 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2252393/SRR4432884.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: 00:08:41 8897416 reads; of these: 8897416 (100.00%) were paired; of these: 1052184 (11.83%) aligned concordantly 0 times 6120788 (68.79%) aligned concordantly exactly 1 time 1724444 (19.38%) aligned concordantly >1 times ---- 1052184 pairs aligned concordantly 0 times; of these: 94723 (9.00%) aligned discordantly 1 time ---- 957461 pairs aligned 0 times concordantly or discordantly; of these: 1914922 mates make up the pairs; of these: 1360647 (71.05%) aligned 0 times 375687 (19.62%) aligned exactly 1 time 178588 (9.33%) aligned >1 times 92.35% overall alignment rate Time searching: 00:08:41 Overall time: 00:08:41 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 8 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] 7868742 / 7936351 = 0.9915 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 10:17:46: # Command line: callpeak -t SRX2252393.bam -f BAM -g 12100000 -n SRX2252393.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2252393.20 # format = BAM # ChIP-seq file = ['SRX2252393.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 10:17:46: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:17:46: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:17:46: # Command line: callpeak -t SRX2252393.bam -f BAM -g 12100000 -n SRX2252393.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2252393.10 # format = BAM # ChIP-seq file = ['SRX2252393.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 10:17:46: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:17:46: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:17:46: # Command line: callpeak -t SRX2252393.bam -f BAM -g 12100000 -n SRX2252393.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2252393.05 # format = BAM # ChIP-seq file = ['SRX2252393.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 10:17:46: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:17:46: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:17:50: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:17:50: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:17:50: #1 total tags in treatment: 64907 INFO @ Sat, 15 Sep 2018 10:17:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:17:50: #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 10:17:50: #1 tags after filtering in treatment: 58296 INFO @ Sat, 15 Sep 2018 10:17:50: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Sep 2018 10:17:50: #1 finished! INFO @ Sat, 15 Sep 2018 10:17:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:17:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:17:50: #2 number of paired peaks: 359 WARNING @ Sat, 15 Sep 2018 10:17:50: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sat, 15 Sep 2018 10:17:50: start model_add_line... INFO @ Sat, 15 Sep 2018 10:17:50: start X-correlation... INFO @ Sat, 15 Sep 2018 10:17:50: end of X-cor INFO @ Sat, 15 Sep 2018 10:17:50: #2 finished! INFO @ Sat, 15 Sep 2018 10:17:50: #2 predicted fragment length is 147 bps INFO @ Sat, 15 Sep 2018 10:17:50: #2 alternative fragment length(s) may be 115,147,267,552,578 bps INFO @ Sat, 15 Sep 2018 10:17:50: #2.2 Generate R script for model : SRX2252393.20_model.r INFO @ Sat, 15 Sep 2018 10:17:50: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:17:50: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:17:50: #1 total tags in treatment: 64907 INFO @ Sat, 15 Sep 2018 10:17:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:17:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) WARNING @ Sat, 15 Sep 2018 10:17:50: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:17:50: #2 You may need to consider one of the other alternative d(s): 115,147,267,552,578 WARNING @ Sat, 15 Sep 2018 10:17:50: #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 10:17:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:17:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:17:50: #1 tags after filtering in treatment: 58296 INFO @ Sat, 15 Sep 2018 10:17:50: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Sep 2018 10:17:50: #1 finished! INFO @ Sat, 15 Sep 2018 10:17:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:17:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:17:50: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:17:50: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:17:50: #1 total tags in treatment: 64907 INFO @ Sat, 15 Sep 2018 10:17:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:17:50: #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 10:17:50: #2 number of paired peaks: 359 WARNING @ Sat, 15 Sep 2018 10:17:50: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sat, 15 Sep 2018 10:17:50: start model_add_line... INFO @ Sat, 15 Sep 2018 10:17:50: start X-correlation... INFO @ Sat, 15 Sep 2018 10:17:50: end of X-cor INFO @ Sat, 15 Sep 2018 10:17:50: #2 finished! INFO @ Sat, 15 Sep 2018 10:17:50: #1 tags after filtering in treatment: 58296 INFO @ Sat, 15 Sep 2018 10:17:50: #2 predicted fragment length is 147 bps INFO @ Sat, 15 Sep 2018 10:17:50: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Sep 2018 10:17:50: #2 alternative fragment length(s) may be 115,147,267,552,578 bps INFO @ Sat, 15 Sep 2018 10:17:50: #1 finished! INFO @ Sat, 15 Sep 2018 10:17:50: #2.2 Generate R script for model : SRX2252393.10_model.r INFO @ Sat, 15 Sep 2018 10:17:50: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:17:50: #2 looking for paired plus/minus strand peaks... WARNING @ Sat, 15 Sep 2018 10:17:50: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:17:50: #2 You may need to consider one of the other alternative d(s): 115,147,267,552,578 WARNING @ Sat, 15 Sep 2018 10:17:50: #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 10:17:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:17:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:17:50: #2 number of paired peaks: 359 WARNING @ Sat, 15 Sep 2018 10:17:50: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sat, 15 Sep 2018 10:17:50: start model_add_line... INFO @ Sat, 15 Sep 2018 10:17:50: start X-correlation... INFO @ Sat, 15 Sep 2018 10:17:50: end of X-cor INFO @ Sat, 15 Sep 2018 10:17:50: #2 finished! INFO @ Sat, 15 Sep 2018 10:17:50: #2 predicted fragment length is 147 bps INFO @ Sat, 15 Sep 2018 10:17:50: #2 alternative fragment length(s) may be 115,147,267,552,578 bps INFO @ Sat, 15 Sep 2018 10:17:50: #2.2 Generate R script for model : SRX2252393.05_model.r WARNING @ Sat, 15 Sep 2018 10:17:50: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 10:17:50: #2 You may need to consider one of the other alternative d(s): 115,147,267,552,578 WARNING @ Sat, 15 Sep 2018 10:17:50: #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 10:17:50: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:17:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Sep 2018 10:17:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:17:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:17:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:17:50: #4 Write output xls file... SRX2252393.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:17:50: #4 Write peak in narrowPeak format file... SRX2252393.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:17:50: #4 Write summits bed file... SRX2252393.20_summits.bed INFO @ Sat, 15 Sep 2018 10:17:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:17:51: #4 Write output xls file... SRX2252393.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:17:51: #4 Write peak in narrowPeak format file... SRX2252393.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:17:51: #4 Write output xls file... SRX2252393.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:17:51: #4 Write summits bed file... SRX2252393.10_summits.bed INFO @ Sat, 15 Sep 2018 10:17:51: #4 Write peak in narrowPeak format file... SRX2252393.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:17:51: Done! INFO @ Sat, 15 Sep 2018 10:17:51: #4 Write summits bed file... SRX2252393.05_summits.bed INFO @ Sat, 15 Sep 2018 10:17:51: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。