Job ID = 11193219 sra ファイルのダウンロード中... Completed: 334091K bytes transferred in 6 seconds (441440K 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 7787817 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977505/SRR1951351.sra Written 7787817 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977505/SRR1951351.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: 00:03:24 7787817 reads; of these: 7787817 (100.00%) were paired; of these: 2917530 (37.46%) aligned concordantly 0 times 4363158 (56.03%) aligned concordantly exactly 1 time 507129 (6.51%) aligned concordantly >1 times ---- 2917530 pairs aligned concordantly 0 times; of these: 205819 (7.05%) aligned discordantly 1 time ---- 2711711 pairs aligned 0 times concordantly or discordantly; of these: 5423422 mates make up the pairs; of these: 5157421 (95.10%) aligned 0 times 203590 (3.75%) aligned exactly 1 time 62411 (1.15%) aligned >1 times 66.89% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 3067342 / 5027226 = 0.6101 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 11:17:43: # Command line: callpeak -t SRX977505.bam -f BAM -g 12100000 -n SRX977505.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977505.05 # format = BAM # ChIP-seq file = ['SRX977505.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 11:17:43: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:17:43: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:17:43: # Command line: callpeak -t SRX977505.bam -f BAM -g 12100000 -n SRX977505.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977505.20 # format = BAM # ChIP-seq file = ['SRX977505.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 11:17:43: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:17:43: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:17:43: # Command line: callpeak -t SRX977505.bam -f BAM -g 12100000 -n SRX977505.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977505.10 # format = BAM # ChIP-seq file = ['SRX977505.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 11:17:43: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:17:43: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:17:48: 1000000 INFO @ Sat, 15 Sep 2018 11:17:49: 1000000 INFO @ Sat, 15 Sep 2018 11:17:49: 1000000 INFO @ Sat, 15 Sep 2018 11:17:54: 2000000 INFO @ Sat, 15 Sep 2018 11:17:54: 2000000 INFO @ Sat, 15 Sep 2018 11:17:54: 2000000 INFO @ Sat, 15 Sep 2018 11:17:59: 3000000 INFO @ Sat, 15 Sep 2018 11:18:00: 3000000 INFO @ Sat, 15 Sep 2018 11:18:00: 3000000 INFO @ Sat, 15 Sep 2018 11:18:05: 4000000 INFO @ Sat, 15 Sep 2018 11:18:05: 4000000 INFO @ Sat, 15 Sep 2018 11:18:05: 4000000 INFO @ Sat, 15 Sep 2018 11:18:06: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:18:06: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:18:06: #1 total tags in treatment: 1925257 INFO @ Sat, 15 Sep 2018 11:18:06: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:18:06: #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 11:18:06: #1 tags after filtering in treatment: 1525621 INFO @ Sat, 15 Sep 2018 11:18:06: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Sep 2018 11:18:06: #1 finished! INFO @ Sat, 15 Sep 2018 11:18:06: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:18:07: #2 number of paired peaks: 206 WARNING @ Sat, 15 Sep 2018 11:18:07: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 15 Sep 2018 11:18:07: start model_add_line... INFO @ Sat, 15 Sep 2018 11:18:07: start X-correlation... INFO @ Sat, 15 Sep 2018 11:18:07: end of X-cor INFO @ Sat, 15 Sep 2018 11:18:07: #2 finished! INFO @ Sat, 15 Sep 2018 11:18:07: #2 predicted fragment length is 26 bps INFO @ Sat, 15 Sep 2018 11:18:07: #2 alternative fragment length(s) may be 4,26,556 bps INFO @ Sat, 15 Sep 2018 11:18:07: #2.2 Generate R script for model : SRX977505.20_model.r WARNING @ Sat, 15 Sep 2018 11:18:07: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:18:07: #2 You may need to consider one of the other alternative d(s): 4,26,556 WARNING @ Sat, 15 Sep 2018 11:18:07: #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 11:18:07: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:18:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:18:07: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:18:07: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:18:07: #1 total tags in treatment: 1925257 INFO @ Sat, 15 Sep 2018 11:18:07: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:18:07: #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 11:18:07: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:18:07: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:18:07: #1 total tags in treatment: 1925257 INFO @ Sat, 15 Sep 2018 11:18:07: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:18:07: #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 11:18:07: #1 tags after filtering in treatment: 1525621 INFO @ Sat, 15 Sep 2018 11:18:07: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Sep 2018 11:18:07: #1 finished! INFO @ Sat, 15 Sep 2018 11:18:07: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:18:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:18:07: #1 tags after filtering in treatment: 1525621 INFO @ Sat, 15 Sep 2018 11:18:07: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Sep 2018 11:18:07: #1 finished! INFO @ Sat, 15 Sep 2018 11:18:07: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:18:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:18:07: #2 number of paired peaks: 206 WARNING @ Sat, 15 Sep 2018 11:18:07: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 15 Sep 2018 11:18:07: start model_add_line... INFO @ Sat, 15 Sep 2018 11:18:07: start X-correlation... INFO @ Sat, 15 Sep 2018 11:18:07: end of X-cor INFO @ Sat, 15 Sep 2018 11:18:07: #2 finished! INFO @ Sat, 15 Sep 2018 11:18:07: #2 predicted fragment length is 26 bps INFO @ Sat, 15 Sep 2018 11:18:07: #2 alternative fragment length(s) may be 4,26,556 bps INFO @ Sat, 15 Sep 2018 11:18:07: #2.2 Generate R script for model : SRX977505.05_model.r WARNING @ Sat, 15 Sep 2018 11:18:07: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:18:07: #2 You may need to consider one of the other alternative d(s): 4,26,556 WARNING @ Sat, 15 Sep 2018 11:18:07: #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 11:18:07: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:18:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:18:07: #2 number of paired peaks: 206 WARNING @ Sat, 15 Sep 2018 11:18:07: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 15 Sep 2018 11:18:07: start model_add_line... INFO @ Sat, 15 Sep 2018 11:18:07: start X-correlation... INFO @ Sat, 15 Sep 2018 11:18:07: end of X-cor INFO @ Sat, 15 Sep 2018 11:18:07: #2 finished! INFO @ Sat, 15 Sep 2018 11:18:07: #2 predicted fragment length is 26 bps INFO @ Sat, 15 Sep 2018 11:18:07: #2 alternative fragment length(s) may be 4,26,556 bps INFO @ Sat, 15 Sep 2018 11:18:07: #2.2 Generate R script for model : SRX977505.10_model.r WARNING @ Sat, 15 Sep 2018 11:18:07: #2 Since the d (26) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:18:07: #2 You may need to consider one of the other alternative d(s): 4,26,556 WARNING @ Sat, 15 Sep 2018 11:18:07: #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 11:18:07: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:18:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:18:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:18:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:18:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:18:11: #4 Write output xls file... SRX977505.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:18:11: #4 Write peak in narrowPeak format file... SRX977505.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:18:11: #4 Write summits bed file... SRX977505.20_summits.bed INFO @ Sat, 15 Sep 2018 11:18:11: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (219 records, 4 fields): 88 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:18:12: #4 Write output xls file... SRX977505.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:18:12: #4 Write peak in narrowPeak format file... SRX977505.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:18:12: #4 Write summits bed file... SRX977505.10_summits.bed INFO @ Sat, 15 Sep 2018 11:18:12: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (633 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:18:12: #4 Write output xls file... SRX977505.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:18:12: #4 Write peak in narrowPeak format file... SRX977505.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:18:12: #4 Write summits bed file... SRX977505.05_summits.bed INFO @ Sat, 15 Sep 2018 11:18:12: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1620 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。