Job ID = 11244874 sra ファイルのダウンロード中... Completed: 444288K bytes transferred in 7 seconds (491780K 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 4533008 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765836/SRR6807569.sra Written 4533008 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3765836/SRR6807569.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: 00:00:01 Multiseed full-index search: 00:06:07 4533008 reads; of these: 4533008 (100.00%) were paired; of these: 170700 (3.77%) aligned concordantly 0 times 3884221 (85.69%) aligned concordantly exactly 1 time 478087 (10.55%) aligned concordantly >1 times ---- 170700 pairs aligned concordantly 0 times; of these: 87142 (51.05%) aligned discordantly 1 time ---- 83558 pairs aligned 0 times concordantly or discordantly; of these: 167116 mates make up the pairs; of these: 78500 (46.97%) aligned 0 times 58442 (34.97%) aligned exactly 1 time 30174 (18.06%) aligned >1 times 99.13% overall alignment rate Time searching: 00:06:08 Overall time: 00:06:08 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] 100287 / 4428436 = 0.0226 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 22:32:00: # Command line: callpeak -t SRX3765836.bam -f BAM -g 12100000 -n SRX3765836.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3765836.05 # format = BAM # ChIP-seq file = ['SRX3765836.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 22:32:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:32:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:32:00: # Command line: callpeak -t SRX3765836.bam -f BAM -g 12100000 -n SRX3765836.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3765836.10 # format = BAM # ChIP-seq file = ['SRX3765836.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 22:32:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:32:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:32:00: # Command line: callpeak -t SRX3765836.bam -f BAM -g 12100000 -n SRX3765836.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3765836.20 # format = BAM # ChIP-seq file = ['SRX3765836.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 22:32:00: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:32:00: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:32:09: 1000000 INFO @ Tue, 09 Oct 2018 22:32:09: 1000000 INFO @ Tue, 09 Oct 2018 22:32:09: 1000000 INFO @ Tue, 09 Oct 2018 22:32:18: 2000000 INFO @ Tue, 09 Oct 2018 22:32:18: 2000000 INFO @ Tue, 09 Oct 2018 22:32:18: 2000000 INFO @ Tue, 09 Oct 2018 22:32:26: 3000000 INFO @ Tue, 09 Oct 2018 22:32:26: 3000000 INFO @ Tue, 09 Oct 2018 22:32:26: 3000000 INFO @ Tue, 09 Oct 2018 22:32:35: 4000000 INFO @ Tue, 09 Oct 2018 22:32:35: 4000000 INFO @ Tue, 09 Oct 2018 22:32:35: 4000000 INFO @ Tue, 09 Oct 2018 22:32:43: 5000000 INFO @ Tue, 09 Oct 2018 22:32:43: 5000000 INFO @ Tue, 09 Oct 2018 22:32:43: 5000000 INFO @ Tue, 09 Oct 2018 22:32:52: 6000000 INFO @ Tue, 09 Oct 2018 22:32:52: 6000000 INFO @ Tue, 09 Oct 2018 22:32:52: 6000000 INFO @ Tue, 09 Oct 2018 22:33:00: 7000000 INFO @ Tue, 09 Oct 2018 22:33:00: 7000000 INFO @ Tue, 09 Oct 2018 22:33:00: 7000000 INFO @ Tue, 09 Oct 2018 22:33:09: 8000000 INFO @ Tue, 09 Oct 2018 22:33:09: 8000000 INFO @ Tue, 09 Oct 2018 22:33:09: 8000000 INFO @ Tue, 09 Oct 2018 22:33:15: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:33:15: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:33:15: #1 total tags in treatment: 4262645 INFO @ Tue, 09 Oct 2018 22:33:15: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:33:15: #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 22:33:15: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:33:15: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:33:15: #1 tag size is determined as 100 bps INFO @ Tue, 09 Oct 2018 22:33:15: #1 total tags in treatment: 4262645 INFO @ Tue, 09 Oct 2018 22:33:15: #1 tag size = 100 INFO @ Tue, 09 Oct 2018 22:33:15: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:33:15: #1 total tags in treatment: 4262645 INFO @ Tue, 09 Oct 2018 22:33:15: #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 22:33:15: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:33:15: #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 22:33:16: #1 tags after filtering in treatment: 3472409 INFO @ Tue, 09 Oct 2018 22:33:16: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 22:33:16: #1 finished! INFO @ Tue, 09 Oct 2018 22:33:16: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:33:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:33:16: #1 tags after filtering in treatment: 3472409 INFO @ Tue, 09 Oct 2018 22:33:16: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 22:33:16: #1 finished! INFO @ Tue, 09 Oct 2018 22:33:16: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:33:16: #1 tags after filtering in treatment: 3472409 INFO @ Tue, 09 Oct 2018 22:33:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:33:16: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 09 Oct 2018 22:33:16: #1 finished! INFO @ Tue, 09 Oct 2018 22:33:16: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:33:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:33:16: #2 number of paired peaks: 103 WARNING @ Tue, 09 Oct 2018 22:33:16: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 09 Oct 2018 22:33:16: start model_add_line... INFO @ Tue, 09 Oct 2018 22:33:16: #2 number of paired peaks: 103 WARNING @ Tue, 09 Oct 2018 22:33:16: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 09 Oct 2018 22:33:16: start model_add_line... INFO @ Tue, 09 Oct 2018 22:33:16: #2 number of paired peaks: 103 WARNING @ Tue, 09 Oct 2018 22:33:16: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 09 Oct 2018 22:33:16: start model_add_line... INFO @ Tue, 09 Oct 2018 22:33:16: start X-correlation... INFO @ Tue, 09 Oct 2018 22:33:16: start X-correlation... INFO @ Tue, 09 Oct 2018 22:33:16: start X-correlation... INFO @ Tue, 09 Oct 2018 22:33:16: end of X-cor INFO @ Tue, 09 Oct 2018 22:33:16: #2 finished! INFO @ Tue, 09 Oct 2018 22:33:16: #2 predicted fragment length is 172 bps INFO @ Tue, 09 Oct 2018 22:33:16: #2 alternative fragment length(s) may be 1,149,165,172,238,563 bps INFO @ Tue, 09 Oct 2018 22:33:16: #2.2 Generate R script for model : SRX3765836.10_model.r INFO @ Tue, 09 Oct 2018 22:33:16: end of X-cor INFO @ Tue, 09 Oct 2018 22:33:16: #2 finished! INFO @ Tue, 09 Oct 2018 22:33:16: #2 predicted fragment length is 172 bps INFO @ Tue, 09 Oct 2018 22:33:16: #2 alternative fragment length(s) may be 1,149,165,172,238,563 bps INFO @ Tue, 09 Oct 2018 22:33:16: #2.2 Generate R script for model : SRX3765836.20_model.r INFO @ Tue, 09 Oct 2018 22:33:16: end of X-cor INFO @ Tue, 09 Oct 2018 22:33:16: #2 finished! INFO @ Tue, 09 Oct 2018 22:33:16: #2 predicted fragment length is 172 bps INFO @ Tue, 09 Oct 2018 22:33:16: #2 alternative fragment length(s) may be 1,149,165,172,238,563 bps INFO @ Tue, 09 Oct 2018 22:33:16: #2.2 Generate R script for model : SRX3765836.05_model.r WARNING @ Tue, 09 Oct 2018 22:33:16: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:33:16: #2 You may need to consider one of the other alternative d(s): 1,149,165,172,238,563 WARNING @ Tue, 09 Oct 2018 22:33:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:33:16: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:33:16: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 09 Oct 2018 22:33:16: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:33:16: #2 You may need to consider one of the other alternative d(s): 1,149,165,172,238,563 WARNING @ Tue, 09 Oct 2018 22:33:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:33:16: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:33:16: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 09 Oct 2018 22:33:16: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 09 Oct 2018 22:33:16: #2 You may need to consider one of the other alternative d(s): 1,149,165,172,238,563 WARNING @ Tue, 09 Oct 2018 22:33:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:33:16: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:33:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:33:23: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:33:23: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:33:23: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 22:33:26: #4 Write output xls file... SRX3765836.10_peaks.xls INFO @ Tue, 09 Oct 2018 22:33:26: #4 Write peak in narrowPeak format file... SRX3765836.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:33:26: #4 Write summits bed file... SRX3765836.10_summits.bed INFO @ Tue, 09 Oct 2018 22:33:26: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:33:26: #4 Write output xls file... SRX3765836.20_peaks.xls INFO @ Tue, 09 Oct 2018 22:33:26: #4 Write peak in narrowPeak format file... SRX3765836.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:33:26: #4 Write summits bed file... SRX3765836.20_summits.bed INFO @ Tue, 09 Oct 2018 22:33:26: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 22:33:26: #4 Write output xls file... SRX3765836.05_peaks.xls INFO @ Tue, 09 Oct 2018 22:33:26: #4 Write peak in narrowPeak format file... SRX3765836.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 22:33:26: #4 Write summits bed file... SRX3765836.05_summits.bed INFO @ Tue, 09 Oct 2018 22:33:26: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。