Job ID = 11162635 sra ファイルのダウンロード中... Completed: 194617K bytes transferred in 7 seconds (215191K 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 6469124 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3709374/SRR6736426.sra Written 6469124 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3709374/SRR6736426.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: 00:04:29 6469124 reads; of these: 6469124 (100.00%) were paired; of these: 1404285 (21.71%) aligned concordantly 0 times 3539860 (54.72%) aligned concordantly exactly 1 time 1524979 (23.57%) aligned concordantly >1 times ---- 1404285 pairs aligned concordantly 0 times; of these: 27791 (1.98%) aligned discordantly 1 time ---- 1376494 pairs aligned 0 times concordantly or discordantly; of these: 2752988 mates make up the pairs; of these: 1850222 (67.21%) aligned 0 times 547880 (19.90%) aligned exactly 1 time 354886 (12.89%) aligned >1 times 85.70% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:30 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] 5001064 / 5081884 = 0.9841 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 @ Wed, 05 Sep 2018 10:44:07: # Command line: callpeak -t SRX3709374.bam -f BAM -g 12100000 -n SRX3709374.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3709374.20 # format = BAM # ChIP-seq file = ['SRX3709374.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 @ Wed, 05 Sep 2018 10:44:07: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:44:07: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:44:07: # Command line: callpeak -t SRX3709374.bam -f BAM -g 12100000 -n SRX3709374.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3709374.05 # format = BAM # ChIP-seq file = ['SRX3709374.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 @ Wed, 05 Sep 2018 10:44:07: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:44:07: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:44:07: # Command line: callpeak -t SRX3709374.bam -f BAM -g 12100000 -n SRX3709374.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3709374.10 # format = BAM # ChIP-seq file = ['SRX3709374.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 @ Wed, 05 Sep 2018 10:44:07: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:44:07: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 05 Sep 2018 10:44:12: 1000000 BigWig に変換しました。 INFO @ Wed, 05 Sep 2018 10:44:12: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:44:12: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:44:12: #1 total tags in treatment: 83165 INFO @ Wed, 05 Sep 2018 10:44:12: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:44:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:44:12: #1 tags after filtering in treatment: 60011 INFO @ Wed, 05 Sep 2018 10:44:12: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 05 Sep 2018 10:44:12: #1 finished! INFO @ Wed, 05 Sep 2018 10:44:12: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:44:12: #2 number of paired peaks: 405 WARNING @ Wed, 05 Sep 2018 10:44:12: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Wed, 05 Sep 2018 10:44:12: start model_add_line... INFO @ Wed, 05 Sep 2018 10:44:12: start X-correlation... INFO @ Wed, 05 Sep 2018 10:44:12: end of X-cor INFO @ Wed, 05 Sep 2018 10:44:12: #2 finished! INFO @ Wed, 05 Sep 2018 10:44:12: #2 predicted fragment length is 73 bps INFO @ Wed, 05 Sep 2018 10:44:12: #2 alternative fragment length(s) may be 73 bps INFO @ Wed, 05 Sep 2018 10:44:12: #2.2 Generate R script for model : SRX3709374.10_model.r WARNING @ Wed, 05 Sep 2018 10:44:12: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 05 Sep 2018 10:44:12: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Wed, 05 Sep 2018 10:44:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 05 Sep 2018 10:44:12: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:44:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:44:12: 1000000 INFO @ Wed, 05 Sep 2018 10:44:13: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:44:13: #4 Write output xls file... SRX3709374.10_peaks.xls INFO @ Wed, 05 Sep 2018 10:44:13: #4 Write peak in narrowPeak format file... SRX3709374.10_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:44:13: #4 Write summits bed file... SRX3709374.10_summits.bed INFO @ Wed, 05 Sep 2018 10:44:13: Done! INFO @ Wed, 05 Sep 2018 10:44:13: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:44:13: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:44:13: #1 total tags in treatment: 83165 INFO @ Wed, 05 Sep 2018 10:44:13: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:44:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:44:13: #1 tags after filtering in treatment: 60011 INFO @ Wed, 05 Sep 2018 10:44:13: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 05 Sep 2018 10:44:13: #1 finished! INFO @ Wed, 05 Sep 2018 10:44:13: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:44:13: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (16 chroms): 5 millis pass2 - checking and writing primary data (138 records, 4 fields): 6 millis INFO @ Wed, 05 Sep 2018 10:44:13: 1000000 INFO @ Wed, 05 Sep 2018 10:44:13: #2 number of paired peaks: 405 WARNING @ Wed, 05 Sep 2018 10:44:13: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Wed, 05 Sep 2018 10:44:13: start model_add_line... INFO @ Wed, 05 Sep 2018 10:44:13: start X-correlation... CompletedMACS2peakCalling INFO @ Wed, 05 Sep 2018 10:44:13: end of X-cor INFO @ Wed, 05 Sep 2018 10:44:13: #2 finished! INFO @ Wed, 05 Sep 2018 10:44:13: #2 predicted fragment length is 73 bps INFO @ Wed, 05 Sep 2018 10:44:13: #2 alternative fragment length(s) may be 73 bps INFO @ Wed, 05 Sep 2018 10:44:13: #2.2 Generate R script for model : SRX3709374.20_model.r WARNING @ Wed, 05 Sep 2018 10:44:13: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 05 Sep 2018 10:44:13: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Wed, 05 Sep 2018 10:44:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 05 Sep 2018 10:44:13: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:44:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:44:13: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:44:13: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:44:13: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:44:13: #1 total tags in treatment: 83165 INFO @ Wed, 05 Sep 2018 10:44:13: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:44:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:44:13: #1 tags after filtering in treatment: 60011 INFO @ Wed, 05 Sep 2018 10:44:13: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 05 Sep 2018 10:44:13: #1 finished! INFO @ Wed, 05 Sep 2018 10:44:13: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:44:13: #4 Write output xls file... SRX3709374.20_peaks.xls INFO @ Wed, 05 Sep 2018 10:44:13: #4 Write peak in narrowPeak format file... SRX3709374.20_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:44:13: #4 Write summits bed file... SRX3709374.20_summits.bed INFO @ Wed, 05 Sep 2018 10:44:13: #2 number of paired peaks: 405 WARNING @ Wed, 05 Sep 2018 10:44:13: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Wed, 05 Sep 2018 10:44:13: start model_add_line... INFO @ Wed, 05 Sep 2018 10:44:13: Done! INFO @ Wed, 05 Sep 2018 10:44:13: start X-correlation... INFO @ Wed, 05 Sep 2018 10:44:13: end of X-cor INFO @ Wed, 05 Sep 2018 10:44:13: #2 finished! INFO @ Wed, 05 Sep 2018 10:44:13: #2 predicted fragment length is 73 bps INFO @ Wed, 05 Sep 2018 10:44:13: #2 alternative fragment length(s) may be 73 bps INFO @ Wed, 05 Sep 2018 10:44:13: #2.2 Generate R script for model : SRX3709374.05_model.r WARNING @ Wed, 05 Sep 2018 10:44:13: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 05 Sep 2018 10:44:13: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Wed, 05 Sep 2018 10:44:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 05 Sep 2018 10:44:13: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:44:13: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (54 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 05 Sep 2018 10:44:13: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:44:13: #4 Write output xls file... SRX3709374.05_peaks.xls INFO @ Wed, 05 Sep 2018 10:44:14: #4 Write peak in narrowPeak format file... SRX3709374.05_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:44:14: #4 Write summits bed file... SRX3709374.05_summits.bed INFO @ Wed, 05 Sep 2018 10:44:14: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (265 records, 4 fields): 5 millis CompletedMACS2peakCalling