Job ID = 11633389 sra ファイルのダウンロード中... Completed: 209653K bytes transferred in 5 seconds (325068K 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 3123340 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236167/ERR1162760.sra Written 3123340 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236167/ERR1162760.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: 00:02:27 3123340 reads; of these: 3123340 (100.00%) were paired; of these: 384865 (12.32%) aligned concordantly 0 times 2418805 (77.44%) aligned concordantly exactly 1 time 319670 (10.23%) aligned concordantly >1 times ---- 384865 pairs aligned concordantly 0 times; of these: 27879 (7.24%) aligned discordantly 1 time ---- 356986 pairs aligned 0 times concordantly or discordantly; of these: 713972 mates make up the pairs; of these: 694295 (97.24%) aligned 0 times 9863 (1.38%) aligned exactly 1 time 9814 (1.37%) aligned >1 times 88.89% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 243805 / 2765240 = 0.0882 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 @ Fri, 15 Feb 2019 08:55:00: # Command line: callpeak -t ERX1236167.bam -f BAM -g 12100000 -n ERX1236167.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236167.05 # format = BAM # ChIP-seq file = ['ERX1236167.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 @ Fri, 15 Feb 2019 08:55:00: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:55:00: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:55:00: # Command line: callpeak -t ERX1236167.bam -f BAM -g 12100000 -n ERX1236167.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236167.10 # format = BAM # ChIP-seq file = ['ERX1236167.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 @ Fri, 15 Feb 2019 08:55:00: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:55:00: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:55:00: # Command line: callpeak -t ERX1236167.bam -f BAM -g 12100000 -n ERX1236167.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236167.20 # format = BAM # ChIP-seq file = ['ERX1236167.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 @ Fri, 15 Feb 2019 08:55:00: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:55:00: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:55:07: 1000000 INFO @ Fri, 15 Feb 2019 08:55:07: 1000000 INFO @ Fri, 15 Feb 2019 08:55:07: 1000000 INFO @ Fri, 15 Feb 2019 08:55:14: 2000000 INFO @ Fri, 15 Feb 2019 08:55:14: 2000000 INFO @ Fri, 15 Feb 2019 08:55:14: 2000000 INFO @ Fri, 15 Feb 2019 08:55:20: 3000000 INFO @ Fri, 15 Feb 2019 08:55:20: 3000000 INFO @ Fri, 15 Feb 2019 08:55:20: 3000000 INFO @ Fri, 15 Feb 2019 08:55:27: 4000000 INFO @ Fri, 15 Feb 2019 08:55:27: 4000000 INFO @ Fri, 15 Feb 2019 08:55:27: 4000000 INFO @ Fri, 15 Feb 2019 08:55:34: 5000000 INFO @ Fri, 15 Feb 2019 08:55:34: 5000000 INFO @ Fri, 15 Feb 2019 08:55:34: 5000000 INFO @ Fri, 15 Feb 2019 08:55:34: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:55:34: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:55:34: #1 total tags in treatment: 2495863 INFO @ Fri, 15 Feb 2019 08:55:34: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:55:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:55:34: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:55:34: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:55:34: #1 total tags in treatment: 2495863 INFO @ Fri, 15 Feb 2019 08:55:34: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:55:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:55:34: #1 tags after filtering in treatment: 2193604 INFO @ Fri, 15 Feb 2019 08:55:34: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 15 Feb 2019 08:55:34: #1 finished! INFO @ Fri, 15 Feb 2019 08:55:34: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:55:34: #1 tags after filtering in treatment: 2193604 INFO @ Fri, 15 Feb 2019 08:55:34: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 15 Feb 2019 08:55:34: #1 finished! INFO @ Fri, 15 Feb 2019 08:55:34: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:55:34: #2 number of paired peaks: 180 WARNING @ Fri, 15 Feb 2019 08:55:34: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Fri, 15 Feb 2019 08:55:34: start model_add_line... INFO @ Fri, 15 Feb 2019 08:55:34: #2 number of paired peaks: 180 WARNING @ Fri, 15 Feb 2019 08:55:34: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Fri, 15 Feb 2019 08:55:34: start model_add_line... INFO @ Fri, 15 Feb 2019 08:55:34: start X-correlation... INFO @ Fri, 15 Feb 2019 08:55:34: end of X-cor INFO @ Fri, 15 Feb 2019 08:55:34: #2 finished! INFO @ Fri, 15 Feb 2019 08:55:34: #2 predicted fragment length is 87 bps INFO @ Fri, 15 Feb 2019 08:55:34: #2 alternative fragment length(s) may be 4,87 bps INFO @ Fri, 15 Feb 2019 08:55:34: #2.2 Generate R script for model : ERX1236167.05_model.r INFO @ Fri, 15 Feb 2019 08:55:34: start X-correlation... INFO @ Fri, 15 Feb 2019 08:55:34: end of X-cor INFO @ Fri, 15 Feb 2019 08:55:34: #2 finished! INFO @ Fri, 15 Feb 2019 08:55:34: #2 predicted fragment length is 87 bps INFO @ Fri, 15 Feb 2019 08:55:34: #2 alternative fragment length(s) may be 4,87 bps INFO @ Fri, 15 Feb 2019 08:55:34: #2.2 Generate R script for model : ERX1236167.20_model.r INFO @ Fri, 15 Feb 2019 08:55:34: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:55:34: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:55:34: #1 total tags in treatment: 2495863 INFO @ Fri, 15 Feb 2019 08:55:34: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:55:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:55:34: #1 tags after filtering in treatment: 2193604 INFO @ Fri, 15 Feb 2019 08:55:34: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 15 Feb 2019 08:55:34: #1 finished! INFO @ Fri, 15 Feb 2019 08:55:34: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:55:35: #2 number of paired peaks: 180 WARNING @ Fri, 15 Feb 2019 08:55:35: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Fri, 15 Feb 2019 08:55:35: start model_add_line... INFO @ Fri, 15 Feb 2019 08:55:35: start X-correlation... INFO @ Fri, 15 Feb 2019 08:55:35: end of X-cor INFO @ Fri, 15 Feb 2019 08:55:35: #2 finished! INFO @ Fri, 15 Feb 2019 08:55:35: #2 predicted fragment length is 87 bps INFO @ Fri, 15 Feb 2019 08:55:35: #2 alternative fragment length(s) may be 4,87 bps INFO @ Fri, 15 Feb 2019 08:55:35: #2.2 Generate R script for model : ERX1236167.10_model.r WARNING @ Fri, 15 Feb 2019 08:55:35: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 08:55:35: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Fri, 15 Feb 2019 08:55:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 08:55:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:55:35: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 15 Feb 2019 08:55:35: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 08:55:35: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Fri, 15 Feb 2019 08:55:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 08:55:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:55:35: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 15 Feb 2019 08:55:35: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 08:55:35: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Fri, 15 Feb 2019 08:55:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 08:55:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 08:55:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 08:55:40: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:55:40: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:55:40: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 08:55:42: #4 Write output xls file... ERX1236167.20_peaks.xls INFO @ Fri, 15 Feb 2019 08:55:42: #4 Write peak in narrowPeak format file... ERX1236167.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:55:42: #4 Write summits bed file... ERX1236167.20_summits.bed INFO @ Fri, 15 Feb 2019 08:55:42: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (194 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 08:55:42: #4 Write output xls file... ERX1236167.05_peaks.xls INFO @ Fri, 15 Feb 2019 08:55:42: #4 Write peak in narrowPeak format file... ERX1236167.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:55:42: #4 Write output xls file... ERX1236167.10_peaks.xls INFO @ Fri, 15 Feb 2019 08:55:42: #4 Write summits bed file... ERX1236167.05_summits.bed INFO @ Fri, 15 Feb 2019 08:55:42: Done! INFO @ Fri, 15 Feb 2019 08:55:42: #4 Write peak in narrowPeak format file... ERX1236167.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 08:55:42: #4 Write summits bed file... ERX1236167.10_summits.bed INFO @ Fri, 15 Feb 2019 08:55:42: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (612 records, 4 fields): 8 millis pass1 - making usageList (16 chroms): 5 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (389 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。