Job ID = 11193203 sra ファイルのダウンロード中... Completed: 267646K bytes transferred in 6 seconds (359542K 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 6122335 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876291/SRR1802394.sra Written 6122335 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876291/SRR1802394.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: 00:02:08 6122335 reads; of these: 6122335 (100.00%) were paired; of these: 3624829 (59.21%) aligned concordantly 0 times 2094393 (34.21%) aligned concordantly exactly 1 time 403113 (6.58%) aligned concordantly >1 times ---- 3624829 pairs aligned concordantly 0 times; of these: 52710 (1.45%) aligned discordantly 1 time ---- 3572119 pairs aligned 0 times concordantly or discordantly; of these: 7144238 mates make up the pairs; of these: 7011111 (98.14%) aligned 0 times 87118 (1.22%) aligned exactly 1 time 46009 (0.64%) aligned >1 times 42.74% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 1804810 / 2533215 = 0.7125 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 11:10:59: # Command line: callpeak -t SRX876291.bam -f BAM -g 12100000 -n SRX876291.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX876291.05 # format = BAM # ChIP-seq file = ['SRX876291.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 11:10:59: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:10:59: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:10:59: # Command line: callpeak -t SRX876291.bam -f BAM -g 12100000 -n SRX876291.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX876291.20 # format = BAM # ChIP-seq file = ['SRX876291.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 11:10:59: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:10:59: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:10:59: # Command line: callpeak -t SRX876291.bam -f BAM -g 12100000 -n SRX876291.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX876291.10 # format = BAM # ChIP-seq file = ['SRX876291.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 11:10:59: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:10:59: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:11:06: 1000000 INFO @ Sat, 15 Sep 2018 11:11:06: 1000000 INFO @ Sat, 15 Sep 2018 11:11:06: 1000000 INFO @ Sat, 15 Sep 2018 11:11:10: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:11:10: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:11:10: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:11:10: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:11:10: #1 total tags in treatment: 725394 INFO @ Sat, 15 Sep 2018 11:11:10: #1 total tags in treatment: 725394 INFO @ Sat, 15 Sep 2018 11:11:10: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:11:10: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:11:10: #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 11:11:10: #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 11:11:10: #1 tags after filtering in treatment: 621300 INFO @ Sat, 15 Sep 2018 11:11:10: #1 tags after filtering in treatment: 621300 INFO @ Sat, 15 Sep 2018 11:11:10: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Sep 2018 11:11:10: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Sep 2018 11:11:10: #1 finished! INFO @ Sat, 15 Sep 2018 11:11:10: #1 finished! INFO @ Sat, 15 Sep 2018 11:11:10: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:11:10: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:11:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:11:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:11:10: #2 number of paired peaks: 109 WARNING @ Sat, 15 Sep 2018 11:11:10: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 15 Sep 2018 11:11:10: start model_add_line... INFO @ Sat, 15 Sep 2018 11:11:10: #2 number of paired peaks: 109 WARNING @ Sat, 15 Sep 2018 11:11:10: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 15 Sep 2018 11:11:10: start model_add_line... INFO @ Sat, 15 Sep 2018 11:11:10: start X-correlation... INFO @ Sat, 15 Sep 2018 11:11:10: start X-correlation... INFO @ Sat, 15 Sep 2018 11:11:10: end of X-cor INFO @ Sat, 15 Sep 2018 11:11:10: #2 finished! INFO @ Sat, 15 Sep 2018 11:11:10: #2 predicted fragment length is 59 bps INFO @ Sat, 15 Sep 2018 11:11:10: #2 alternative fragment length(s) may be 4,31,59,365,502,536,557,584 bps INFO @ Sat, 15 Sep 2018 11:11:10: #2.2 Generate R script for model : SRX876291.05_model.r INFO @ Sat, 15 Sep 2018 11:11:10: end of X-cor INFO @ Sat, 15 Sep 2018 11:11:10: #2 finished! INFO @ Sat, 15 Sep 2018 11:11:10: #2 predicted fragment length is 59 bps INFO @ Sat, 15 Sep 2018 11:11:10: #2 alternative fragment length(s) may be 4,31,59,365,502,536,557,584 bps INFO @ Sat, 15 Sep 2018 11:11:10: #2.2 Generate R script for model : SRX876291.20_model.r WARNING @ Sat, 15 Sep 2018 11:11:10: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:11:10: #2 You may need to consider one of the other alternative d(s): 4,31,59,365,502,536,557,584 WARNING @ Sat, 15 Sep 2018 11:11:10: #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 11:11:10: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:11:10: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 15 Sep 2018 11:11:10: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:11:10: #2 You may need to consider one of the other alternative d(s): 4,31,59,365,502,536,557,584 WARNING @ Sat, 15 Sep 2018 11:11:10: #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 11:11:10: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:11:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:11:11: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:11:11: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:11:11: #1 total tags in treatment: 725394 INFO @ Sat, 15 Sep 2018 11:11:11: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:11:11: #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 11:11:11: #1 tags after filtering in treatment: 621300 INFO @ Sat, 15 Sep 2018 11:11:11: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Sep 2018 11:11:11: #1 finished! INFO @ Sat, 15 Sep 2018 11:11:11: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:11:11: #2 number of paired peaks: 109 WARNING @ Sat, 15 Sep 2018 11:11:11: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Sat, 15 Sep 2018 11:11:11: start model_add_line... INFO @ Sat, 15 Sep 2018 11:11:11: start X-correlation... INFO @ Sat, 15 Sep 2018 11:11:11: end of X-cor INFO @ Sat, 15 Sep 2018 11:11:11: #2 finished! INFO @ Sat, 15 Sep 2018 11:11:11: #2 predicted fragment length is 59 bps INFO @ Sat, 15 Sep 2018 11:11:11: #2 alternative fragment length(s) may be 4,31,59,365,502,536,557,584 bps INFO @ Sat, 15 Sep 2018 11:11:11: #2.2 Generate R script for model : SRX876291.10_model.r WARNING @ Sat, 15 Sep 2018 11:11:11: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:11:11: #2 You may need to consider one of the other alternative d(s): 4,31,59,365,502,536,557,584 WARNING @ Sat, 15 Sep 2018 11:11:11: #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 11:11:11: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:11:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:11:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:11:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:11:12: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:11:12: #4 Write output xls file... SRX876291.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:11:12: #4 Write peak in narrowPeak format file... SRX876291.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:11:12: #4 Write summits bed file... SRX876291.05_summits.bed INFO @ Sat, 15 Sep 2018 11:11:12: Done! INFO @ Sat, 15 Sep 2018 11:11:12: #4 Write output xls file... SRX876291.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:11:12: #4 Write peak in narrowPeak format file... SRX876291.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:11:12: #4 Write summits bed file... SRX876291.20_summits.bed INFO @ Sat, 15 Sep 2018 11:11:12: Done! pass1 - making usageList (9 chroms): 9 millis pass1 - making usageList (16 chroms): 9 millis pass2 - checking and writing primary data (16 records, 4 fields): 3 millis pass2 - checking and writing primary data (515 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:11:13: #4 Write output xls file... SRX876291.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:11:13: #4 Write peak in narrowPeak format file... SRX876291.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:11:13: #4 Write summits bed file... SRX876291.10_summits.bed INFO @ Sat, 15 Sep 2018 11:11:13: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。