Job ID = 2007973 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,680,040 reads read : 3,360,080 reads written : 3,360,080 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:02:59 1680040 reads; of these: 1680040 (100.00%) were paired; of these: 278927 (16.60%) aligned concordantly 0 times 1272400 (75.74%) aligned concordantly exactly 1 time 128713 (7.66%) aligned concordantly >1 times ---- 278927 pairs aligned concordantly 0 times; of these: 32469 (11.64%) aligned discordantly 1 time ---- 246458 pairs aligned 0 times concordantly or discordantly; of these: 492916 mates make up the pairs; of these: 465276 (94.39%) aligned 0 times 17750 (3.60%) aligned exactly 1 time 9890 (2.01%) aligned >1 times 86.15% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 265173 / 1429179 = 0.1855 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, 05 Jul 2019 17:05:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.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, 05 Jul 2019 17:05:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:05:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:05:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.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, 05 Jul 2019 17:05:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:05:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:05:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.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, 05 Jul 2019 17:05:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:05:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:06:08: 1000000 INFO @ Fri, 05 Jul 2019 17:06:09: 1000000 INFO @ Fri, 05 Jul 2019 17:06:09: 1000000 INFO @ Fri, 05 Jul 2019 17:06:18: 2000000 INFO @ Fri, 05 Jul 2019 17:06:22: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:06:22: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:06:22: #1 total tags in treatment: 1139088 INFO @ Fri, 05 Jul 2019 17:06:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:06:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:06:22: #1 tags after filtering in treatment: 1078864 INFO @ Fri, 05 Jul 2019 17:06:22: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:06:22: #1 finished! INFO @ Fri, 05 Jul 2019 17:06:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:06:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:06:22: #2 number of paired peaks: 171 WARNING @ Fri, 05 Jul 2019 17:06:22: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 05 Jul 2019 17:06:22: start model_add_line... INFO @ Fri, 05 Jul 2019 17:06:22: start X-correlation... INFO @ Fri, 05 Jul 2019 17:06:22: end of X-cor INFO @ Fri, 05 Jul 2019 17:06:22: #2 finished! INFO @ Fri, 05 Jul 2019 17:06:22: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 17:06:22: #2 alternative fragment length(s) may be 0,69,106,140,191,222,240,279,514,539,557 bps INFO @ Fri, 05 Jul 2019 17:06:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.05_model.r WARNING @ Fri, 05 Jul 2019 17:06:22: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:06:22: #2 You may need to consider one of the other alternative d(s): 0,69,106,140,191,222,240,279,514,539,557 WARNING @ Fri, 05 Jul 2019 17:06:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:06:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:06:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:06:23: 2000000 INFO @ Fri, 05 Jul 2019 17:06:24: 2000000 INFO @ Fri, 05 Jul 2019 17:06:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:06:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:06:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:06:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.05_summits.bed INFO @ Fri, 05 Jul 2019 17:06:27: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (107 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:06:28: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:06:28: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:06:28: #1 total tags in treatment: 1139088 INFO @ Fri, 05 Jul 2019 17:06:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:06:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:06:28: #1 tags after filtering in treatment: 1078864 INFO @ Fri, 05 Jul 2019 17:06:28: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:06:28: #1 finished! INFO @ Fri, 05 Jul 2019 17:06:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:06:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:06:28: #2 number of paired peaks: 171 WARNING @ Fri, 05 Jul 2019 17:06:28: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 05 Jul 2019 17:06:28: start model_add_line... INFO @ Fri, 05 Jul 2019 17:06:28: start X-correlation... INFO @ Fri, 05 Jul 2019 17:06:28: end of X-cor INFO @ Fri, 05 Jul 2019 17:06:28: #2 finished! INFO @ Fri, 05 Jul 2019 17:06:28: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 17:06:28: #2 alternative fragment length(s) may be 0,69,106,140,191,222,240,279,514,539,557 bps INFO @ Fri, 05 Jul 2019 17:06:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.20_model.r WARNING @ Fri, 05 Jul 2019 17:06:28: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:06:28: #2 You may need to consider one of the other alternative d(s): 0,69,106,140,191,222,240,279,514,539,557 WARNING @ Fri, 05 Jul 2019 17:06:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:06:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:06:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:06:29: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:06:29: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:06:29: #1 total tags in treatment: 1139088 INFO @ Fri, 05 Jul 2019 17:06:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:06:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:06:29: #1 tags after filtering in treatment: 1078864 INFO @ Fri, 05 Jul 2019 17:06:29: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:06:29: #1 finished! INFO @ Fri, 05 Jul 2019 17:06:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:06:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:06:29: #2 number of paired peaks: 171 WARNING @ Fri, 05 Jul 2019 17:06:29: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 05 Jul 2019 17:06:29: start model_add_line... INFO @ Fri, 05 Jul 2019 17:06:29: start X-correlation... INFO @ Fri, 05 Jul 2019 17:06:29: end of X-cor INFO @ Fri, 05 Jul 2019 17:06:29: #2 finished! INFO @ Fri, 05 Jul 2019 17:06:29: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 17:06:29: #2 alternative fragment length(s) may be 0,69,106,140,191,222,240,279,514,539,557 bps INFO @ Fri, 05 Jul 2019 17:06:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.10_model.r WARNING @ Fri, 05 Jul 2019 17:06:29: #2 Since the d (191) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:06:29: #2 You may need to consider one of the other alternative d(s): 0,69,106,140,191,222,240,279,514,539,557 WARNING @ Fri, 05 Jul 2019 17:06:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:06:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:06:29: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:06:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:06:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:06:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:06:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:06:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.20_summits.bed INFO @ Fri, 05 Jul 2019 17:06:34: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 17:06:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:06:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:06:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471764/ERX471764.10_summits.bed INFO @ Fri, 05 Jul 2019 17:06:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (31 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。