Job ID = 2009907 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,748,894 reads read : 9,497,788 reads written : 9,497,788 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5008404.sra.cache’: 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: 00:05:38 4748894 reads; of these: 4748894 (100.00%) were paired; of these: 586082 (12.34%) aligned concordantly 0 times 3415546 (71.92%) aligned concordantly exactly 1 time 747266 (15.74%) aligned concordantly >1 times ---- 586082 pairs aligned concordantly 0 times; of these: 70399 (12.01%) aligned discordantly 1 time ---- 515683 pairs aligned 0 times concordantly or discordantly; of these: 1031366 mates make up the pairs; of these: 787069 (76.31%) aligned 0 times 169157 (16.40%) aligned exactly 1 time 75140 (7.29%) aligned >1 times 91.71% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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] 116392 / 4218907 = 0.0276 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 20:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.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 20:45:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:45:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:45:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.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 20:45:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:45:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:45:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.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 20:45:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:45:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:45:37: 1000000 INFO @ Fri, 05 Jul 2019 20:45:41: 1000000 INFO @ Fri, 05 Jul 2019 20:45:42: 1000000 INFO @ Fri, 05 Jul 2019 20:45:46: 2000000 INFO @ Fri, 05 Jul 2019 20:45:54: 2000000 INFO @ Fri, 05 Jul 2019 20:45:55: 3000000 INFO @ Fri, 05 Jul 2019 20:45:55: 2000000 INFO @ Fri, 05 Jul 2019 20:46:04: 4000000 INFO @ Fri, 05 Jul 2019 20:46:06: 3000000 INFO @ Fri, 05 Jul 2019 20:46:07: 3000000 INFO @ Fri, 05 Jul 2019 20:46:12: 5000000 INFO @ Fri, 05 Jul 2019 20:46:18: 4000000 INFO @ Fri, 05 Jul 2019 20:46:19: 4000000 INFO @ Fri, 05 Jul 2019 20:46:21: 6000000 INFO @ Fri, 05 Jul 2019 20:46:30: 7000000 INFO @ Fri, 05 Jul 2019 20:46:30: 5000000 INFO @ Fri, 05 Jul 2019 20:46:31: 5000000 INFO @ Fri, 05 Jul 2019 20:46:39: 8000000 INFO @ Fri, 05 Jul 2019 20:46:42: 6000000 INFO @ Fri, 05 Jul 2019 20:46:43: 6000000 INFO @ Fri, 05 Jul 2019 20:46:43: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:46:43: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:46:43: #1 total tags in treatment: 4046821 INFO @ Fri, 05 Jul 2019 20:46:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:46:43: #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 20:46:43: #1 tags after filtering in treatment: 2884228 INFO @ Fri, 05 Jul 2019 20:46:43: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 20:46:43: #1 finished! INFO @ Fri, 05 Jul 2019 20:46:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:46:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:46:43: #2 number of paired peaks: 111 WARNING @ Fri, 05 Jul 2019 20:46:43: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Fri, 05 Jul 2019 20:46:43: start model_add_line... INFO @ Fri, 05 Jul 2019 20:46:43: start X-correlation... INFO @ Fri, 05 Jul 2019 20:46:43: end of X-cor INFO @ Fri, 05 Jul 2019 20:46:43: #2 finished! INFO @ Fri, 05 Jul 2019 20:46:43: #2 predicted fragment length is 1 bps INFO @ Fri, 05 Jul 2019 20:46:43: #2 alternative fragment length(s) may be 1,47,61,78,94,134,162,178,216,233,259,300,319,520,543,566,584 bps INFO @ Fri, 05 Jul 2019 20:46:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.05_model.r WARNING @ Fri, 05 Jul 2019 20:46:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 20:46:43: #2 You may need to consider one of the other alternative d(s): 1,47,61,78,94,134,162,178,216,233,259,300,319,520,543,566,584 WARNING @ Fri, 05 Jul 2019 20:46:43: #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 20:46:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:46:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:46:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:46:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.05_peaks.xls INFO @ Fri, 05 Jul 2019 20:46:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:46:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.05_summits.bed INFO @ Fri, 05 Jul 2019 20:46:52: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:46:53: 7000000 INFO @ Fri, 05 Jul 2019 20:46:54: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 20:47:05: 8000000 INFO @ Fri, 05 Jul 2019 20:47:06: 8000000 INFO @ Fri, 05 Jul 2019 20:47:10: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:47:10: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:47:10: #1 total tags in treatment: 4046821 INFO @ Fri, 05 Jul 2019 20:47:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:47:10: #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 20:47:10: #1 tags after filtering in treatment: 2884228 INFO @ Fri, 05 Jul 2019 20:47:10: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 20:47:10: #1 finished! INFO @ Fri, 05 Jul 2019 20:47:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:47:10: #2 number of paired peaks: 111 WARNING @ Fri, 05 Jul 2019 20:47:10: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Fri, 05 Jul 2019 20:47:10: start model_add_line... INFO @ Fri, 05 Jul 2019 20:47:10: start X-correlation... INFO @ Fri, 05 Jul 2019 20:47:10: end of X-cor INFO @ Fri, 05 Jul 2019 20:47:10: #2 finished! INFO @ Fri, 05 Jul 2019 20:47:10: #2 predicted fragment length is 1 bps INFO @ Fri, 05 Jul 2019 20:47:10: #2 alternative fragment length(s) may be 1,47,61,78,94,134,162,178,216,233,259,300,319,520,543,566,584 bps INFO @ Fri, 05 Jul 2019 20:47:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.10_model.r WARNING @ Fri, 05 Jul 2019 20:47:10: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 20:47:10: #2 You may need to consider one of the other alternative d(s): 1,47,61,78,94,134,162,178,216,233,259,300,319,520,543,566,584 WARNING @ Fri, 05 Jul 2019 20:47:10: #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 20:47:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:47:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:47:11: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:47:11: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:47:11: #1 total tags in treatment: 4046821 INFO @ Fri, 05 Jul 2019 20:47:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:47:11: #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 20:47:11: #1 tags after filtering in treatment: 2884228 INFO @ Fri, 05 Jul 2019 20:47:11: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 20:47:11: #1 finished! INFO @ Fri, 05 Jul 2019 20:47:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:47:11: #2 number of paired peaks: 111 WARNING @ Fri, 05 Jul 2019 20:47:11: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Fri, 05 Jul 2019 20:47:11: start model_add_line... INFO @ Fri, 05 Jul 2019 20:47:11: start X-correlation... INFO @ Fri, 05 Jul 2019 20:47:11: end of X-cor INFO @ Fri, 05 Jul 2019 20:47:11: #2 finished! INFO @ Fri, 05 Jul 2019 20:47:11: #2 predicted fragment length is 1 bps INFO @ Fri, 05 Jul 2019 20:47:11: #2 alternative fragment length(s) may be 1,47,61,78,94,134,162,178,216,233,259,300,319,520,543,566,584 bps INFO @ Fri, 05 Jul 2019 20:47:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.20_model.r WARNING @ Fri, 05 Jul 2019 20:47:11: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 20:47:11: #2 You may need to consider one of the other alternative d(s): 1,47,61,78,94,134,162,178,216,233,259,300,319,520,543,566,584 WARNING @ Fri, 05 Jul 2019 20:47:11: #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 20:47:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:47:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:47:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:47:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 20:47:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.10_peaks.xls INFO @ Fri, 05 Jul 2019 20:47:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:47:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.10_summits.bed INFO @ Fri, 05 Jul 2019 20:47:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.20_peaks.xls INFO @ Fri, 05 Jul 2019 20:47:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:47:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339845/SRX2339845.20_summits.bed INFO @ Fri, 05 Jul 2019 20:47:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling