Job ID = 2009995 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 8,748,840 reads read : 17,497,680 reads written : 17,497,680 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5008418.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: 00:06:44 8748840 reads; of these: 8748840 (100.00%) were paired; of these: 907923 (10.38%) aligned concordantly 0 times 6313187 (72.16%) aligned concordantly exactly 1 time 1527730 (17.46%) aligned concordantly >1 times ---- 907923 pairs aligned concordantly 0 times; of these: 177517 (19.55%) aligned discordantly 1 time ---- 730406 pairs aligned 0 times concordantly or discordantly; of these: 1460812 mates make up the pairs; of these: 1169398 (80.05%) aligned 0 times 166085 (11.37%) aligned exactly 1 time 125329 (8.58%) aligned >1 times 93.32% overall alignment rate Time searching: 00:06:44 Overall time: 00:06:44 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_sort_core] merging from 8 files... [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] 531588 / 7981555 = 0.0666 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 20:58:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.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 20:58:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:58:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:58:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.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 20:58:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:58:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:58:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.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 20:58:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:58:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:58:20: 1000000 INFO @ Fri, 05 Jul 2019 20:58:22: 1000000 INFO @ Fri, 05 Jul 2019 20:58:22: 1000000 INFO @ Fri, 05 Jul 2019 20:58:30: 2000000 INFO @ Fri, 05 Jul 2019 20:58:31: 2000000 INFO @ Fri, 05 Jul 2019 20:58:34: 2000000 INFO @ Fri, 05 Jul 2019 20:58:39: 3000000 INFO @ Fri, 05 Jul 2019 20:58:41: 3000000 INFO @ Fri, 05 Jul 2019 20:58:46: 3000000 INFO @ Fri, 05 Jul 2019 20:58:49: 4000000 INFO @ Fri, 05 Jul 2019 20:58:50: 4000000 INFO @ Fri, 05 Jul 2019 20:58:57: 4000000 INFO @ Fri, 05 Jul 2019 20:58:57: 5000000 INFO @ Fri, 05 Jul 2019 20:58:59: 5000000 INFO @ Fri, 05 Jul 2019 20:59:05: 6000000 INFO @ Fri, 05 Jul 2019 20:59:08: 6000000 INFO @ Fri, 05 Jul 2019 20:59:08: 5000000 INFO @ Fri, 05 Jul 2019 20:59:13: 7000000 INFO @ Fri, 05 Jul 2019 20:59:17: 7000000 INFO @ Fri, 05 Jul 2019 20:59:19: 6000000 INFO @ Fri, 05 Jul 2019 20:59:21: 8000000 INFO @ Fri, 05 Jul 2019 20:59:26: 8000000 INFO @ Fri, 05 Jul 2019 20:59:29: 9000000 INFO @ Fri, 05 Jul 2019 20:59:31: 7000000 INFO @ Fri, 05 Jul 2019 20:59:35: 9000000 INFO @ Fri, 05 Jul 2019 20:59:37: 10000000 INFO @ Fri, 05 Jul 2019 20:59:42: 8000000 INFO @ Fri, 05 Jul 2019 20:59:44: 10000000 INFO @ Fri, 05 Jul 2019 20:59:45: 11000000 INFO @ Fri, 05 Jul 2019 20:59:52: 12000000 INFO @ Fri, 05 Jul 2019 20:59:53: 11000000 INFO @ Fri, 05 Jul 2019 20:59:53: 9000000 INFO @ Fri, 05 Jul 2019 21:00:00: 13000000 INFO @ Fri, 05 Jul 2019 21:00:02: 12000000 INFO @ Fri, 05 Jul 2019 21:00:05: 10000000 INFO @ Fri, 05 Jul 2019 21:00:08: 14000000 INFO @ Fri, 05 Jul 2019 21:00:11: 13000000 INFO @ Fri, 05 Jul 2019 21:00:16: 15000000 INFO @ Fri, 05 Jul 2019 21:00:16: 11000000 INFO @ Fri, 05 Jul 2019 21:00:18: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:00:18: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:00:18: #1 total tags in treatment: 7313919 INFO @ Fri, 05 Jul 2019 21:00:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:00:18: #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 21:00:18: #1 tags after filtering in treatment: 4461789 INFO @ Fri, 05 Jul 2019 21:00:18: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 05 Jul 2019 21:00:18: #1 finished! INFO @ Fri, 05 Jul 2019 21:00:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:00:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:00:19: #2 number of paired peaks: 162 WARNING @ Fri, 05 Jul 2019 21:00:19: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Fri, 05 Jul 2019 21:00:19: start model_add_line... INFO @ Fri, 05 Jul 2019 21:00:19: start X-correlation... INFO @ Fri, 05 Jul 2019 21:00:19: end of X-cor INFO @ Fri, 05 Jul 2019 21:00:19: #2 finished! INFO @ Fri, 05 Jul 2019 21:00:19: #2 predicted fragment length is 46 bps INFO @ Fri, 05 Jul 2019 21:00:19: #2 alternative fragment length(s) may be 21,46,102,161,179,217,265,267,271,288,329,346,375,398,425,455,481,509,523,552 bps INFO @ Fri, 05 Jul 2019 21:00:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.10_model.r WARNING @ Fri, 05 Jul 2019 21:00:19: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:00:19: #2 You may need to consider one of the other alternative d(s): 21,46,102,161,179,217,265,267,271,288,329,346,375,398,425,455,481,509,523,552 WARNING @ Fri, 05 Jul 2019 21:00:19: #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 21:00:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:00:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:00:20: 14000000 INFO @ Fri, 05 Jul 2019 21:00:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:00:27: 12000000 INFO @ Fri, 05 Jul 2019 21:00:29: 15000000 INFO @ Fri, 05 Jul 2019 21:00:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.10_peaks.xls INFO @ Fri, 05 Jul 2019 21:00:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:00:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.10_summits.bed INFO @ Fri, 05 Jul 2019 21:00:30: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 21:00:32: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:00:32: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:00:32: #1 total tags in treatment: 7313919 INFO @ Fri, 05 Jul 2019 21:00:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:00:32: #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 21:00:32: #1 tags after filtering in treatment: 4461789 INFO @ Fri, 05 Jul 2019 21:00:32: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 05 Jul 2019 21:00:32: #1 finished! INFO @ Fri, 05 Jul 2019 21:00:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:00:32: #2 number of paired peaks: 162 WARNING @ Fri, 05 Jul 2019 21:00:32: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Fri, 05 Jul 2019 21:00:32: start model_add_line... INFO @ Fri, 05 Jul 2019 21:00:32: start X-correlation... INFO @ Fri, 05 Jul 2019 21:00:32: end of X-cor INFO @ Fri, 05 Jul 2019 21:00:32: #2 finished! INFO @ Fri, 05 Jul 2019 21:00:32: #2 predicted fragment length is 46 bps INFO @ Fri, 05 Jul 2019 21:00:32: #2 alternative fragment length(s) may be 21,46,102,161,179,217,265,267,271,288,329,346,375,398,425,455,481,509,523,552 bps INFO @ Fri, 05 Jul 2019 21:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.20_model.r WARNING @ Fri, 05 Jul 2019 21:00:32: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:00:32: #2 You may need to consider one of the other alternative d(s): 21,46,102,161,179,217,265,267,271,288,329,346,375,398,425,455,481,509,523,552 WARNING @ Fri, 05 Jul 2019 21:00:32: #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 21:00:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:00:32: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:00:38: 13000000 INFO @ Fri, 05 Jul 2019 21:00:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:00:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.20_peaks.xls INFO @ Fri, 05 Jul 2019 21:00:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:00:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.20_summits.bed INFO @ Fri, 05 Jul 2019 21:00:44: Done! pass1 - making usageList (4 chroms): 2 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:00:48: 14000000 INFO @ Fri, 05 Jul 2019 21:00:59: 15000000 INFO @ Fri, 05 Jul 2019 21:01:01: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:01:01: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:01:01: #1 total tags in treatment: 7313919 INFO @ Fri, 05 Jul 2019 21:01:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:01:01: #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 21:01:01: #1 tags after filtering in treatment: 4461789 INFO @ Fri, 05 Jul 2019 21:01:01: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 05 Jul 2019 21:01:01: #1 finished! INFO @ Fri, 05 Jul 2019 21:01:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:01:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:01:02: #2 number of paired peaks: 162 WARNING @ Fri, 05 Jul 2019 21:01:02: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Fri, 05 Jul 2019 21:01:02: start model_add_line... INFO @ Fri, 05 Jul 2019 21:01:02: start X-correlation... INFO @ Fri, 05 Jul 2019 21:01:02: end of X-cor INFO @ Fri, 05 Jul 2019 21:01:02: #2 finished! INFO @ Fri, 05 Jul 2019 21:01:02: #2 predicted fragment length is 46 bps INFO @ Fri, 05 Jul 2019 21:01:02: #2 alternative fragment length(s) may be 21,46,102,161,179,217,265,267,271,288,329,346,375,398,425,455,481,509,523,552 bps INFO @ Fri, 05 Jul 2019 21:01:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.05_model.r WARNING @ Fri, 05 Jul 2019 21:01:02: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 21:01:02: #2 You may need to consider one of the other alternative d(s): 21,46,102,161,179,217,265,267,271,288,329,346,375,398,425,455,481,509,523,552 WARNING @ Fri, 05 Jul 2019 21:01:02: #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 21:01:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:01:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:01:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.05_peaks.xls INFO @ Fri, 05 Jul 2019 21:01:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:01:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339859/SRX2339859.05_summits.bed INFO @ Fri, 05 Jul 2019 21:01:13: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (41 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。