Job ID = 2010626 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 16,066,248 reads read : 32,132,496 reads written : 32,132,496 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: 00:07:53 16066248 reads; of these: 16066248 (100.00%) were paired; of these: 10403304 (64.75%) aligned concordantly 0 times 3810647 (23.72%) aligned concordantly exactly 1 time 1852297 (11.53%) aligned concordantly >1 times ---- 10403304 pairs aligned concordantly 0 times; of these: 11861 (0.11%) aligned discordantly 1 time ---- 10391443 pairs aligned 0 times concordantly or discordantly; of these: 20782886 mates make up the pairs; of these: 20183587 (97.12%) aligned 0 times 92284 (0.44%) aligned exactly 1 time 507015 (2.44%) aligned >1 times 37.19% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 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] 2274373 / 5670752 = 0.4011 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, 06 Jul 2019 00:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.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, 06 Jul 2019 00:04:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:04:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:04:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.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, 06 Jul 2019 00:04:05: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:04:05: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:04:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.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, 06 Jul 2019 00:04:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:04:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:04:12: 1000000 INFO @ Sat, 06 Jul 2019 00:04:12: 1000000 INFO @ Sat, 06 Jul 2019 00:04:16: 1000000 INFO @ Sat, 06 Jul 2019 00:04:19: 2000000 INFO @ Sat, 06 Jul 2019 00:04:21: 2000000 INFO @ Sat, 06 Jul 2019 00:04:25: 2000000 INFO @ Sat, 06 Jul 2019 00:04:26: 3000000 INFO @ Sat, 06 Jul 2019 00:04:28: 3000000 INFO @ Sat, 06 Jul 2019 00:04:35: 3000000 INFO @ Sat, 06 Jul 2019 00:04:35: 4000000 INFO @ Sat, 06 Jul 2019 00:04:37: 4000000 INFO @ Sat, 06 Jul 2019 00:04:42: 5000000 INFO @ Sat, 06 Jul 2019 00:04:45: 4000000 INFO @ Sat, 06 Jul 2019 00:04:47: 5000000 INFO @ Sat, 06 Jul 2019 00:04:48: 6000000 INFO @ Sat, 06 Jul 2019 00:04:55: 7000000 INFO @ Sat, 06 Jul 2019 00:04:55: 5000000 INFO @ Sat, 06 Jul 2019 00:04:56: 6000000 INFO @ Sat, 06 Jul 2019 00:04:58: #1 tag size is determined as 76 bps INFO @ Sat, 06 Jul 2019 00:04:58: #1 tag size = 76 INFO @ Sat, 06 Jul 2019 00:04:58: #1 total tags in treatment: 3392355 INFO @ Sat, 06 Jul 2019 00:04:58: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:04:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:04:58: #1 tags after filtering in treatment: 2116702 INFO @ Sat, 06 Jul 2019 00:04:58: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 06 Jul 2019 00:04:58: #1 finished! INFO @ Sat, 06 Jul 2019 00:04:58: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:04:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:04:58: #2 number of paired peaks: 280 WARNING @ Sat, 06 Jul 2019 00:04:58: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Sat, 06 Jul 2019 00:04:58: start model_add_line... INFO @ Sat, 06 Jul 2019 00:04:58: start X-correlation... INFO @ Sat, 06 Jul 2019 00:04:58: end of X-cor INFO @ Sat, 06 Jul 2019 00:04:58: #2 finished! INFO @ Sat, 06 Jul 2019 00:04:58: #2 predicted fragment length is 105 bps INFO @ Sat, 06 Jul 2019 00:04:58: #2 alternative fragment length(s) may be 2,43,105,125 bps INFO @ Sat, 06 Jul 2019 00:04:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.05_model.r WARNING @ Sat, 06 Jul 2019 00:04:58: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 00:04:58: #2 You may need to consider one of the other alternative d(s): 2,43,105,125 WARNING @ Sat, 06 Jul 2019 00:04:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 00:04:58: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:04:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 00:05:05: 6000000 INFO @ Sat, 06 Jul 2019 00:05:06: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 00:05:06: 7000000 INFO @ Sat, 06 Jul 2019 00:05:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.05_peaks.xls INFO @ Sat, 06 Jul 2019 00:05:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:05:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.05_summits.bed INFO @ Sat, 06 Jul 2019 00:05:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (308 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:05:10: #1 tag size is determined as 76 bps INFO @ Sat, 06 Jul 2019 00:05:10: #1 tag size = 76 INFO @ Sat, 06 Jul 2019 00:05:10: #1 total tags in treatment: 3392355 INFO @ Sat, 06 Jul 2019 00:05:10: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:05:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:05:10: #1 tags after filtering in treatment: 2116702 INFO @ Sat, 06 Jul 2019 00:05:10: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 06 Jul 2019 00:05:10: #1 finished! INFO @ Sat, 06 Jul 2019 00:05:10: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:05:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:05:11: #2 number of paired peaks: 280 WARNING @ Sat, 06 Jul 2019 00:05:11: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Sat, 06 Jul 2019 00:05:11: start model_add_line... INFO @ Sat, 06 Jul 2019 00:05:11: start X-correlation... INFO @ Sat, 06 Jul 2019 00:05:11: end of X-cor INFO @ Sat, 06 Jul 2019 00:05:11: #2 finished! INFO @ Sat, 06 Jul 2019 00:05:11: #2 predicted fragment length is 105 bps INFO @ Sat, 06 Jul 2019 00:05:11: #2 alternative fragment length(s) may be 2,43,105,125 bps INFO @ Sat, 06 Jul 2019 00:05:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.10_model.r WARNING @ Sat, 06 Jul 2019 00:05:11: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 00:05:11: #2 You may need to consider one of the other alternative d(s): 2,43,105,125 WARNING @ Sat, 06 Jul 2019 00:05:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 00:05:11: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:05:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 00:05:14: 7000000 INFO @ Sat, 06 Jul 2019 00:05:18: #1 tag size is determined as 76 bps INFO @ Sat, 06 Jul 2019 00:05:18: #1 tag size = 76 INFO @ Sat, 06 Jul 2019 00:05:18: #1 total tags in treatment: 3392355 INFO @ Sat, 06 Jul 2019 00:05:18: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:05:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:05:18: #1 tags after filtering in treatment: 2116702 INFO @ Sat, 06 Jul 2019 00:05:18: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 06 Jul 2019 00:05:18: #1 finished! INFO @ Sat, 06 Jul 2019 00:05:18: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:05:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:05:18: #2 number of paired peaks: 280 WARNING @ Sat, 06 Jul 2019 00:05:18: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Sat, 06 Jul 2019 00:05:18: start model_add_line... INFO @ Sat, 06 Jul 2019 00:05:18: start X-correlation... INFO @ Sat, 06 Jul 2019 00:05:18: end of X-cor INFO @ Sat, 06 Jul 2019 00:05:18: #2 finished! INFO @ Sat, 06 Jul 2019 00:05:18: #2 predicted fragment length is 105 bps INFO @ Sat, 06 Jul 2019 00:05:18: #2 alternative fragment length(s) may be 2,43,105,125 bps INFO @ Sat, 06 Jul 2019 00:05:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.20_model.r WARNING @ Sat, 06 Jul 2019 00:05:18: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 00:05:18: #2 You may need to consider one of the other alternative d(s): 2,43,105,125 WARNING @ Sat, 06 Jul 2019 00:05:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 00:05:18: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:05:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 00:05:18: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:05:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.10_peaks.xls INFO @ Sat, 06 Jul 2019 00:05:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:05:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.10_summits.bed INFO @ Sat, 06 Jul 2019 00:05:21: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (184 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:05:26: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 00:05:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.20_peaks.xls INFO @ Sat, 06 Jul 2019 00:05:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:05:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX3828984/SRX3828984.20_summits.bed INFO @ Sat, 06 Jul 2019 00:05:28: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 2 millis BigWig に変換しました。 CompletedMACS2peakCalling