Job ID = 2010726 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,602,052 reads read : 5,204,104 reads written : 5,204,104 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: 00:02:05 2602052 reads; of these: 2602052 (100.00%) were paired; of these: 864476 (33.22%) aligned concordantly 0 times 1568445 (60.28%) aligned concordantly exactly 1 time 169131 (6.50%) aligned concordantly >1 times ---- 864476 pairs aligned concordantly 0 times; of these: 30850 (3.57%) aligned discordantly 1 time ---- 833626 pairs aligned 0 times concordantly or discordantly; of these: 1667252 mates make up the pairs; of these: 1596408 (95.75%) aligned 0 times 50601 (3.03%) aligned exactly 1 time 20243 (1.21%) aligned >1 times 69.32% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 12799 / 1762822 = 0.0073 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 00:10:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.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 00:10:02: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:10:02: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:10:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.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 00:10:03: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:10:03: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:10:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.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 00:10:04: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:10:04: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:10:13: 1000000 INFO @ Sat, 06 Jul 2019 00:10:14: 1000000 INFO @ Sat, 06 Jul 2019 00:10:15: 1000000 INFO @ Sat, 06 Jul 2019 00:10:23: 2000000 INFO @ Sat, 06 Jul 2019 00:10:25: 2000000 INFO @ Sat, 06 Jul 2019 00:10:25: 2000000 INFO @ Sat, 06 Jul 2019 00:10:32: 3000000 INFO @ Sat, 06 Jul 2019 00:10:35: 3000000 INFO @ Sat, 06 Jul 2019 00:10:35: 3000000 INFO @ Sat, 06 Jul 2019 00:10:37: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:10:37: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:10:37: #1 total tags in treatment: 1724961 INFO @ Sat, 06 Jul 2019 00:10:37: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:10:37: #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 00:10:37: #1 tags after filtering in treatment: 1568632 INFO @ Sat, 06 Jul 2019 00:10:37: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 06 Jul 2019 00:10:37: #1 finished! INFO @ Sat, 06 Jul 2019 00:10:37: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:10:37: #2 number of paired peaks: 139 WARNING @ Sat, 06 Jul 2019 00:10:37: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 06 Jul 2019 00:10:37: start model_add_line... INFO @ Sat, 06 Jul 2019 00:10:37: start X-correlation... INFO @ Sat, 06 Jul 2019 00:10:37: end of X-cor INFO @ Sat, 06 Jul 2019 00:10:37: #2 finished! INFO @ Sat, 06 Jul 2019 00:10:37: #2 predicted fragment length is 128 bps INFO @ Sat, 06 Jul 2019 00:10:37: #2 alternative fragment length(s) may be 2,26,65,107,128,191 bps INFO @ Sat, 06 Jul 2019 00:10:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.05_model.r WARNING @ Sat, 06 Jul 2019 00:10:37: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 00:10:37: #2 You may need to consider one of the other alternative d(s): 2,26,65,107,128,191 WARNING @ Sat, 06 Jul 2019 00:10:37: #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 00:10:37: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:10:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 00:10:40: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:10:40: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:10:40: #1 total tags in treatment: 1724961 INFO @ Sat, 06 Jul 2019 00:10:40: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:10:40: #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 00:10:40: #1 tags after filtering in treatment: 1568632 INFO @ Sat, 06 Jul 2019 00:10:40: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 06 Jul 2019 00:10:40: #1 finished! INFO @ Sat, 06 Jul 2019 00:10:40: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:10:40: #2 number of paired peaks: 139 WARNING @ Sat, 06 Jul 2019 00:10:40: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 06 Jul 2019 00:10:40: start model_add_line... INFO @ Sat, 06 Jul 2019 00:10:40: start X-correlation... INFO @ Sat, 06 Jul 2019 00:10:40: end of X-cor INFO @ Sat, 06 Jul 2019 00:10:40: #2 finished! INFO @ Sat, 06 Jul 2019 00:10:40: #2 predicted fragment length is 128 bps INFO @ Sat, 06 Jul 2019 00:10:40: #2 alternative fragment length(s) may be 2,26,65,107,128,191 bps INFO @ Sat, 06 Jul 2019 00:10:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.10_model.r WARNING @ Sat, 06 Jul 2019 00:10:40: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 00:10:40: #2 You may need to consider one of the other alternative d(s): 2,26,65,107,128,191 WARNING @ Sat, 06 Jul 2019 00:10:40: #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 00:10:40: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:10:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 00:10:41: #1 tag size is determined as 75 bps INFO @ Sat, 06 Jul 2019 00:10:41: #1 tag size = 75 INFO @ Sat, 06 Jul 2019 00:10:41: #1 total tags in treatment: 1724961 INFO @ Sat, 06 Jul 2019 00:10:41: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:10:41: #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 00:10:41: #1 tags after filtering in treatment: 1568632 INFO @ Sat, 06 Jul 2019 00:10:41: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 06 Jul 2019 00:10:41: #1 finished! INFO @ Sat, 06 Jul 2019 00:10:41: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:10:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:10:41: #2 number of paired peaks: 139 WARNING @ Sat, 06 Jul 2019 00:10:41: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 06 Jul 2019 00:10:41: start model_add_line... INFO @ Sat, 06 Jul 2019 00:10:41: start X-correlation... INFO @ Sat, 06 Jul 2019 00:10:41: end of X-cor INFO @ Sat, 06 Jul 2019 00:10:41: #2 finished! INFO @ Sat, 06 Jul 2019 00:10:41: #2 predicted fragment length is 128 bps INFO @ Sat, 06 Jul 2019 00:10:41: #2 alternative fragment length(s) may be 2,26,65,107,128,191 bps INFO @ Sat, 06 Jul 2019 00:10:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.20_model.r WARNING @ Sat, 06 Jul 2019 00:10:41: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 00:10:41: #2 You may need to consider one of the other alternative d(s): 2,26,65,107,128,191 WARNING @ Sat, 06 Jul 2019 00:10:41: #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 00:10:41: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 00:10:43: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 00:10:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.05_peaks.xls INFO @ Sat, 06 Jul 2019 00:10:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:10:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.05_summits.bed INFO @ Sat, 06 Jul 2019 00:10:45: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (447 records, 4 fields): 8 millis INFO @ Sat, 06 Jul 2019 00:10:46: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:10:46: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 00:10:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.10_peaks.xls INFO @ Sat, 06 Jul 2019 00:10:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:10:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.10_summits.bed INFO @ Sat, 06 Jul 2019 00:10:48: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.20_peaks.xls INFO @ Sat, 06 Jul 2019 00:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:10:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386908/SRX386908.20_summits.bed INFO @ Sat, 06 Jul 2019 00:10:49: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (62 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。