Job ID = 2007997 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,096,121 reads read : 4,192,242 reads written : 4,192,242 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: 00:02:47 2096121 reads; of these: 2096121 (100.00%) were paired; of these: 127472 (6.08%) aligned concordantly 0 times 1815082 (86.59%) aligned concordantly exactly 1 time 153567 (7.33%) aligned concordantly >1 times ---- 127472 pairs aligned concordantly 0 times; of these: 56914 (44.65%) aligned discordantly 1 time ---- 70558 pairs aligned 0 times concordantly or discordantly; of these: 141116 mates make up the pairs; of these: 104238 (73.87%) aligned 0 times 24034 (17.03%) aligned exactly 1 time 12844 (9.10%) aligned >1 times 97.51% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 36108 / 2017016 = 0.0179 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 17:09:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.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 17:09:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:09:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:09:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.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 17:09:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:09:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.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 17:09:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:09:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:09:55: 1000000 INFO @ Fri, 05 Jul 2019 17:09:57: 1000000 INFO @ Fri, 05 Jul 2019 17:09:58: 1000000 INFO @ Fri, 05 Jul 2019 17:10:03: 2000000 INFO @ Fri, 05 Jul 2019 17:10:06: 2000000 INFO @ Fri, 05 Jul 2019 17:10:10: 2000000 INFO @ Fri, 05 Jul 2019 17:10:11: 3000000 INFO @ Fri, 05 Jul 2019 17:10:18: 4000000 INFO @ Fri, 05 Jul 2019 17:10:18: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:10:18: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:10:18: #1 total tags in treatment: 1932967 INFO @ Fri, 05 Jul 2019 17:10:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:10:18: #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 17:10:18: #1 tags after filtering in treatment: 1739453 INFO @ Fri, 05 Jul 2019 17:10:18: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 05 Jul 2019 17:10:18: #1 finished! INFO @ Fri, 05 Jul 2019 17:10:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:10:19: #2 number of paired peaks: 261 WARNING @ Fri, 05 Jul 2019 17:10:19: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 05 Jul 2019 17:10:19: start model_add_line... INFO @ Fri, 05 Jul 2019 17:10:19: start X-correlation... INFO @ Fri, 05 Jul 2019 17:10:19: end of X-cor INFO @ Fri, 05 Jul 2019 17:10:19: #2 finished! INFO @ Fri, 05 Jul 2019 17:10:19: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 17:10:19: #2 alternative fragment length(s) may be 120,134 bps INFO @ Fri, 05 Jul 2019 17:10:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.10_model.r WARNING @ Fri, 05 Jul 2019 17:10:19: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:10:19: #2 You may need to consider one of the other alternative d(s): 120,134 WARNING @ Fri, 05 Jul 2019 17:10:19: #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 17:10:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:10:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:10:20: 3000000 INFO @ Fri, 05 Jul 2019 17:10:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:10:25: 3000000 INFO @ Fri, 05 Jul 2019 17:10:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:10:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:10:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.10_summits.bed INFO @ Fri, 05 Jul 2019 17:10:26: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (406 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:10:32: 4000000 INFO @ Fri, 05 Jul 2019 17:10:32: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:10:32: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:10:32: #1 total tags in treatment: 1932967 INFO @ Fri, 05 Jul 2019 17:10:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:10:32: #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 17:10:32: #1 tags after filtering in treatment: 1739453 INFO @ Fri, 05 Jul 2019 17:10:32: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 05 Jul 2019 17:10:32: #1 finished! INFO @ Fri, 05 Jul 2019 17:10:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:10:32: #2 number of paired peaks: 261 WARNING @ Fri, 05 Jul 2019 17:10:32: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 05 Jul 2019 17:10:32: start model_add_line... INFO @ Fri, 05 Jul 2019 17:10:32: start X-correlation... INFO @ Fri, 05 Jul 2019 17:10:32: end of X-cor INFO @ Fri, 05 Jul 2019 17:10:32: #2 finished! INFO @ Fri, 05 Jul 2019 17:10:32: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 17:10:32: #2 alternative fragment length(s) may be 120,134 bps INFO @ Fri, 05 Jul 2019 17:10:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.20_model.r WARNING @ Fri, 05 Jul 2019 17:10:32: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:10:32: #2 You may need to consider one of the other alternative d(s): 120,134 WARNING @ Fri, 05 Jul 2019 17:10:32: #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 17:10:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:10:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:10:36: 4000000 INFO @ Fri, 05 Jul 2019 17:10:37: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:10:37: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:10:37: #1 total tags in treatment: 1932967 INFO @ Fri, 05 Jul 2019 17:10:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:10:37: #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 17:10:37: #1 tags after filtering in treatment: 1739453 INFO @ Fri, 05 Jul 2019 17:10:37: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 05 Jul 2019 17:10:37: #1 finished! INFO @ Fri, 05 Jul 2019 17:10:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:10:37: #2 number of paired peaks: 261 WARNING @ Fri, 05 Jul 2019 17:10:37: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 05 Jul 2019 17:10:37: start model_add_line... INFO @ Fri, 05 Jul 2019 17:10:37: start X-correlation... INFO @ Fri, 05 Jul 2019 17:10:37: end of X-cor INFO @ Fri, 05 Jul 2019 17:10:37: #2 finished! INFO @ Fri, 05 Jul 2019 17:10:37: #2 predicted fragment length is 120 bps INFO @ Fri, 05 Jul 2019 17:10:37: #2 alternative fragment length(s) may be 120,134 bps INFO @ Fri, 05 Jul 2019 17:10:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.05_model.r WARNING @ Fri, 05 Jul 2019 17:10:37: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:10:37: #2 You may need to consider one of the other alternative d(s): 120,134 WARNING @ Fri, 05 Jul 2019 17:10:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 17:10:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:10:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:10:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:10:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:10:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:10:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.20_summits.bed INFO @ Fri, 05 Jul 2019 17:10:40: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:10:43: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:10:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:10:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:10:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471787/ERX471787.05_summits.bed INFO @ Fri, 05 Jul 2019 17:10:45: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (695 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。