Job ID = 2008029 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,661,474 reads read : 3,322,948 reads written : 3,322,948 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: 00:02:06 1661474 reads; of these: 1661474 (100.00%) were paired; of these: 233782 (14.07%) aligned concordantly 0 times 1308182 (78.74%) aligned concordantly exactly 1 time 119510 (7.19%) aligned concordantly >1 times ---- 233782 pairs aligned concordantly 0 times; of these: 26265 (11.23%) aligned discordantly 1 time ---- 207517 pairs aligned 0 times concordantly or discordantly; of these: 415034 mates make up the pairs; of these: 389363 (93.81%) aligned 0 times 17619 (4.25%) aligned exactly 1 time 8052 (1.94%) aligned >1 times 88.28% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 225353 / 1450294 = 0.1554 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 17:19:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.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 17:19:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:19:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:19:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.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 17:19:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:19:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:19:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.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 17:19:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:19:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:20:10: 1000000 INFO @ Fri, 05 Jul 2019 17:20:12: 1000000 INFO @ Fri, 05 Jul 2019 17:20:13: 1000000 INFO @ Fri, 05 Jul 2019 17:20:22: 2000000 INFO @ Fri, 05 Jul 2019 17:20:25: 2000000 INFO @ Fri, 05 Jul 2019 17:20:26: 2000000 INFO @ Fri, 05 Jul 2019 17:20:28: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:20:28: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:20:28: #1 total tags in treatment: 1204100 INFO @ Fri, 05 Jul 2019 17:20:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:20:28: #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 17:20:28: #1 tags after filtering in treatment: 1149172 INFO @ Fri, 05 Jul 2019 17:20:28: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:20:28: #1 finished! INFO @ Fri, 05 Jul 2019 17:20:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:20:28: #2 number of paired peaks: 176 WARNING @ Fri, 05 Jul 2019 17:20:28: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Fri, 05 Jul 2019 17:20:28: start model_add_line... INFO @ Fri, 05 Jul 2019 17:20:28: start X-correlation... INFO @ Fri, 05 Jul 2019 17:20:28: end of X-cor INFO @ Fri, 05 Jul 2019 17:20:28: #2 finished! INFO @ Fri, 05 Jul 2019 17:20:28: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 17:20:28: #2 alternative fragment length(s) may be 0,30,52,78,91,142,146,181,202,220,248,265,315,335,396,448,457,484,499,520,543,587 bps INFO @ Fri, 05 Jul 2019 17:20:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.05_model.r WARNING @ Fri, 05 Jul 2019 17:20:28: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:20:28: #2 You may need to consider one of the other alternative d(s): 0,30,52,78,91,142,146,181,202,220,248,265,315,335,396,448,457,484,499,520,543,587 WARNING @ Fri, 05 Jul 2019 17:20:28: #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 17:20:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:20:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:20:30: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:20:30: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:20:30: #1 total tags in treatment: 1204100 INFO @ Fri, 05 Jul 2019 17:20:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:20:30: #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 17:20:30: #1 tags after filtering in treatment: 1149172 INFO @ Fri, 05 Jul 2019 17:20:30: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:20:30: #1 finished! INFO @ Fri, 05 Jul 2019 17:20:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:20:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:20:30: #2 number of paired peaks: 176 WARNING @ Fri, 05 Jul 2019 17:20:30: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Fri, 05 Jul 2019 17:20:30: start model_add_line... INFO @ Fri, 05 Jul 2019 17:20:30: start X-correlation... INFO @ Fri, 05 Jul 2019 17:20:30: end of X-cor INFO @ Fri, 05 Jul 2019 17:20:30: #2 finished! INFO @ Fri, 05 Jul 2019 17:20:30: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 17:20:30: #2 alternative fragment length(s) may be 0,30,52,78,91,142,146,181,202,220,248,265,315,335,396,448,457,484,499,520,543,587 bps INFO @ Fri, 05 Jul 2019 17:20:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.20_model.r WARNING @ Fri, 05 Jul 2019 17:20:30: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:20:30: #2 You may need to consider one of the other alternative d(s): 0,30,52,78,91,142,146,181,202,220,248,265,315,335,396,448,457,484,499,520,543,587 WARNING @ Fri, 05 Jul 2019 17:20:30: #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 17:20:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:20:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:20:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:20:33: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:20:33: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:20:33: #1 total tags in treatment: 1204100 INFO @ Fri, 05 Jul 2019 17:20:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:20:33: #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 17:20:33: #1 tags after filtering in treatment: 1149172 INFO @ Fri, 05 Jul 2019 17:20:33: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:20:33: #1 finished! INFO @ Fri, 05 Jul 2019 17:20:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:20:33: #2 number of paired peaks: 176 WARNING @ Fri, 05 Jul 2019 17:20:33: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Fri, 05 Jul 2019 17:20:33: start model_add_line... INFO @ Fri, 05 Jul 2019 17:20:33: start X-correlation... INFO @ Fri, 05 Jul 2019 17:20:33: end of X-cor INFO @ Fri, 05 Jul 2019 17:20:33: #2 finished! INFO @ Fri, 05 Jul 2019 17:20:33: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 17:20:33: #2 alternative fragment length(s) may be 0,30,52,78,91,142,146,181,202,220,248,265,315,335,396,448,457,484,499,520,543,587 bps INFO @ Fri, 05 Jul 2019 17:20:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.10_model.r WARNING @ Fri, 05 Jul 2019 17:20:33: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 17:20:33: #2 You may need to consider one of the other alternative d(s): 0,30,52,78,91,142,146,181,202,220,248,265,315,335,396,448,457,484,499,520,543,587 WARNING @ Fri, 05 Jul 2019 17:20:33: #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 17:20:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:20:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.05_summits.bed INFO @ Fri, 05 Jul 2019 17:20:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:20:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:20:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:20:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:20:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.20_summits.bed INFO @ Fri, 05 Jul 2019 17:20:35: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:20:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:20:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:20:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:20:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471815/ERX471815.10_summits.bed INFO @ Fri, 05 Jul 2019 17:20:38: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (15 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。