Job ID = 2008000 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,682,410 reads read : 3,364,820 reads written : 3,364,820 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: 00:01:56 1682410 reads; of these: 1682410 (100.00%) were paired; of these: 141870 (8.43%) aligned concordantly 0 times 1411217 (83.88%) aligned concordantly exactly 1 time 129323 (7.69%) aligned concordantly >1 times ---- 141870 pairs aligned concordantly 0 times; of these: 35264 (24.86%) aligned discordantly 1 time ---- 106606 pairs aligned 0 times concordantly or discordantly; of these: 213212 mates make up the pairs; of these: 184272 (86.43%) aligned 0 times 18681 (8.76%) aligned exactly 1 time 10259 (4.81%) aligned >1 times 94.52% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 130062 / 1568487 = 0.0829 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 17:06:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.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 17:06:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:06:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.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 17:06:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:06:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:06:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.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 17:06:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:06:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:06:52: 1000000 INFO @ Fri, 05 Jul 2019 17:06:52: 1000000 INFO @ Fri, 05 Jul 2019 17:06:53: 1000000 INFO @ Fri, 05 Jul 2019 17:07:00: 2000000 INFO @ Fri, 05 Jul 2019 17:07:01: 2000000 INFO @ Fri, 05 Jul 2019 17:07:04: 2000000 INFO @ Fri, 05 Jul 2019 17:07:07: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:07:07: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:07:07: #1 total tags in treatment: 1411836 INFO @ Fri, 05 Jul 2019 17:07:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:07:07: #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 17:07:07: #1 tags after filtering in treatment: 1337960 INFO @ Fri, 05 Jul 2019 17:07:07: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:07:07: #1 finished! INFO @ Fri, 05 Jul 2019 17:07:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:07:07: #2 number of paired peaks: 157 WARNING @ Fri, 05 Jul 2019 17:07:07: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Fri, 05 Jul 2019 17:07:07: start model_add_line... INFO @ Fri, 05 Jul 2019 17:07:07: start X-correlation... INFO @ Fri, 05 Jul 2019 17:07:07: end of X-cor INFO @ Fri, 05 Jul 2019 17:07:07: #2 finished! INFO @ Fri, 05 Jul 2019 17:07:07: #2 predicted fragment length is 235 bps INFO @ Fri, 05 Jul 2019 17:07:07: #2 alternative fragment length(s) may be 1,161,172,190,206,235,498,558,583 bps INFO @ Fri, 05 Jul 2019 17:07:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.20_model.r INFO @ Fri, 05 Jul 2019 17:07:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:07:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:07:09: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:07:09: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:07:09: #1 total tags in treatment: 1411836 INFO @ Fri, 05 Jul 2019 17:07:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:07:09: #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 17:07:09: #1 tags after filtering in treatment: 1337960 INFO @ Fri, 05 Jul 2019 17:07:09: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:07:09: #1 finished! INFO @ Fri, 05 Jul 2019 17:07:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:07:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:07:10: #2 number of paired peaks: 157 WARNING @ Fri, 05 Jul 2019 17:07:10: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Fri, 05 Jul 2019 17:07:10: start model_add_line... INFO @ Fri, 05 Jul 2019 17:07:10: start X-correlation... INFO @ Fri, 05 Jul 2019 17:07:10: end of X-cor INFO @ Fri, 05 Jul 2019 17:07:10: #2 finished! INFO @ Fri, 05 Jul 2019 17:07:10: #2 predicted fragment length is 235 bps INFO @ Fri, 05 Jul 2019 17:07:10: #2 alternative fragment length(s) may be 1,161,172,190,206,235,498,558,583 bps INFO @ Fri, 05 Jul 2019 17:07:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.10_model.r INFO @ Fri, 05 Jul 2019 17:07:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:07:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:07:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:07:13: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:07:13: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:07:13: #1 total tags in treatment: 1411836 INFO @ Fri, 05 Jul 2019 17:07:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:07:13: #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 17:07:13: #1 tags after filtering in treatment: 1337960 INFO @ Fri, 05 Jul 2019 17:07:13: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:07:13: #1 finished! INFO @ Fri, 05 Jul 2019 17:07:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:07:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:07:13: #2 number of paired peaks: 157 WARNING @ Fri, 05 Jul 2019 17:07:13: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Fri, 05 Jul 2019 17:07:13: start model_add_line... INFO @ Fri, 05 Jul 2019 17:07:13: start X-correlation... INFO @ Fri, 05 Jul 2019 17:07:13: end of X-cor INFO @ Fri, 05 Jul 2019 17:07:13: #2 finished! INFO @ Fri, 05 Jul 2019 17:07:13: #2 predicted fragment length is 235 bps INFO @ Fri, 05 Jul 2019 17:07:13: #2 alternative fragment length(s) may be 1,161,172,190,206,235,498,558,583 bps INFO @ Fri, 05 Jul 2019 17:07:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.05_model.r INFO @ Fri, 05 Jul 2019 17:07:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:07:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:07:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:07:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:07:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.20_summits.bed INFO @ Fri, 05 Jul 2019 17:07:14: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:07:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:07:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:07:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:07:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.10_summits.bed INFO @ Fri, 05 Jul 2019 17:07:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:07:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471789/ERX471789.05_summits.bed INFO @ Fri, 05 Jul 2019 17:07:19: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (150 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。