Job ID = 2008021 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,855,888 reads read : 3,711,776 reads written : 3,711,776 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: 00:01:59 1855888 reads; of these: 1855888 (100.00%) were paired; of these: 260506 (14.04%) aligned concordantly 0 times 1466895 (79.04%) aligned concordantly exactly 1 time 128487 (6.92%) aligned concordantly >1 times ---- 260506 pairs aligned concordantly 0 times; of these: 30603 (11.75%) aligned discordantly 1 time ---- 229903 pairs aligned 0 times concordantly or discordantly; of these: 459806 mates make up the pairs; of these: 433490 (94.28%) aligned 0 times 17622 (3.83%) aligned exactly 1 time 8694 (1.89%) aligned >1 times 88.32% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 239435 / 1622057 = 0.1476 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 17:18:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.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 17:18:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:18:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:18:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.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 17:18:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:18:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:18:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.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 17:18:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:18:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:18:54: 1000000 INFO @ Fri, 05 Jul 2019 17:18:55: 1000000 INFO @ Fri, 05 Jul 2019 17:18:57: 1000000 INFO @ Fri, 05 Jul 2019 17:19:04: 2000000 INFO @ Fri, 05 Jul 2019 17:19:05: 2000000 INFO @ Fri, 05 Jul 2019 17:19:07: 2000000 INFO @ Fri, 05 Jul 2019 17:19:11: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:19:11: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:19:11: #1 total tags in treatment: 1357896 INFO @ Fri, 05 Jul 2019 17:19:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:19:11: #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 17:19:11: #1 tags after filtering in treatment: 1296761 INFO @ Fri, 05 Jul 2019 17:19:11: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:19:11: #1 finished! INFO @ Fri, 05 Jul 2019 17:19:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:19:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:19:11: #2 number of paired peaks: 168 WARNING @ Fri, 05 Jul 2019 17:19:11: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 05 Jul 2019 17:19:11: start model_add_line... INFO @ Fri, 05 Jul 2019 17:19:11: start X-correlation... INFO @ Fri, 05 Jul 2019 17:19:11: end of X-cor INFO @ Fri, 05 Jul 2019 17:19:11: #2 finished! INFO @ Fri, 05 Jul 2019 17:19:11: #2 predicted fragment length is 219 bps INFO @ Fri, 05 Jul 2019 17:19:11: #2 alternative fragment length(s) may be 0,35,58,89,124,138,157,183,219,249,275,303,328,371,424,444,470,492,516,540,573 bps INFO @ Fri, 05 Jul 2019 17:19:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.10_model.r INFO @ Fri, 05 Jul 2019 17:19:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:19:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:19:13: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:19:13: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:19:13: #1 total tags in treatment: 1357896 INFO @ Fri, 05 Jul 2019 17:19:13: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:19:13: #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 17:19:13: #1 tags after filtering in treatment: 1296761 INFO @ Fri, 05 Jul 2019 17:19:13: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:19:13: #1 finished! INFO @ Fri, 05 Jul 2019 17:19:13: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:19:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:19:13: #2 number of paired peaks: 168 WARNING @ Fri, 05 Jul 2019 17:19:13: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 05 Jul 2019 17:19:13: start model_add_line... INFO @ Fri, 05 Jul 2019 17:19:13: start X-correlation... INFO @ Fri, 05 Jul 2019 17:19:13: end of X-cor INFO @ Fri, 05 Jul 2019 17:19:13: #2 finished! INFO @ Fri, 05 Jul 2019 17:19:13: #2 predicted fragment length is 219 bps INFO @ Fri, 05 Jul 2019 17:19:13: #2 alternative fragment length(s) may be 0,35,58,89,124,138,157,183,219,249,275,303,328,371,424,444,470,492,516,540,573 bps INFO @ Fri, 05 Jul 2019 17:19:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.05_model.r INFO @ Fri, 05 Jul 2019 17:19:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:19:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:19:15: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:19:15: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:19:15: #1 total tags in treatment: 1357896 INFO @ Fri, 05 Jul 2019 17:19:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:19:15: #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 17:19:15: #1 tags after filtering in treatment: 1296761 INFO @ Fri, 05 Jul 2019 17:19:15: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:19:15: #1 finished! INFO @ Fri, 05 Jul 2019 17:19:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:19:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:19:15: #2 number of paired peaks: 168 WARNING @ Fri, 05 Jul 2019 17:19:15: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Fri, 05 Jul 2019 17:19:15: start model_add_line... INFO @ Fri, 05 Jul 2019 17:19:15: start X-correlation... INFO @ Fri, 05 Jul 2019 17:19:15: end of X-cor INFO @ Fri, 05 Jul 2019 17:19:15: #2 finished! INFO @ Fri, 05 Jul 2019 17:19:15: #2 predicted fragment length is 219 bps INFO @ Fri, 05 Jul 2019 17:19:15: #2 alternative fragment length(s) may be 0,35,58,89,124,138,157,183,219,249,275,303,328,371,424,444,470,492,516,540,573 bps INFO @ Fri, 05 Jul 2019 17:19:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.20_model.r INFO @ Fri, 05 Jul 2019 17:19:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:19:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:19:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.10_summits.bed INFO @ Fri, 05 Jul 2019 17:19:17: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (23 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:19:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:19:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:19:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:19:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.05_summits.bed INFO @ Fri, 05 Jul 2019 17:19:19: Done! pass1 - making usageList (15 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (61 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:19:19: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:19:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:19:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:19:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471808/ERX471808.20_summits.bed INFO @ Fri, 05 Jul 2019 17:19:21: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (7 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。