Job ID = 2008054 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,848,726 reads read : 3,697,452 reads written : 3,697,452 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: 00:01:53 1848726 reads; of these: 1848726 (100.00%) were paired; of these: 363217 (19.65%) aligned concordantly 0 times 1352054 (73.13%) aligned concordantly exactly 1 time 133455 (7.22%) aligned concordantly >1 times ---- 363217 pairs aligned concordantly 0 times; of these: 41195 (11.34%) aligned discordantly 1 time ---- 322022 pairs aligned 0 times concordantly or discordantly; of these: 644044 mates make up the pairs; of these: 611689 (94.98%) aligned 0 times 20539 (3.19%) aligned exactly 1 time 11816 (1.83%) aligned >1 times 83.46% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 277676 / 1522458 = 0.1824 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 17:23:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.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 17:23:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:23:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:23:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.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 17:23:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:23:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:23:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.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 17:23:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:23:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:23:45: 1000000 INFO @ Fri, 05 Jul 2019 17:23:46: 1000000 INFO @ Fri, 05 Jul 2019 17:23:46: 1000000 INFO @ Fri, 05 Jul 2019 17:23:56: 2000000 INFO @ Fri, 05 Jul 2019 17:23:56: 2000000 INFO @ Fri, 05 Jul 2019 17:23:58: 2000000 INFO @ Fri, 05 Jul 2019 17:24:01: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:24:01: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:24:01: #1 total tags in treatment: 1212046 INFO @ Fri, 05 Jul 2019 17:24:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:24:01: #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 17:24:01: #1 tags after filtering in treatment: 1147744 INFO @ Fri, 05 Jul 2019 17:24:01: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:24:01: #1 finished! INFO @ Fri, 05 Jul 2019 17:24:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:24:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:24:01: #2 number of paired peaks: 170 WARNING @ Fri, 05 Jul 2019 17:24:01: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Fri, 05 Jul 2019 17:24:01: start model_add_line... INFO @ Fri, 05 Jul 2019 17:24:01: start X-correlation... INFO @ Fri, 05 Jul 2019 17:24:01: end of X-cor INFO @ Fri, 05 Jul 2019 17:24:01: #2 finished! INFO @ Fri, 05 Jul 2019 17:24:01: #2 predicted fragment length is 202 bps INFO @ Fri, 05 Jul 2019 17:24:01: #2 alternative fragment length(s) may be 1,140,181,202,239,267,301,448,589 bps INFO @ Fri, 05 Jul 2019 17:24:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.20_model.r INFO @ Fri, 05 Jul 2019 17:24:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:24:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:24:01: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:24:01: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:24:01: #1 total tags in treatment: 1212046 INFO @ Fri, 05 Jul 2019 17:24:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:24:01: #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 17:24:01: #1 tags after filtering in treatment: 1147744 INFO @ Fri, 05 Jul 2019 17:24:01: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:24:01: #1 finished! INFO @ Fri, 05 Jul 2019 17:24:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:24:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:24:01: #2 number of paired peaks: 170 WARNING @ Fri, 05 Jul 2019 17:24:01: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Fri, 05 Jul 2019 17:24:01: start model_add_line... INFO @ Fri, 05 Jul 2019 17:24:01: start X-correlation... INFO @ Fri, 05 Jul 2019 17:24:01: end of X-cor INFO @ Fri, 05 Jul 2019 17:24:01: #2 finished! INFO @ Fri, 05 Jul 2019 17:24:01: #2 predicted fragment length is 202 bps INFO @ Fri, 05 Jul 2019 17:24:01: #2 alternative fragment length(s) may be 1,140,181,202,239,267,301,448,589 bps INFO @ Fri, 05 Jul 2019 17:24:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.05_model.r INFO @ Fri, 05 Jul 2019 17:24:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:24:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:24:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:24:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:24:05: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:24:05: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:24:05: #1 total tags in treatment: 1212046 INFO @ Fri, 05 Jul 2019 17:24:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:24:05: #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 17:24:05: #1 tags after filtering in treatment: 1147744 INFO @ Fri, 05 Jul 2019 17:24:05: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:24:05: #1 finished! INFO @ Fri, 05 Jul 2019 17:24:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:24:05: #2 number of paired peaks: 170 WARNING @ Fri, 05 Jul 2019 17:24:05: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Fri, 05 Jul 2019 17:24:05: start model_add_line... INFO @ Fri, 05 Jul 2019 17:24:05: start X-correlation... INFO @ Fri, 05 Jul 2019 17:24:05: end of X-cor INFO @ Fri, 05 Jul 2019 17:24:05: #2 finished! INFO @ Fri, 05 Jul 2019 17:24:05: #2 predicted fragment length is 202 bps INFO @ Fri, 05 Jul 2019 17:24:05: #2 alternative fragment length(s) may be 1,140,181,202,239,267,301,448,589 bps INFO @ Fri, 05 Jul 2019 17:24:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.10_model.r INFO @ Fri, 05 Jul 2019 17:24:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:24:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:24:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:24:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:24:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.20_summits.bed INFO @ Fri, 05 Jul 2019 17:24:06: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:24:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:24:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:24:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.05_summits.bed INFO @ Fri, 05 Jul 2019 17:24:07: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (123 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:24:09: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:24:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:24:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471837/ERX471837.10_summits.bed INFO @ Fri, 05 Jul 2019 17:24:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (37 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。