Job ID = 2007851 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 191,778 reads read : 383,556 reads written : 383,556 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: 00:00:05 191778 reads; of these: 191778 (100.00%) were paired; of these: 33446 (17.44%) aligned concordantly 0 times 147466 (76.89%) aligned concordantly exactly 1 time 10866 (5.67%) aligned concordantly >1 times ---- 33446 pairs aligned concordantly 0 times; of these: 15306 (45.76%) aligned discordantly 1 time ---- 18140 pairs aligned 0 times concordantly or discordantly; of these: 36280 mates make up the pairs; of these: 31117 (85.77%) aligned 0 times 2651 (7.31%) aligned exactly 1 time 2512 (6.92%) aligned >1 times 91.89% overall alignment rate Time searching: 00:00:05 Overall time: 00:00:05 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] 1354 / 171847 = 0.0079 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 16:33:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.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 16:33:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:33:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:33:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.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 16:33:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:33:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:33:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.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 16:33:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:33:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:33:49: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:33:49: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:33:49: #1 total tags in treatment: 157079 INFO @ Fri, 05 Jul 2019 16:33:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:33:49: #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 16:33:49: #1 tags after filtering in treatment: 155575 INFO @ Fri, 05 Jul 2019 16:33:49: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:33:49: #1 finished! INFO @ Fri, 05 Jul 2019 16:33:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:33:49: #2 number of paired peaks: 179 WARNING @ Fri, 05 Jul 2019 16:33:49: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 05 Jul 2019 16:33:49: start model_add_line... INFO @ Fri, 05 Jul 2019 16:33:49: start X-correlation... INFO @ Fri, 05 Jul 2019 16:33:49: end of X-cor INFO @ Fri, 05 Jul 2019 16:33:49: #2 finished! INFO @ Fri, 05 Jul 2019 16:33:49: #2 predicted fragment length is 227 bps INFO @ Fri, 05 Jul 2019 16:33:49: #2 alternative fragment length(s) may be 227 bps INFO @ Fri, 05 Jul 2019 16:33:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.05_model.r INFO @ Fri, 05 Jul 2019 16:33:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:33:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:33:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:33:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:33:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.05_summits.bed INFO @ Fri, 05 Jul 2019 16:33:50: Done! INFO @ Fri, 05 Jul 2019 16:33:50: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:33:50: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:33:50: #1 total tags in treatment: 157079 INFO @ Fri, 05 Jul 2019 16:33:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:33:50: #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 16:33:50: #1 tags after filtering in treatment: 155575 INFO @ Fri, 05 Jul 2019 16:33:50: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:33:50: #1 finished! INFO @ Fri, 05 Jul 2019 16:33:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:33:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:33:50: #2 number of paired peaks: 179 WARNING @ Fri, 05 Jul 2019 16:33:50: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 05 Jul 2019 16:33:50: start model_add_line... INFO @ Fri, 05 Jul 2019 16:33:50: start X-correlation... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:33:50: end of X-cor INFO @ Fri, 05 Jul 2019 16:33:50: #2 finished! INFO @ Fri, 05 Jul 2019 16:33:50: #2 predicted fragment length is 227 bps INFO @ Fri, 05 Jul 2019 16:33:50: #2 alternative fragment length(s) may be 227 bps INFO @ Fri, 05 Jul 2019 16:33:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.10_model.r INFO @ Fri, 05 Jul 2019 16:33:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:33:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:33:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:33:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:33:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:33:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.10_summits.bed INFO @ Fri, 05 Jul 2019 16:33:51: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:33:51: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:33:51: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:33:51: #1 total tags in treatment: 157079 INFO @ Fri, 05 Jul 2019 16:33:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:33:51: #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 16:33:51: #1 tags after filtering in treatment: 155575 INFO @ Fri, 05 Jul 2019 16:33:51: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 05 Jul 2019 16:33:51: #1 finished! INFO @ Fri, 05 Jul 2019 16:33:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:33:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:33:51: #2 number of paired peaks: 179 WARNING @ Fri, 05 Jul 2019 16:33:51: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 05 Jul 2019 16:33:51: start model_add_line... INFO @ Fri, 05 Jul 2019 16:33:51: start X-correlation... INFO @ Fri, 05 Jul 2019 16:33:51: end of X-cor INFO @ Fri, 05 Jul 2019 16:33:51: #2 finished! INFO @ Fri, 05 Jul 2019 16:33:51: #2 predicted fragment length is 227 bps INFO @ Fri, 05 Jul 2019 16:33:51: #2 alternative fragment length(s) may be 227 bps INFO @ Fri, 05 Jul 2019 16:33:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.20_model.r INFO @ Fri, 05 Jul 2019 16:33:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:33:51: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX462394/ERX462394.20_summits.bed INFO @ Fri, 05 Jul 2019 16:33:52: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 7 millis BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling CompletedMACS2peakCalling