Job ID = 2011731 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,671,884 reads read : 7,343,768 reads written : 7,343,768 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1171740.sra.cache’: 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: 00:01:44 3671884 reads; of these: 3671884 (100.00%) were paired; of these: 3322969 (90.50%) aligned concordantly 0 times 225695 (6.15%) aligned concordantly exactly 1 time 123220 (3.36%) aligned concordantly >1 times ---- 3322969 pairs aligned concordantly 0 times; of these: 306649 (9.23%) aligned discordantly 1 time ---- 3016320 pairs aligned 0 times concordantly or discordantly; of these: 6032640 mates make up the pairs; of these: 4982947 (82.60%) aligned 0 times 713650 (11.83%) aligned exactly 1 time 336043 (5.57%) aligned >1 times 32.15% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 80555 / 377472 = 0.2134 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 @ Sat, 06 Jul 2019 02:16:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.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 @ Sat, 06 Jul 2019 02:16:46: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:16:46: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:16:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.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 @ Sat, 06 Jul 2019 02:16:47: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:16:47: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:16:53: 1000000 INFO @ Sat, 06 Jul 2019 02:16:54: 1000000 INFO @ Sat, 06 Jul 2019 02:16:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.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 @ Sat, 06 Jul 2019 02:16:55: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:16:55: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:16:59: 2000000 INFO @ Sat, 06 Jul 2019 02:17:00: 2000000 INFO @ Sat, 06 Jul 2019 02:17:00: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:17:00: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:17:00: #1 total tags in treatment: 273588 INFO @ Sat, 06 Jul 2019 02:17:00: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:17:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:17:00: #1 tags after filtering in treatment: 185203 INFO @ Sat, 06 Jul 2019 02:17:00: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 06 Jul 2019 02:17:00: #1 finished! INFO @ Sat, 06 Jul 2019 02:17:00: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:17:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:17:00: #2 number of paired peaks: 735 WARNING @ Sat, 06 Jul 2019 02:17:00: Fewer paired peaks (735) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 735 pairs to build model! INFO @ Sat, 06 Jul 2019 02:17:00: start model_add_line... INFO @ Sat, 06 Jul 2019 02:17:00: start X-correlation... INFO @ Sat, 06 Jul 2019 02:17:00: end of X-cor INFO @ Sat, 06 Jul 2019 02:17:00: #2 finished! INFO @ Sat, 06 Jul 2019 02:17:00: #2 predicted fragment length is 281 bps INFO @ Sat, 06 Jul 2019 02:17:00: #2 alternative fragment length(s) may be 4,281 bps INFO @ Sat, 06 Jul 2019 02:17:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.05_model.r INFO @ Sat, 06 Jul 2019 02:17:00: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:17:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:17:01: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:17:01: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:17:01: #1 total tags in treatment: 273588 INFO @ Sat, 06 Jul 2019 02:17:01: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:17:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:17:01: #1 tags after filtering in treatment: 185203 INFO @ Sat, 06 Jul 2019 02:17:01: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 06 Jul 2019 02:17:01: #1 finished! INFO @ Sat, 06 Jul 2019 02:17:01: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:17:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:17:01: #2 number of paired peaks: 735 WARNING @ Sat, 06 Jul 2019 02:17:01: Fewer paired peaks (735) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 735 pairs to build model! INFO @ Sat, 06 Jul 2019 02:17:01: start model_add_line... INFO @ Sat, 06 Jul 2019 02:17:01: start X-correlation... INFO @ Sat, 06 Jul 2019 02:17:01: end of X-cor INFO @ Sat, 06 Jul 2019 02:17:01: #2 finished! INFO @ Sat, 06 Jul 2019 02:17:01: #2 predicted fragment length is 281 bps INFO @ Sat, 06 Jul 2019 02:17:01: #2 alternative fragment length(s) may be 4,281 bps INFO @ Sat, 06 Jul 2019 02:17:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.10_model.r INFO @ Sat, 06 Jul 2019 02:17:01: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:17:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:17:01: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:17:02: 1000000 INFO @ Sat, 06 Jul 2019 02:17:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.05_peaks.xls INFO @ Sat, 06 Jul 2019 02:17:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:17:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.05_summits.bed INFO @ Sat, 06 Jul 2019 02:17:02: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (462 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:17:02: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.10_peaks.xls INFO @ Sat, 06 Jul 2019 02:17:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:17:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.10_summits.bed INFO @ Sat, 06 Jul 2019 02:17:03: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (346 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:17:08: 2000000 INFO @ Sat, 06 Jul 2019 02:17:09: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:17:09: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:17:09: #1 total tags in treatment: 273588 INFO @ Sat, 06 Jul 2019 02:17:09: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:17:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:17:09: #1 tags after filtering in treatment: 185203 INFO @ Sat, 06 Jul 2019 02:17:09: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 06 Jul 2019 02:17:09: #1 finished! INFO @ Sat, 06 Jul 2019 02:17:09: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:17:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:17:10: #2 number of paired peaks: 735 WARNING @ Sat, 06 Jul 2019 02:17:10: Fewer paired peaks (735) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 735 pairs to build model! INFO @ Sat, 06 Jul 2019 02:17:10: start model_add_line... INFO @ Sat, 06 Jul 2019 02:17:10: start X-correlation... INFO @ Sat, 06 Jul 2019 02:17:10: end of X-cor INFO @ Sat, 06 Jul 2019 02:17:10: #2 finished! INFO @ Sat, 06 Jul 2019 02:17:10: #2 predicted fragment length is 281 bps INFO @ Sat, 06 Jul 2019 02:17:10: #2 alternative fragment length(s) may be 4,281 bps INFO @ Sat, 06 Jul 2019 02:17:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.20_model.r INFO @ Sat, 06 Jul 2019 02:17:10: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:17:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:17:11: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:17:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.20_peaks.xls INFO @ Sat, 06 Jul 2019 02:17:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:17:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX472782/SRX472782.20_summits.bed INFO @ Sat, 06 Jul 2019 02:17:11: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (171 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。