Job ID = 2010002 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,943,672 reads read : 9,887,344 reads written : 9,887,344 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5008424.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: 00:03:34 4943672 reads; of these: 4943672 (100.00%) were paired; of these: 1528497 (30.92%) aligned concordantly 0 times 2532386 (51.22%) aligned concordantly exactly 1 time 882789 (17.86%) aligned concordantly >1 times ---- 1528497 pairs aligned concordantly 0 times; of these: 37278 (2.44%) aligned discordantly 1 time ---- 1491219 pairs aligned 0 times concordantly or discordantly; of these: 2982438 mates make up the pairs; of these: 2826034 (94.76%) aligned 0 times 95900 (3.22%) aligned exactly 1 time 60504 (2.03%) aligned >1 times 71.42% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 183778 / 3444761 = 0.0534 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 20:54:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.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 20:54:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:54:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:54:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.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 20:54:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:54:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:54:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.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 20:54:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:54:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:54:40: 1000000 INFO @ Fri, 05 Jul 2019 20:54:40: 1000000 INFO @ Fri, 05 Jul 2019 20:54:41: 1000000 INFO @ Fri, 05 Jul 2019 20:54:46: 2000000 INFO @ Fri, 05 Jul 2019 20:54:47: 2000000 INFO @ Fri, 05 Jul 2019 20:54:47: 2000000 INFO @ Fri, 05 Jul 2019 20:54:53: 3000000 INFO @ Fri, 05 Jul 2019 20:54:54: 3000000 INFO @ Fri, 05 Jul 2019 20:54:54: 3000000 INFO @ Fri, 05 Jul 2019 20:54:59: 4000000 INFO @ Fri, 05 Jul 2019 20:55:00: 4000000 INFO @ Fri, 05 Jul 2019 20:55:01: 4000000 INFO @ Fri, 05 Jul 2019 20:55:05: 5000000 INFO @ Fri, 05 Jul 2019 20:55:06: 5000000 INFO @ Fri, 05 Jul 2019 20:55:07: 5000000 INFO @ Fri, 05 Jul 2019 20:55:11: 6000000 INFO @ Fri, 05 Jul 2019 20:55:12: 6000000 INFO @ Fri, 05 Jul 2019 20:55:14: 6000000 INFO @ Fri, 05 Jul 2019 20:55:15: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:55:15: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:55:15: #1 total tags in treatment: 3231697 INFO @ Fri, 05 Jul 2019 20:55:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:55:15: #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 20:55:15: #1 tags after filtering in treatment: 2223094 INFO @ Fri, 05 Jul 2019 20:55:15: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 05 Jul 2019 20:55:15: #1 finished! INFO @ Fri, 05 Jul 2019 20:55:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:55:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:55:15: #2 number of paired peaks: 110 WARNING @ Fri, 05 Jul 2019 20:55:15: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Fri, 05 Jul 2019 20:55:15: start model_add_line... INFO @ Fri, 05 Jul 2019 20:55:15: start X-correlation... INFO @ Fri, 05 Jul 2019 20:55:15: end of X-cor INFO @ Fri, 05 Jul 2019 20:55:15: #2 finished! INFO @ Fri, 05 Jul 2019 20:55:15: #2 predicted fragment length is 178 bps INFO @ Fri, 05 Jul 2019 20:55:15: #2 alternative fragment length(s) may be 3,178,197,219,548 bps INFO @ Fri, 05 Jul 2019 20:55:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.10_model.r INFO @ Fri, 05 Jul 2019 20:55:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:55:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:55:16: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:55:16: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:55:16: #1 total tags in treatment: 3231697 INFO @ Fri, 05 Jul 2019 20:55:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:55:16: #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 20:55:16: #1 tags after filtering in treatment: 2223094 INFO @ Fri, 05 Jul 2019 20:55:16: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 05 Jul 2019 20:55:16: #1 finished! INFO @ Fri, 05 Jul 2019 20:55:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:55:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:55:16: #2 number of paired peaks: 110 WARNING @ Fri, 05 Jul 2019 20:55:16: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Fri, 05 Jul 2019 20:55:16: start model_add_line... INFO @ Fri, 05 Jul 2019 20:55:16: start X-correlation... INFO @ Fri, 05 Jul 2019 20:55:16: end of X-cor INFO @ Fri, 05 Jul 2019 20:55:16: #2 finished! INFO @ Fri, 05 Jul 2019 20:55:16: #2 predicted fragment length is 178 bps INFO @ Fri, 05 Jul 2019 20:55:16: #2 alternative fragment length(s) may be 3,178,197,219,548 bps INFO @ Fri, 05 Jul 2019 20:55:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.20_model.r INFO @ Fri, 05 Jul 2019 20:55:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:55:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:55:19: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:55:19: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:55:19: #1 total tags in treatment: 3231697 INFO @ Fri, 05 Jul 2019 20:55:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:55:19: #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 20:55:19: #1 tags after filtering in treatment: 2223094 INFO @ Fri, 05 Jul 2019 20:55:19: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 05 Jul 2019 20:55:19: #1 finished! INFO @ Fri, 05 Jul 2019 20:55:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:55:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:55:19: #2 number of paired peaks: 110 WARNING @ Fri, 05 Jul 2019 20:55:19: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Fri, 05 Jul 2019 20:55:19: start model_add_line... INFO @ Fri, 05 Jul 2019 20:55:19: start X-correlation... INFO @ Fri, 05 Jul 2019 20:55:19: end of X-cor INFO @ Fri, 05 Jul 2019 20:55:19: #2 finished! INFO @ Fri, 05 Jul 2019 20:55:19: #2 predicted fragment length is 178 bps INFO @ Fri, 05 Jul 2019 20:55:19: #2 alternative fragment length(s) may be 3,178,197,219,548 bps INFO @ Fri, 05 Jul 2019 20:55:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.05_model.r INFO @ Fri, 05 Jul 2019 20:55:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:55:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:55:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:55:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:55:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.10_peaks.xls INFO @ Fri, 05 Jul 2019 20:55:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:55:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.10_summits.bed INFO @ Fri, 05 Jul 2019 20:55:27: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (513 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 20:55:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.20_peaks.xls INFO @ Fri, 05 Jul 2019 20:55:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:55:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.20_summits.bed INFO @ Fri, 05 Jul 2019 20:55:28: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 20:55:28: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:55:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.05_peaks.xls INFO @ Fri, 05 Jul 2019 20:55:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:55:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339865/SRX2339865.05_summits.bed INFO @ Fri, 05 Jul 2019 20:55:31: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (803 records, 4 fields): 6 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。