Job ID = 2008262 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 339,088 reads read : 678,176 reads written : 678,176 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628988.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: 00:00:16 339088 reads; of these: 339088 (100.00%) were paired; of these: 22783 (6.72%) aligned concordantly 0 times 292293 (86.20%) aligned concordantly exactly 1 time 24012 (7.08%) aligned concordantly >1 times ---- 22783 pairs aligned concordantly 0 times; of these: 1972 (8.66%) aligned discordantly 1 time ---- 20811 pairs aligned 0 times concordantly or discordantly; of these: 41622 mates make up the pairs; of these: 39436 (94.75%) aligned 0 times 1017 (2.44%) aligned exactly 1 time 1169 (2.81%) aligned >1 times 94.18% overall alignment rate Time searching: 00:00:16 Overall time: 00:00:16 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] 292875 / 317952 = 0.9211 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 18:09:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.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 18:09:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:09:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:09:52: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:09:52: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:09:52: #1 total tags in treatment: 24649 INFO @ Fri, 05 Jul 2019 18:09:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:09:52: #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 18:09:52: #1 tags after filtering in treatment: 24032 INFO @ Fri, 05 Jul 2019 18:09:52: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 18:09:52: #1 finished! INFO @ Fri, 05 Jul 2019 18:09:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:09:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:09:52: #2 number of paired peaks: 264 WARNING @ Fri, 05 Jul 2019 18:09:52: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Fri, 05 Jul 2019 18:09:52: start model_add_line... INFO @ Fri, 05 Jul 2019 18:09:52: start X-correlation... INFO @ Fri, 05 Jul 2019 18:09:52: end of X-cor INFO @ Fri, 05 Jul 2019 18:09:52: #2 finished! INFO @ Fri, 05 Jul 2019 18:09:52: #2 predicted fragment length is 314 bps INFO @ Fri, 05 Jul 2019 18:09:52: #2 alternative fragment length(s) may be 97,120,167,185,224,270,292,314,336,360,379,401,424,462,484,513,549 bps INFO @ Fri, 05 Jul 2019 18:09:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.05_model.r INFO @ Fri, 05 Jul 2019 18:09:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:09:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:09:52: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:09:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:09:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:09:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.05_summits.bed INFO @ Fri, 05 Jul 2019 18:09:52: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 18:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.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 18:09:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:09:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:09:53: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:09:53: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:09:53: #1 total tags in treatment: 24649 INFO @ Fri, 05 Jul 2019 18:09:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:09:53: #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 18:09:53: #1 tags after filtering in treatment: 24032 INFO @ Fri, 05 Jul 2019 18:09:53: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 18:09:53: #1 finished! INFO @ Fri, 05 Jul 2019 18:09:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:09:53: #2 number of paired peaks: 264 WARNING @ Fri, 05 Jul 2019 18:09:53: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Fri, 05 Jul 2019 18:09:53: start model_add_line... INFO @ Fri, 05 Jul 2019 18:09:53: start X-correlation... INFO @ Fri, 05 Jul 2019 18:09:53: end of X-cor INFO @ Fri, 05 Jul 2019 18:09:53: #2 finished! INFO @ Fri, 05 Jul 2019 18:09:53: #2 predicted fragment length is 314 bps INFO @ Fri, 05 Jul 2019 18:09:53: #2 alternative fragment length(s) may be 97,120,167,185,224,270,292,314,336,360,379,401,424,462,484,513,549 bps INFO @ Fri, 05 Jul 2019 18:09:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.10_model.r INFO @ Fri, 05 Jul 2019 18:09:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:09:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:09:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:09:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.10_summits.bed INFO @ Fri, 05 Jul 2019 18:09:54: Done! CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 05 Jul 2019 18:09:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.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 18:09:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:09:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:09:54: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:09:54: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:09:54: #1 total tags in treatment: 24649 INFO @ Fri, 05 Jul 2019 18:09:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:09:54: #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 18:09:54: #1 tags after filtering in treatment: 24032 INFO @ Fri, 05 Jul 2019 18:09:54: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 05 Jul 2019 18:09:54: #1 finished! INFO @ Fri, 05 Jul 2019 18:09:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:09:54: #2 looking for paired plus/minus strand peaks... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:09:54: #2 number of paired peaks: 264 WARNING @ Fri, 05 Jul 2019 18:09:54: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Fri, 05 Jul 2019 18:09:54: start model_add_line... INFO @ Fri, 05 Jul 2019 18:09:54: start X-correlation... INFO @ Fri, 05 Jul 2019 18:09:54: end of X-cor INFO @ Fri, 05 Jul 2019 18:09:54: #2 finished! INFO @ Fri, 05 Jul 2019 18:09:54: #2 predicted fragment length is 314 bps INFO @ Fri, 05 Jul 2019 18:09:54: #2 alternative fragment length(s) may be 97,120,167,185,224,270,292,314,336,360,379,401,424,462,484,513,549 bps INFO @ Fri, 05 Jul 2019 18:09:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.20_model.r INFO @ Fri, 05 Jul 2019 18:09:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:09:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:09:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:09:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:09:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585784/ERX585784.20_summits.bed INFO @ Fri, 05 Jul 2019 18:09:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling