Job ID = 2008342 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 138,195 reads read : 276,390 reads written : 276,390 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: 00:00:06 138195 reads; of these: 138195 (100.00%) were paired; of these: 22017 (15.93%) aligned concordantly 0 times 104017 (75.27%) aligned concordantly exactly 1 time 12161 (8.80%) aligned concordantly >1 times ---- 22017 pairs aligned concordantly 0 times; of these: 2515 (11.42%) aligned discordantly 1 time ---- 19502 pairs aligned 0 times concordantly or discordantly; of these: 39004 mates make up the pairs; of these: 37066 (95.03%) aligned 0 times 633 (1.62%) aligned exactly 1 time 1305 (3.35%) aligned >1 times 86.59% overall alignment rate Time searching: 00:00:06 Overall time: 00:00:06 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] 110626 / 118014 = 0.9374 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 18:39:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.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 18:39:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:39:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:39:28: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:39:28: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:39:28: #1 total tags in treatment: 7697 INFO @ Fri, 05 Jul 2019 18:39:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:39:28: #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 18:39:28: #1 tags after filtering in treatment: 7093 INFO @ Fri, 05 Jul 2019 18:39:28: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 05 Jul 2019 18:39:28: #1 finished! INFO @ Fri, 05 Jul 2019 18:39:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:39:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:39:28: #2 number of paired peaks: 286 WARNING @ Fri, 05 Jul 2019 18:39:28: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Fri, 05 Jul 2019 18:39:28: start model_add_line... INFO @ Fri, 05 Jul 2019 18:39:28: start X-correlation... INFO @ Fri, 05 Jul 2019 18:39:28: end of X-cor INFO @ Fri, 05 Jul 2019 18:39:28: #2 finished! INFO @ Fri, 05 Jul 2019 18:39:28: #2 predicted fragment length is 275 bps INFO @ Fri, 05 Jul 2019 18:39:28: #2 alternative fragment length(s) may be 47,108,175,275 bps INFO @ Fri, 05 Jul 2019 18:39:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.05_model.r INFO @ Fri, 05 Jul 2019 18:39:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.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 18:39:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:39:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:39:28: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:39:28: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:39:28: #1 total tags in treatment: 7697 INFO @ Fri, 05 Jul 2019 18:39:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:39:28: #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 18:39:28: #1 tags after filtering in treatment: 7093 INFO @ Fri, 05 Jul 2019 18:39:28: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 05 Jul 2019 18:39:28: #1 finished! INFO @ Fri, 05 Jul 2019 18:39:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:39:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:39:29: #2 number of paired peaks: 286 WARNING @ Fri, 05 Jul 2019 18:39:29: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Fri, 05 Jul 2019 18:39:29: start model_add_line... INFO @ Fri, 05 Jul 2019 18:39:29: start X-correlation... INFO @ Fri, 05 Jul 2019 18:39:29: end of X-cor INFO @ Fri, 05 Jul 2019 18:39:29: #2 finished! INFO @ Fri, 05 Jul 2019 18:39:29: #2 predicted fragment length is 275 bps INFO @ Fri, 05 Jul 2019 18:39:29: #2 alternative fragment length(s) may be 47,108,175,275 bps INFO @ Fri, 05 Jul 2019 18:39:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.10_model.r INFO @ Fri, 05 Jul 2019 18:39:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:39:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:39:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:39:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:39:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:39:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:39:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:39:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.05_summits.bed INFO @ Fri, 05 Jul 2019 18:39:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:39:34: Done! INFO @ Fri, 05 Jul 2019 18:39:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.10_summits.bed INFO @ Fri, 05 Jul 2019 18:39:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 18:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.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 18:39:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:39:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:39:37: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:39:37: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:39:37: #1 total tags in treatment: 7697 INFO @ Fri, 05 Jul 2019 18:39:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:39:37: #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 18:39:37: #1 tags after filtering in treatment: 7093 INFO @ Fri, 05 Jul 2019 18:39:37: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 05 Jul 2019 18:39:37: #1 finished! INFO @ Fri, 05 Jul 2019 18:39:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:39:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:39:37: #2 number of paired peaks: 286 WARNING @ Fri, 05 Jul 2019 18:39:37: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Fri, 05 Jul 2019 18:39:37: start model_add_line... INFO @ Fri, 05 Jul 2019 18:39:37: start X-correlation... INFO @ Fri, 05 Jul 2019 18:39:37: end of X-cor INFO @ Fri, 05 Jul 2019 18:39:37: #2 finished! INFO @ Fri, 05 Jul 2019 18:39:37: #2 predicted fragment length is 275 bps INFO @ Fri, 05 Jul 2019 18:39:37: #2 alternative fragment length(s) may be 47,108,175,275 bps INFO @ Fri, 05 Jul 2019 18:39:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.20_model.r INFO @ Fri, 05 Jul 2019 18:39:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:39:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:39:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:39:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:39:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:39:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585848/ERX585848.20_summits.bed INFO @ Fri, 05 Jul 2019 18:39:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling