Job ID = 2008247 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 19,444,183 reads read : 38,888,366 reads written : 38,888,366 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628991.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: 00:15:38 19444183 reads; of these: 19444183 (100.00%) were paired; of these: 1607242 (8.27%) aligned concordantly 0 times 16455551 (84.63%) aligned concordantly exactly 1 time 1381390 (7.10%) aligned concordantly >1 times ---- 1607242 pairs aligned concordantly 0 times; of these: 125537 (7.81%) aligned discordantly 1 time ---- 1481705 pairs aligned 0 times concordantly or discordantly; of these: 2963410 mates make up the pairs; of these: 2857423 (96.42%) aligned 0 times 68248 (2.30%) aligned exactly 1 time 37739 (1.27%) aligned >1 times 92.65% overall alignment rate Time searching: 00:15:38 Overall time: 00:15:38 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_sort_core] merging from 16 files... [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] 16716881 / 17933890 = 0.9321 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 18:56:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.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 18:56:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.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 18:56:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:09: 1000000 INFO @ Fri, 05 Jul 2019 18:56:09: 1000000 INFO @ Fri, 05 Jul 2019 18:56:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.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 18:56:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:16: 2000000 INFO @ Fri, 05 Jul 2019 18:56:16: 2000000 INFO @ Fri, 05 Jul 2019 18:56:18: 1000000 INFO @ Fri, 05 Jul 2019 18:56:20: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:56:20: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:56:20: #1 total tags in treatment: 1167094 INFO @ Fri, 05 Jul 2019 18:56:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:20: #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 18:56:20: #1 tags after filtering in treatment: 902941 INFO @ Fri, 05 Jul 2019 18:56:20: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 05 Jul 2019 18:56:20: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:20: #2 number of paired peaks: 154 WARNING @ Fri, 05 Jul 2019 18:56:20: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 05 Jul 2019 18:56:20: start model_add_line... INFO @ Fri, 05 Jul 2019 18:56:20: start X-correlation... INFO @ Fri, 05 Jul 2019 18:56:20: end of X-cor INFO @ Fri, 05 Jul 2019 18:56:20: #2 finished! INFO @ Fri, 05 Jul 2019 18:56:20: #2 predicted fragment length is 175 bps INFO @ Fri, 05 Jul 2019 18:56:20: #2 alternative fragment length(s) may be 62,105,159,175,205,229,264,276,314,388,436,470,506,544,573 bps INFO @ Fri, 05 Jul 2019 18:56:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.05_model.r INFO @ Fri, 05 Jul 2019 18:56:20: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:56:20: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:56:20: #1 total tags in treatment: 1167094 INFO @ Fri, 05 Jul 2019 18:56:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:20: #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 18:56:20: #1 tags after filtering in treatment: 902941 INFO @ Fri, 05 Jul 2019 18:56:20: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 05 Jul 2019 18:56:20: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:21: #2 number of paired peaks: 154 WARNING @ Fri, 05 Jul 2019 18:56:21: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 05 Jul 2019 18:56:21: start model_add_line... INFO @ Fri, 05 Jul 2019 18:56:21: start X-correlation... INFO @ Fri, 05 Jul 2019 18:56:21: end of X-cor INFO @ Fri, 05 Jul 2019 18:56:21: #2 finished! INFO @ Fri, 05 Jul 2019 18:56:21: #2 predicted fragment length is 175 bps INFO @ Fri, 05 Jul 2019 18:56:21: #2 alternative fragment length(s) may be 62,105,159,175,205,229,264,276,314,388,436,470,506,544,573 bps INFO @ Fri, 05 Jul 2019 18:56:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.10_model.r INFO @ Fri, 05 Jul 2019 18:56:24: 2000000 INFO @ Fri, 05 Jul 2019 18:56:28: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:56:28: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:56:28: #1 total tags in treatment: 1167094 INFO @ Fri, 05 Jul 2019 18:56:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:28: #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 18:56:28: #1 tags after filtering in treatment: 902941 INFO @ Fri, 05 Jul 2019 18:56:28: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 05 Jul 2019 18:56:28: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:28: #2 number of paired peaks: 154 WARNING @ Fri, 05 Jul 2019 18:56:28: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 05 Jul 2019 18:56:28: start model_add_line... INFO @ Fri, 05 Jul 2019 18:56:28: start X-correlation... INFO @ Fri, 05 Jul 2019 18:56:28: end of X-cor INFO @ Fri, 05 Jul 2019 18:56:28: #2 finished! INFO @ Fri, 05 Jul 2019 18:56:28: #2 predicted fragment length is 175 bps INFO @ Fri, 05 Jul 2019 18:56:28: #2 alternative fragment length(s) may be 62,105,159,175,205,229,264,276,314,388,436,470,506,544,573 bps INFO @ Fri, 05 Jul 2019 18:56:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.20_model.r INFO @ Fri, 05 Jul 2019 18:56:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:56:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:56:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:56:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:56:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 18:56:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 18:56:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:56:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:56:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 18:56:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.20_peaks.xls INFO @ Fri, 05 Jul 2019 18:56:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.05_peaks.xls INFO @ Fri, 05 Jul 2019 18:56:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.10_peaks.xls INFO @ Fri, 05 Jul 2019 18:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.20_summits.bed INFO @ Fri, 05 Jul 2019 18:56:37: Done! INFO @ Fri, 05 Jul 2019 18:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.05_summits.bed INFO @ Fri, 05 Jul 2019 18:56:37: Done! INFO @ Fri, 05 Jul 2019 18:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 18:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585771/ERX585771.10_summits.bed INFO @ Fri, 05 Jul 2019 18:56:37: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (15 chroms)pass1 - making usageList (10 chroms)pass1 - making usageList (0 chroms): 2 millis : 2 millis : 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass2 - checking and writing primary data (29 records, 4 fields): 7 millis pass2 - checking and writing primary data (168 records, 4 fields): 7 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。