Job ID = 2007963 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,788,571 reads read : 3,577,142 reads written : 3,577,142 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: 00:01:56 1788571 reads; of these: 1788571 (100.00%) were paired; of these: 248890 (13.92%) aligned concordantly 0 times 1439534 (80.49%) aligned concordantly exactly 1 time 100147 (5.60%) aligned concordantly >1 times ---- 248890 pairs aligned concordantly 0 times; of these: 95692 (38.45%) aligned discordantly 1 time ---- 153198 pairs aligned 0 times concordantly or discordantly; of these: 306396 mates make up the pairs; of these: 268831 (87.74%) aligned 0 times 21609 (7.05%) aligned exactly 1 time 15956 (5.21%) aligned >1 times 92.48% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 85510 / 1632029 = 0.0524 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 17:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.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 17:00:45: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:00:45: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:00:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.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 17:00:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:00:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:00:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.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 17:00:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:00:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:00:53: 1000000 INFO @ Fri, 05 Jul 2019 17:00:55: 1000000 INFO @ Fri, 05 Jul 2019 17:00:56: 1000000 INFO @ Fri, 05 Jul 2019 17:01:02: 2000000 INFO @ Fri, 05 Jul 2019 17:01:02: 2000000 INFO @ Fri, 05 Jul 2019 17:01:06: 2000000 INFO @ Fri, 05 Jul 2019 17:01:10: 3000000 INFO @ Fri, 05 Jul 2019 17:01:11: 3000000 INFO @ Fri, 05 Jul 2019 17:01:11: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:01:11: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:01:11: #1 total tags in treatment: 1456597 INFO @ Fri, 05 Jul 2019 17:01:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:01:11: #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 17:01:11: #1 tags after filtering in treatment: 1367888 INFO @ Fri, 05 Jul 2019 17:01:11: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:01:11: #1 finished! INFO @ Fri, 05 Jul 2019 17:01:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:01:11: #2 number of paired peaks: 17 WARNING @ Fri, 05 Jul 2019 17:01:11: Too few paired peaks (17) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 05 Jul 2019 17:01:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 8 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:01:12: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:01:12: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:01:12: #1 total tags in treatment: 1456597 INFO @ Fri, 05 Jul 2019 17:01:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:01:12: #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 17:01:12: #1 tags after filtering in treatment: 1367888 INFO @ Fri, 05 Jul 2019 17:01:12: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:01:12: #1 finished! INFO @ Fri, 05 Jul 2019 17:01:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:01:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:01:12: #2 number of paired peaks: 17 WARNING @ Fri, 05 Jul 2019 17:01:12: Too few paired peaks (17) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 05 Jul 2019 17:01:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:01:16: 3000000 INFO @ Fri, 05 Jul 2019 17:01:18: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:01:18: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:01:18: #1 total tags in treatment: 1456597 INFO @ Fri, 05 Jul 2019 17:01:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:01:18: #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 17:01:18: #1 tags after filtering in treatment: 1367888 INFO @ Fri, 05 Jul 2019 17:01:18: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:01:18: #1 finished! INFO @ Fri, 05 Jul 2019 17:01:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:01:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:01:18: #2 number of paired peaks: 17 WARNING @ Fri, 05 Jul 2019 17:01:18: Too few paired peaks (17) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Fri, 05 Jul 2019 17:01:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471754/ERX471754.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。