Job ID = 2010687 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,793,849 reads read : 15,587,698 reads written : 15,587,698 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: 00:04:57 7793849 reads; of these: 7793849 (100.00%) were paired; of these: 2733598 (35.07%) aligned concordantly 0 times 4333039 (55.60%) aligned concordantly exactly 1 time 727212 (9.33%) aligned concordantly >1 times ---- 2733598 pairs aligned concordantly 0 times; of these: 5866 (0.21%) aligned discordantly 1 time ---- 2727732 pairs aligned 0 times concordantly or discordantly; of these: 5455464 mates make up the pairs; of these: 3386350 (62.07%) aligned 0 times 1755282 (32.17%) aligned exactly 1 time 313832 (5.75%) aligned >1 times 78.28% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 263735 / 5065529 = 0.0521 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 @ Sat, 06 Jul 2019 00:03:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.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 @ Sat, 06 Jul 2019 00:03:56: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:03:56: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:03:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.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 @ Sat, 06 Jul 2019 00:03:57: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:03:57: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:03:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.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 @ Sat, 06 Jul 2019 00:03:58: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:03:58: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:04:04: 1000000 INFO @ Sat, 06 Jul 2019 00:04:04: 1000000 INFO @ Sat, 06 Jul 2019 00:04:05: 1000000 INFO @ Sat, 06 Jul 2019 00:04:11: 2000000 INFO @ Sat, 06 Jul 2019 00:04:12: 2000000 INFO @ Sat, 06 Jul 2019 00:04:12: 2000000 INFO @ Sat, 06 Jul 2019 00:04:18: 3000000 INFO @ Sat, 06 Jul 2019 00:04:18: 3000000 INFO @ Sat, 06 Jul 2019 00:04:20: 3000000 INFO @ Sat, 06 Jul 2019 00:04:24: 4000000 INFO @ Sat, 06 Jul 2019 00:04:25: 4000000 INFO @ Sat, 06 Jul 2019 00:04:27: 4000000 INFO @ Sat, 06 Jul 2019 00:04:30: 5000000 INFO @ Sat, 06 Jul 2019 00:04:32: 5000000 INFO @ Sat, 06 Jul 2019 00:04:34: 5000000 INFO @ Sat, 06 Jul 2019 00:04:36: 6000000 INFO @ Sat, 06 Jul 2019 00:04:38: 6000000 INFO @ Sat, 06 Jul 2019 00:04:42: 6000000 INFO @ Sat, 06 Jul 2019 00:04:42: 7000000 INFO @ Sat, 06 Jul 2019 00:04:45: 7000000 INFO @ Sat, 06 Jul 2019 00:04:48: 8000000 INFO @ Sat, 06 Jul 2019 00:04:49: 7000000 INFO @ Sat, 06 Jul 2019 00:04:51: 8000000 INFO @ Sat, 06 Jul 2019 00:04:54: 9000000 INFO @ Sat, 06 Jul 2019 00:04:56: 8000000 INFO @ Sat, 06 Jul 2019 00:04:58: 9000000 INFO @ Sat, 06 Jul 2019 00:05:01: 10000000 INFO @ Sat, 06 Jul 2019 00:05:04: 9000000 INFO @ Sat, 06 Jul 2019 00:05:05: 10000000 INFO @ Sat, 06 Jul 2019 00:05:08: 11000000 INFO @ Sat, 06 Jul 2019 00:05:11: 10000000 INFO @ Sat, 06 Jul 2019 00:05:11: 11000000 INFO @ Sat, 06 Jul 2019 00:05:12: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:05:12: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:05:12: #1 total tags in treatment: 4796558 INFO @ Sat, 06 Jul 2019 00:05:12: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:05:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:05:12: #1 tags after filtering in treatment: 3190242 INFO @ Sat, 06 Jul 2019 00:05:12: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 06 Jul 2019 00:05:12: #1 finished! INFO @ Sat, 06 Jul 2019 00:05:12: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:05:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:05:13: #2 number of paired peaks: 3 WARNING @ Sat, 06 Jul 2019 00:05:13: Too few paired peaks (3) 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 @ Sat, 06 Jul 2019 00:05:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.20_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/SRX3865908/SRX3865908.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:05:16: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:05:16: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:05:16: #1 total tags in treatment: 4796558 INFO @ Sat, 06 Jul 2019 00:05:16: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:05:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:05:16: #1 tags after filtering in treatment: 3190242 INFO @ Sat, 06 Jul 2019 00:05:16: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 06 Jul 2019 00:05:16: #1 finished! INFO @ Sat, 06 Jul 2019 00:05:16: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:05:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:05:16: #2 number of paired peaks: 3 WARNING @ Sat, 06 Jul 2019 00:05:16: Too few paired peaks (3) 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 @ Sat, 06 Jul 2019 00:05:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.10_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/SRX3865908/SRX3865908.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:05:18: 11000000 INFO @ Sat, 06 Jul 2019 00:05:22: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 00:05:22: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 00:05:22: #1 total tags in treatment: 4796558 INFO @ Sat, 06 Jul 2019 00:05:22: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:05:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:05:22: #1 tags after filtering in treatment: 3190242 INFO @ Sat, 06 Jul 2019 00:05:22: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 06 Jul 2019 00:05:22: #1 finished! INFO @ Sat, 06 Jul 2019 00:05:22: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:05:23: #2 number of paired peaks: 3 WARNING @ Sat, 06 Jul 2019 00:05:23: Too few paired peaks (3) 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 @ Sat, 06 Jul 2019 00:05:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.05_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/SRX3865908/SRX3865908.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865908/SRX3865908.05_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。