Job ID = 2010653 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,067,069 reads read : 10,134,138 reads written : 10,134,138 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: 00:03:46 5067069 reads; of these: 5067069 (100.00%) were paired; of these: 392638 (7.75%) aligned concordantly 0 times 4482482 (88.46%) aligned concordantly exactly 1 time 191949 (3.79%) aligned concordantly >1 times ---- 392638 pairs aligned concordantly 0 times; of these: 126181 (32.14%) aligned discordantly 1 time ---- 266457 pairs aligned 0 times concordantly or discordantly; of these: 532914 mates make up the pairs; of these: 432494 (81.16%) aligned 0 times 82404 (15.46%) aligned exactly 1 time 18016 (3.38%) aligned >1 times 95.73% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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] 166627 / 4784355 = 0.0348 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 23:57:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.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 23:57:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:57:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:57:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.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 23:57:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:57:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:57:23: 1000000 INFO @ Fri, 05 Jul 2019 23:57:24: 1000000 INFO @ Fri, 05 Jul 2019 23:57:30: 2000000 INFO @ Fri, 05 Jul 2019 23:57:33: 2000000 INFO @ Fri, 05 Jul 2019 23:57:37: 3000000 INFO @ Fri, 05 Jul 2019 23:57:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.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 23:57:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:57:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:57:43: 3000000 INFO @ Fri, 05 Jul 2019 23:57:44: 4000000 INFO @ Fri, 05 Jul 2019 23:57:51: 5000000 INFO @ Fri, 05 Jul 2019 23:57:52: 1000000 INFO @ Fri, 05 Jul 2019 23:57:54: 4000000 INFO @ Fri, 05 Jul 2019 23:57:58: 6000000 INFO @ Fri, 05 Jul 2019 23:58:04: 2000000 INFO @ Fri, 05 Jul 2019 23:58:05: 5000000 INFO @ Fri, 05 Jul 2019 23:58:05: 7000000 INFO @ Fri, 05 Jul 2019 23:58:12: 8000000 INFO @ Fri, 05 Jul 2019 23:58:15: 3000000 INFO @ Fri, 05 Jul 2019 23:58:16: 6000000 INFO @ Fri, 05 Jul 2019 23:58:19: 9000000 INFO @ Fri, 05 Jul 2019 23:58:22: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:58:22: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:58:22: #1 total tags in treatment: 4508319 INFO @ Fri, 05 Jul 2019 23:58:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:58:22: #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 23:58:22: #1 tags after filtering in treatment: 2922695 INFO @ Fri, 05 Jul 2019 23:58:22: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 23:58:22: #1 finished! INFO @ Fri, 05 Jul 2019 23:58:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:58:22: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:58:22: Too few paired peaks (0) 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 23:58:22: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:58:26: 4000000 INFO @ Fri, 05 Jul 2019 23:58:27: 7000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.10_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/SRX3865843/SRX3865843.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:58:37: 8000000 INFO @ Fri, 05 Jul 2019 23:58:37: 5000000 INFO @ Fri, 05 Jul 2019 23:58:48: 9000000 INFO @ Fri, 05 Jul 2019 23:58:48: 6000000 INFO @ Fri, 05 Jul 2019 23:58:51: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:58:51: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:58:51: #1 total tags in treatment: 4508319 INFO @ Fri, 05 Jul 2019 23:58:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:58:51: #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 23:58:51: #1 tags after filtering in treatment: 2922695 INFO @ Fri, 05 Jul 2019 23:58:51: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 23:58:51: #1 finished! INFO @ Fri, 05 Jul 2019 23:58:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:58:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:58:51: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:58:51: Too few paired peaks (0) 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 23:58:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.05_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/SRX3865843/SRX3865843.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:58:58: 7000000 INFO @ Fri, 05 Jul 2019 23:59:09: 8000000 INFO @ Fri, 05 Jul 2019 23:59:19: 9000000 INFO @ Fri, 05 Jul 2019 23:59:23: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:59:23: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:59:23: #1 total tags in treatment: 4508319 INFO @ Fri, 05 Jul 2019 23:59:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:59:23: #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 23:59:23: #1 tags after filtering in treatment: 2922695 INFO @ Fri, 05 Jul 2019 23:59:23: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 23:59:23: #1 finished! INFO @ Fri, 05 Jul 2019 23:59:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:59:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:59:23: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 23:59:23: Too few paired peaks (0) 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 23:59:23: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.20_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865843/SRX3865843.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。