Job ID = 2009739 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,639,508 reads read : 11,279,016 reads written : 11,279,016 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: 00:04:15 5639508 reads; of these: 5639508 (100.00%) were paired; of these: 645816 (11.45%) aligned concordantly 0 times 4332971 (76.83%) aligned concordantly exactly 1 time 660721 (11.72%) aligned concordantly >1 times ---- 645816 pairs aligned concordantly 0 times; of these: 186832 (28.93%) aligned discordantly 1 time ---- 458984 pairs aligned 0 times concordantly or discordantly; of these: 917968 mates make up the pairs; of these: 753126 (82.04%) aligned 0 times 76464 (8.33%) aligned exactly 1 time 88378 (9.63%) aligned >1 times 93.32% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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 8 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] 1282020 / 5116619 = 0.2506 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 19:54:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.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 19:54:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:54:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:54:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.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 19:54:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:54:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:54:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.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 19:54:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:54:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:54:26: 1000000 INFO @ Fri, 05 Jul 2019 19:54:28: 1000000 INFO @ Fri, 05 Jul 2019 19:54:29: 1000000 INFO @ Fri, 05 Jul 2019 19:54:34: 2000000 INFO @ Fri, 05 Jul 2019 19:54:36: 2000000 INFO @ Fri, 05 Jul 2019 19:54:38: 2000000 INFO @ Fri, 05 Jul 2019 19:54:43: 3000000 INFO @ Fri, 05 Jul 2019 19:54:45: 3000000 INFO @ Fri, 05 Jul 2019 19:54:47: 3000000 INFO @ Fri, 05 Jul 2019 19:54:51: 4000000 INFO @ Fri, 05 Jul 2019 19:54:54: 4000000 INFO @ Fri, 05 Jul 2019 19:54:56: 4000000 INFO @ Fri, 05 Jul 2019 19:55:00: 5000000 INFO @ Fri, 05 Jul 2019 19:55:03: 5000000 INFO @ Fri, 05 Jul 2019 19:55:06: 5000000 INFO @ Fri, 05 Jul 2019 19:55:09: 6000000 INFO @ Fri, 05 Jul 2019 19:55:12: 6000000 INFO @ Fri, 05 Jul 2019 19:55:15: 6000000 INFO @ Fri, 05 Jul 2019 19:55:17: 7000000 INFO @ Fri, 05 Jul 2019 19:55:20: 7000000 INFO @ Fri, 05 Jul 2019 19:55:24: 7000000 INFO @ Fri, 05 Jul 2019 19:55:26: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:55:26: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:55:26: #1 total tags in treatment: 3740420 INFO @ Fri, 05 Jul 2019 19:55:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:55:26: #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 19:55:26: #1 tags after filtering in treatment: 3094056 INFO @ Fri, 05 Jul 2019 19:55:26: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 05 Jul 2019 19:55:26: #1 finished! INFO @ Fri, 05 Jul 2019 19:55:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:55:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:55:26: #2 number of paired peaks: 84 WARNING @ Fri, 05 Jul 2019 19:55:26: Too few paired peaks (84) 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 19:55:26: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.05_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/SRX1462588/SRX1462588.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:55:28: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:55:28: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:55:28: #1 total tags in treatment: 3740420 INFO @ Fri, 05 Jul 2019 19:55:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:55:28: #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 19:55:28: #1 tags after filtering in treatment: 3094056 INFO @ Fri, 05 Jul 2019 19:55:28: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 05 Jul 2019 19:55:28: #1 finished! INFO @ Fri, 05 Jul 2019 19:55:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:55:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:55:28: #2 number of paired peaks: 84 WARNING @ Fri, 05 Jul 2019 19:55:28: Too few paired peaks (84) 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 19:55:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.10_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/SRX1462588/SRX1462588.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:55:33: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 19:55:33: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 19:55:33: #1 total tags in treatment: 3740420 INFO @ Fri, 05 Jul 2019 19:55:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:55:33: #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 19:55:33: #1 tags after filtering in treatment: 3094056 INFO @ Fri, 05 Jul 2019 19:55:33: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 05 Jul 2019 19:55:33: #1 finished! INFO @ Fri, 05 Jul 2019 19:55:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:55:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:55:33: #2 number of paired peaks: 84 WARNING @ Fri, 05 Jul 2019 19:55:33: Too few paired peaks (84) 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 19:55:33: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.20_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/SRX1462588/SRX1462588.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX1462588/SRX1462588.20_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。