Job ID = 2008325 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,656,378 reads read : 13,312,756 reads written : 13,312,756 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: 00:06:58 6656378 reads; of these: 6656378 (100.00%) were paired; of these: 535019 (8.04%) aligned concordantly 0 times 5799953 (87.13%) aligned concordantly exactly 1 time 321406 (4.83%) aligned concordantly >1 times ---- 535019 pairs aligned concordantly 0 times; of these: 97525 (18.23%) aligned discordantly 1 time ---- 437494 pairs aligned 0 times concordantly or discordantly; of these: 874988 mates make up the pairs; of these: 839979 (96.00%) aligned 0 times 22814 (2.61%) aligned exactly 1 time 12195 (1.39%) aligned >1 times 93.69% overall alignment rate Time searching: 00:06:58 Overall time: 00:06:58 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] 4479578 / 6178982 = 0.7250 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 18:59:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.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 18:59:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:59:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:59:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.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 18:59:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:59:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:00:09: 1000000 INFO @ Fri, 05 Jul 2019 19:00:10: 1000000 INFO @ Fri, 05 Jul 2019 19:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.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 19:00:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:00:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:00:19: 2000000 INFO @ Fri, 05 Jul 2019 19:00:20: 1000000 INFO @ Fri, 05 Jul 2019 19:00:21: 2000000 INFO @ Fri, 05 Jul 2019 19:00:29: 3000000 INFO @ Fri, 05 Jul 2019 19:00:30: 2000000 INFO @ Fri, 05 Jul 2019 19:00:32: 3000000 INFO @ Fri, 05 Jul 2019 19:00:34: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 19:00:34: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 19:00:34: #1 total tags in treatment: 1667745 INFO @ Fri, 05 Jul 2019 19:00:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:00:34: #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 19:00:34: #1 tags after filtering in treatment: 1183569 INFO @ Fri, 05 Jul 2019 19:00:34: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 19:00:34: #1 finished! INFO @ Fri, 05 Jul 2019 19:00:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:00:34: #2 number of paired peaks: 3 WARNING @ Fri, 05 Jul 2019 19:00:34: 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 @ Fri, 05 Jul 2019 19:00:34: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 19:00:38: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 19:00:38: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 19:00:38: #1 total tags in treatment: 1667745 INFO @ Fri, 05 Jul 2019 19:00:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:00:38: #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 19:00:38: #1 tags after filtering in treatment: 1183569 INFO @ Fri, 05 Jul 2019 19:00:38: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 19:00:38: #1 finished! INFO @ Fri, 05 Jul 2019 19:00:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:00:38: #2 number of paired peaks: 3 WARNING @ Fri, 05 Jul 2019 19:00:38: 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 @ Fri, 05 Jul 2019 19:00:38: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 19:00:39: 3000000 INFO @ Fri, 05 Jul 2019 19:00:44: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 19:00:44: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 19:00:44: #1 total tags in treatment: 1667745 INFO @ Fri, 05 Jul 2019 19:00:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:00:44: #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 19:00:44: #1 tags after filtering in treatment: 1183569 INFO @ Fri, 05 Jul 2019 19:00:44: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 19:00:44: #1 finished! INFO @ Fri, 05 Jul 2019 19:00:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:00:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:00:44: #2 number of paired peaks: 3 WARNING @ Fri, 05 Jul 2019 19:00:44: 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 @ Fri, 05 Jul 2019 19:00:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.10_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585833/ERX585833.20_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。