Job ID = 2008297 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,940,174 reads read : 9,880,348 reads written : 9,880,348 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628957.sra.cache’: 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: 00:00:01 Multiseed full-index search: 00:06:09 4940174 reads; of these: 4940174 (100.00%) were paired; of these: 860301 (17.41%) aligned concordantly 0 times 3773945 (76.39%) aligned concordantly exactly 1 time 305928 (6.19%) aligned concordantly >1 times ---- 860301 pairs aligned concordantly 0 times; of these: 170182 (19.78%) aligned discordantly 1 time ---- 690119 pairs aligned 0 times concordantly or discordantly; of these: 1380238 mates make up the pairs; of these: 1222348 (88.56%) aligned 0 times 123028 (8.91%) aligned exactly 1 time 34862 (2.53%) aligned >1 times 87.63% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 431321 / 4230825 = 0.1019 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 18:33:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.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 18:33:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:33:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.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 18:33:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:33:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.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 18:33:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:33:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:33:12: 1000000 INFO @ Fri, 05 Jul 2019 18:33:16: 1000000 INFO @ Fri, 05 Jul 2019 18:33:17: 1000000 INFO @ Fri, 05 Jul 2019 18:33:21: 2000000 INFO @ Fri, 05 Jul 2019 18:33:27: 2000000 INFO @ Fri, 05 Jul 2019 18:33:29: 2000000 INFO @ Fri, 05 Jul 2019 18:33:29: 3000000 INFO @ Fri, 05 Jul 2019 18:33:38: 3000000 INFO @ Fri, 05 Jul 2019 18:33:38: 4000000 INFO @ Fri, 05 Jul 2019 18:33:40: 3000000 INFO @ Fri, 05 Jul 2019 18:33:46: 5000000 INFO @ Fri, 05 Jul 2019 18:33:48: 4000000 INFO @ Fri, 05 Jul 2019 18:33:51: 4000000 INFO @ Fri, 05 Jul 2019 18:33:54: 6000000 INFO @ Fri, 05 Jul 2019 18:33:59: 5000000 INFO @ Fri, 05 Jul 2019 18:34:03: 5000000 INFO @ Fri, 05 Jul 2019 18:34:03: 7000000 INFO @ Fri, 05 Jul 2019 18:34:09: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:34:09: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:34:09: #1 total tags in treatment: 3654385 INFO @ Fri, 05 Jul 2019 18:34:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:34:09: #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 18:34:10: #1 tags after filtering in treatment: 2513998 INFO @ Fri, 05 Jul 2019 18:34:10: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 05 Jul 2019 18:34:10: #1 finished! INFO @ Fri, 05 Jul 2019 18:34:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:34:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:34:10: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:34:10: 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 18:34:10: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 18:34:10: 6000000 INFO @ Fri, 05 Jul 2019 18:34:14: 6000000 cut: /home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.05_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/ERX585808/ERX585808.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:34:21: 7000000 INFO @ Fri, 05 Jul 2019 18:34:25: 7000000 INFO @ Fri, 05 Jul 2019 18:34:30: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:34:30: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:34:30: #1 total tags in treatment: 3654385 INFO @ Fri, 05 Jul 2019 18:34:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:34:30: #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 18:34:30: #1 tags after filtering in treatment: 2513998 INFO @ Fri, 05 Jul 2019 18:34:30: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 05 Jul 2019 18:34:30: #1 finished! INFO @ Fri, 05 Jul 2019 18:34:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:34:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:34:30: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:34:30: 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 18:34:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.10_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/ERX585808/ERX585808.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:34:34: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:34:34: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:34:34: #1 total tags in treatment: 3654385 INFO @ Fri, 05 Jul 2019 18:34:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:34:34: #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 18:34:34: #1 tags after filtering in treatment: 2513998 INFO @ Fri, 05 Jul 2019 18:34:34: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 05 Jul 2019 18:34:34: #1 finished! INFO @ Fri, 05 Jul 2019 18:34:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:34:34: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:34:34: 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 18:34:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.20_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/ERX585808/ERX585808.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585808/ERX585808.20_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。