Job ID = 2011670 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,873,637 reads read : 27,747,274 reads written : 27,747,274 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1146737.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: 00:00:00 Multiseed full-index search: 00:10:41 13873637 reads; of these: 13873637 (100.00%) were paired; of these: 1202181 (8.67%) aligned concordantly 0 times 10347330 (74.58%) aligned concordantly exactly 1 time 2324126 (16.75%) aligned concordantly >1 times ---- 1202181 pairs aligned concordantly 0 times; of these: 382878 (31.85%) aligned discordantly 1 time ---- 819303 pairs aligned 0 times concordantly or discordantly; of these: 1638606 mates make up the pairs; of these: 1149509 (70.15%) aligned 0 times 231440 (14.12%) aligned exactly 1 time 257657 (15.72%) aligned >1 times 95.86% overall alignment rate Time searching: 00:10:41 Overall time: 00:10:41 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 12 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] 1577975 / 12883412 = 0.1225 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 02:15:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.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 02:15:07: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:15:07: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.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 02:15:08: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:15:08: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:15:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.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 02:15:09: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:15:09: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:15:15: 1000000 INFO @ Sat, 06 Jul 2019 02:15:16: 1000000 INFO @ Sat, 06 Jul 2019 02:15:17: 1000000 INFO @ Sat, 06 Jul 2019 02:15:22: 2000000 INFO @ Sat, 06 Jul 2019 02:15:23: 2000000 INFO @ Sat, 06 Jul 2019 02:15:24: 2000000 INFO @ Sat, 06 Jul 2019 02:15:30: 3000000 INFO @ Sat, 06 Jul 2019 02:15:31: 3000000 INFO @ Sat, 06 Jul 2019 02:15:32: 3000000 INFO @ Sat, 06 Jul 2019 02:15:37: 4000000 INFO @ Sat, 06 Jul 2019 02:15:39: 4000000 INFO @ Sat, 06 Jul 2019 02:15:40: 4000000 INFO @ Sat, 06 Jul 2019 02:15:45: 5000000 INFO @ Sat, 06 Jul 2019 02:15:46: 5000000 INFO @ Sat, 06 Jul 2019 02:15:47: 5000000 INFO @ Sat, 06 Jul 2019 02:15:53: 6000000 INFO @ Sat, 06 Jul 2019 02:15:54: 6000000 INFO @ Sat, 06 Jul 2019 02:15:55: 6000000 INFO @ Sat, 06 Jul 2019 02:16:00: 7000000 INFO @ Sat, 06 Jul 2019 02:16:02: 7000000 INFO @ Sat, 06 Jul 2019 02:16:03: 7000000 INFO @ Sat, 06 Jul 2019 02:16:08: 8000000 INFO @ Sat, 06 Jul 2019 02:16:09: 8000000 INFO @ Sat, 06 Jul 2019 02:16:10: 8000000 INFO @ Sat, 06 Jul 2019 02:16:16: 9000000 INFO @ Sat, 06 Jul 2019 02:16:17: 9000000 INFO @ Sat, 06 Jul 2019 02:16:18: 9000000 INFO @ Sat, 06 Jul 2019 02:16:23: 10000000 INFO @ Sat, 06 Jul 2019 02:16:25: 10000000 INFO @ Sat, 06 Jul 2019 02:16:26: 10000000 INFO @ Sat, 06 Jul 2019 02:16:31: 11000000 INFO @ Sat, 06 Jul 2019 02:16:32: 11000000 INFO @ Sat, 06 Jul 2019 02:16:33: 11000000 INFO @ Sat, 06 Jul 2019 02:16:39: 12000000 INFO @ Sat, 06 Jul 2019 02:16:40: 12000000 INFO @ Sat, 06 Jul 2019 02:16:41: 12000000 INFO @ Sat, 06 Jul 2019 02:16:46: 13000000 INFO @ Sat, 06 Jul 2019 02:16:48: 13000000 INFO @ Sat, 06 Jul 2019 02:16:49: 13000000 INFO @ Sat, 06 Jul 2019 02:16:54: 14000000 INFO @ Sat, 06 Jul 2019 02:16:55: 14000000 INFO @ Sat, 06 Jul 2019 02:16:56: 14000000 INFO @ Sat, 06 Jul 2019 02:17:02: 15000000 INFO @ Sat, 06 Jul 2019 02:17:03: 15000000 INFO @ Sat, 06 Jul 2019 02:17:04: 15000000 INFO @ Sat, 06 Jul 2019 02:17:09: 16000000 INFO @ Sat, 06 Jul 2019 02:17:11: 16000000 INFO @ Sat, 06 Jul 2019 02:17:11: 16000000 INFO @ Sat, 06 Jul 2019 02:17:17: 17000000 INFO @ Sat, 06 Jul 2019 02:17:19: 17000000 INFO @ Sat, 06 Jul 2019 02:17:19: 17000000 INFO @ Sat, 06 Jul 2019 02:17:24: 18000000 INFO @ Sat, 06 Jul 2019 02:17:27: 18000000 INFO @ Sat, 06 Jul 2019 02:17:27: 18000000 INFO @ Sat, 06 Jul 2019 02:17:32: 19000000 INFO @ Sat, 06 Jul 2019 02:17:34: 19000000 INFO @ Sat, 06 Jul 2019 02:17:35: 19000000 INFO @ Sat, 06 Jul 2019 02:17:39: 20000000 INFO @ Sat, 06 Jul 2019 02:17:42: 20000000 INFO @ Sat, 06 Jul 2019 02:17:42: 20000000 INFO @ Sat, 06 Jul 2019 02:17:47: 21000000 INFO @ Sat, 06 Jul 2019 02:17:49: 21000000 INFO @ Sat, 06 Jul 2019 02:17:50: 21000000 INFO @ Sat, 06 Jul 2019 02:17:54: 22000000 INFO @ Sat, 06 Jul 2019 02:17:57: 22000000 INFO @ Sat, 06 Jul 2019 02:17:58: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:18:02: 23000000 INFO @ Sat, 06 Jul 2019 02:18:05: 23000000 INFO @ Sat, 06 Jul 2019 02:18:06: 23000000 INFO @ Sat, 06 Jul 2019 02:18:06: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:18:06: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:18:06: #1 total tags in treatment: 11116076 INFO @ Sat, 06 Jul 2019 02:18:06: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:18:06: #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 02:18:06: #1 tags after filtering in treatment: 7814142 INFO @ Sat, 06 Jul 2019 02:18:06: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 06 Jul 2019 02:18:06: #1 finished! INFO @ Sat, 06 Jul 2019 02:18:06: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:18:06: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:18:06: 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 @ Sat, 06 Jul 2019 02:18:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.05_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/SRX455447/SRX455447.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:18:08: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:18:08: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:18:08: #1 total tags in treatment: 11116076 INFO @ Sat, 06 Jul 2019 02:18:08: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:18:08: #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 02:18:08: #1 tags after filtering in treatment: 7814142 INFO @ Sat, 06 Jul 2019 02:18:08: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 06 Jul 2019 02:18:08: #1 finished! INFO @ Sat, 06 Jul 2019 02:18:08: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:18:09: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:18:09: 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 @ Sat, 06 Jul 2019 02:18:09: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:18:09: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:18:09: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:18:09: #1 total tags in treatment: 11116076 INFO @ Sat, 06 Jul 2019 02:18:09: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:18:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) cut: /home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.20_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/SRX455447/SRX455447.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:18:09: #1 tags after filtering in treatment: 7814142 INFO @ Sat, 06 Jul 2019 02:18:09: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 06 Jul 2019 02:18:09: #1 finished! INFO @ Sat, 06 Jul 2019 02:18:09: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:18:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:18:10: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:18:10: 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 @ Sat, 06 Jul 2019 02:18:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.10_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/SRX455447/SRX455447.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455447/SRX455447.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。