Job ID = 2010920 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 16,204,436 reads read : 32,408,872 reads written : 32,408,872 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1105632.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: 00:19:08 16204436 reads; of these: 16204436 (100.00%) were paired; of these: 8385304 (51.75%) aligned concordantly 0 times 5020526 (30.98%) aligned concordantly exactly 1 time 2798606 (17.27%) aligned concordantly >1 times ---- 8385304 pairs aligned concordantly 0 times; of these: 98124 (1.17%) aligned discordantly 1 time ---- 8287180 pairs aligned 0 times concordantly or discordantly; of these: 16574360 mates make up the pairs; of these: 14834500 (89.50%) aligned 0 times 835708 (5.04%) aligned exactly 1 time 904152 (5.46%) aligned >1 times 54.23% overall alignment rate Time searching: 00:19:08 Overall time: 00:19:08 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] 1820604 / 7861256 = 0.2316 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 01:50:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.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 01:50:50: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:50:50: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:50:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.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 01:50:51: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:50:51: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:50:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.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 01:50:52: #1 read tag files... INFO @ Sat, 06 Jul 2019 01:50:52: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 01:51:02: 1000000 INFO @ Sat, 06 Jul 2019 01:51:03: 1000000 INFO @ Sat, 06 Jul 2019 01:51:04: 1000000 INFO @ Sat, 06 Jul 2019 01:51:15: 2000000 INFO @ Sat, 06 Jul 2019 01:51:16: 2000000 INFO @ Sat, 06 Jul 2019 01:51:17: 2000000 INFO @ Sat, 06 Jul 2019 01:51:27: 3000000 INFO @ Sat, 06 Jul 2019 01:51:28: 3000000 INFO @ Sat, 06 Jul 2019 01:51:29: 3000000 INFO @ Sat, 06 Jul 2019 01:51:39: 4000000 INFO @ Sat, 06 Jul 2019 01:51:40: 4000000 INFO @ Sat, 06 Jul 2019 01:51:41: 4000000 INFO @ Sat, 06 Jul 2019 01:51:51: 5000000 INFO @ Sat, 06 Jul 2019 01:51:52: 5000000 INFO @ Sat, 06 Jul 2019 01:51:53: 5000000 INFO @ Sat, 06 Jul 2019 01:52:04: 6000000 INFO @ Sat, 06 Jul 2019 01:52:04: 6000000 INFO @ Sat, 06 Jul 2019 01:52:06: 6000000 INFO @ Sat, 06 Jul 2019 01:52:16: 7000000 INFO @ Sat, 06 Jul 2019 01:52:17: 7000000 INFO @ Sat, 06 Jul 2019 01:52:18: 7000000 INFO @ Sat, 06 Jul 2019 01:52:28: 8000000 INFO @ Sat, 06 Jul 2019 01:52:28: 8000000 INFO @ Sat, 06 Jul 2019 01:52:29: 8000000 INFO @ Sat, 06 Jul 2019 01:52:39: 9000000 INFO @ Sat, 06 Jul 2019 01:52:40: 9000000 INFO @ Sat, 06 Jul 2019 01:52:40: 9000000 INFO @ Sat, 06 Jul 2019 01:52:50: 10000000 INFO @ Sat, 06 Jul 2019 01:52:51: 10000000 INFO @ Sat, 06 Jul 2019 01:52:51: 10000000 INFO @ Sat, 06 Jul 2019 01:53:02: 11000000 INFO @ Sat, 06 Jul 2019 01:53:04: 11000000 INFO @ Sat, 06 Jul 2019 01:53:04: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 01:53:15: 12000000 INFO @ Sat, 06 Jul 2019 01:53:15: 12000000 INFO @ Sat, 06 Jul 2019 01:53:17: 12000000 BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 01:53:28: 13000000 INFO @ Sat, 06 Jul 2019 01:53:28: 13000000 INFO @ Sat, 06 Jul 2019 01:53:29: 13000000 INFO @ Sat, 06 Jul 2019 01:53:40: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:53:40: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:53:40: #1 total tags in treatment: 6013865 INFO @ Sat, 06 Jul 2019 01:53:40: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:53:40: #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 01:53:40: #1 tags after filtering in treatment: 4127286 INFO @ Sat, 06 Jul 2019 01:53:40: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 06 Jul 2019 01:53:40: #1 finished! INFO @ Sat, 06 Jul 2019 01:53:40: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:53:41: #2 number of paired peaks: 35 WARNING @ Sat, 06 Jul 2019 01:53:41: Too few paired peaks (35) 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 01:53:41: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 01:53:41: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:53:41: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:53:41: #1 total tags in treatment: 6013865 INFO @ Sat, 06 Jul 2019 01:53:41: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:53:41: #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 01:53:41: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 01:53:41: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 01:53:41: #1 total tags in treatment: 6013865 INFO @ Sat, 06 Jul 2019 01:53:41: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 01:53:41: #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 01:53:41: #1 tags after filtering in treatment: 4127286 INFO @ Sat, 06 Jul 2019 01:53:41: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 06 Jul 2019 01:53:41: #1 finished! INFO @ Sat, 06 Jul 2019 01:53:41: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:53:41: #1 tags after filtering in treatment: 4127286 INFO @ Sat, 06 Jul 2019 01:53:41: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 06 Jul 2019 01:53:41: #1 finished! INFO @ Sat, 06 Jul 2019 01:53:41: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 01:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 01:53:41: #2 number of paired peaks: 35 WARNING @ Sat, 06 Jul 2019 01:53:41: Too few paired peaks (35) 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 01:53:41: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 01:53:41: #2 number of paired peaks: 35 WARNING @ Sat, 06 Jul 2019 01:53:41: Too few paired peaks (35) 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 01:53:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.20_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.20_model.r’: No such file or directory rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.10_model.r’rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.05_model.r’: No such file or directorycannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.20_*.xls’ : No such file or directory: No such file or directory rm: rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.10_*.xls’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.05_*.xls’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.20_peaks.narrowPeak’: No such file or directory: No such file or directory: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.10_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX424391/SRX424391.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling