Job ID = 2011660 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 29,470,032 reads read : 58,940,064 reads written : 58,940,064 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1146728.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: 00:20:25 29470032 reads; of these: 29470032 (100.00%) were paired; of these: 5195399 (17.63%) aligned concordantly 0 times 20265508 (68.77%) aligned concordantly exactly 1 time 4009125 (13.60%) aligned concordantly >1 times ---- 5195399 pairs aligned concordantly 0 times; of these: 383334 (7.38%) aligned discordantly 1 time ---- 4812065 pairs aligned 0 times concordantly or discordantly; of these: 9624130 mates make up the pairs; of these: 9204473 (95.64%) aligned 0 times 186982 (1.94%) aligned exactly 1 time 232675 (2.42%) aligned >1 times 84.38% overall alignment rate Time searching: 00:20:25 Overall time: 00:20:26 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 24 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] 10587174 / 24548452 = 0.4313 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 02:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.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 02:30:01: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:30:01: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.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 02:30:01: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:30:01: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:30:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.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 02:30:02: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:30:02: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:30:10: 1000000 INFO @ Sat, 06 Jul 2019 02:30:11: 1000000 INFO @ Sat, 06 Jul 2019 02:30:11: 1000000 INFO @ Sat, 06 Jul 2019 02:30:18: 2000000 INFO @ Sat, 06 Jul 2019 02:30:20: 2000000 INFO @ Sat, 06 Jul 2019 02:30:21: 2000000 INFO @ Sat, 06 Jul 2019 02:30:26: 3000000 INFO @ Sat, 06 Jul 2019 02:30:30: 3000000 INFO @ Sat, 06 Jul 2019 02:30:30: 3000000 INFO @ Sat, 06 Jul 2019 02:30:34: 4000000 INFO @ Sat, 06 Jul 2019 02:30:39: 4000000 INFO @ Sat, 06 Jul 2019 02:30:39: 4000000 INFO @ Sat, 06 Jul 2019 02:30:42: 5000000 INFO @ Sat, 06 Jul 2019 02:30:48: 5000000 INFO @ Sat, 06 Jul 2019 02:30:48: 5000000 INFO @ Sat, 06 Jul 2019 02:30:50: 6000000 INFO @ Sat, 06 Jul 2019 02:30:57: 6000000 INFO @ Sat, 06 Jul 2019 02:30:58: 6000000 INFO @ Sat, 06 Jul 2019 02:30:58: 7000000 INFO @ Sat, 06 Jul 2019 02:31:06: 8000000 INFO @ Sat, 06 Jul 2019 02:31:06: 7000000 INFO @ Sat, 06 Jul 2019 02:31:06: 7000000 INFO @ Sat, 06 Jul 2019 02:31:13: 9000000 INFO @ Sat, 06 Jul 2019 02:31:14: 8000000 INFO @ Sat, 06 Jul 2019 02:31:15: 8000000 INFO @ Sat, 06 Jul 2019 02:31:21: 10000000 INFO @ Sat, 06 Jul 2019 02:31:23: 9000000 INFO @ Sat, 06 Jul 2019 02:31:24: 9000000 INFO @ Sat, 06 Jul 2019 02:31:28: 11000000 INFO @ Sat, 06 Jul 2019 02:31:32: 10000000 INFO @ Sat, 06 Jul 2019 02:31:32: 10000000 INFO @ Sat, 06 Jul 2019 02:31:36: 12000000 INFO @ Sat, 06 Jul 2019 02:31:40: 11000000 INFO @ Sat, 06 Jul 2019 02:31:41: 11000000 INFO @ Sat, 06 Jul 2019 02:31:44: 13000000 INFO @ Sat, 06 Jul 2019 02:31:49: 12000000 INFO @ Sat, 06 Jul 2019 02:31:49: 12000000 INFO @ Sat, 06 Jul 2019 02:31:51: 14000000 INFO @ Sat, 06 Jul 2019 02:31:57: 13000000 INFO @ Sat, 06 Jul 2019 02:31:57: 13000000 INFO @ Sat, 06 Jul 2019 02:31:59: 15000000 INFO @ Sat, 06 Jul 2019 02:32:05: 14000000 INFO @ Sat, 06 Jul 2019 02:32:05: 14000000 INFO @ Sat, 06 Jul 2019 02:32:06: 16000000 INFO @ Sat, 06 Jul 2019 02:32:12: 15000000 INFO @ Sat, 06 Jul 2019 02:32:12: 15000000 INFO @ Sat, 06 Jul 2019 02:32:14: 17000000 INFO @ Sat, 06 Jul 2019 02:32:18: 16000000 INFO @ Sat, 06 Jul 2019 02:32:20: 16000000 INFO @ Sat, 06 Jul 2019 02:32:21: 18000000 INFO @ Sat, 06 Jul 2019 02:32:24: 17000000 INFO @ Sat, 06 Jul 2019 02:32:27: 17000000 INFO @ Sat, 06 Jul 2019 02:32:29: 19000000 INFO @ Sat, 06 Jul 2019 02:32:31: 18000000 INFO @ Sat, 06 Jul 2019 02:32:35: 18000000 INFO @ Sat, 06 Jul 2019 02:32:36: 20000000 INFO @ Sat, 06 Jul 2019 02:32:37: 19000000 INFO @ Sat, 06 Jul 2019 02:32:42: 19000000 INFO @ Sat, 06 Jul 2019 02:32:44: 21000000 INFO @ Sat, 06 Jul 2019 02:32:44: 20000000 INFO @ Sat, 06 Jul 2019 02:32:50: 21000000 INFO @ Sat, 06 Jul 2019 02:32:50: 20000000 INFO @ Sat, 06 Jul 2019 02:32:51: 22000000 INFO @ Sat, 06 Jul 2019 02:32:56: 22000000 INFO @ Sat, 06 Jul 2019 02:32:58: 21000000 INFO @ Sat, 06 Jul 2019 02:32:59: 23000000 INFO @ Sat, 06 Jul 2019 02:33:02: 23000000 INFO @ Sat, 06 Jul 2019 02:33:06: 22000000 INFO @ Sat, 06 Jul 2019 02:33:06: 24000000 INFO @ Sat, 06 Jul 2019 02:33:08: 24000000 INFO @ Sat, 06 Jul 2019 02:33:13: 23000000 INFO @ Sat, 06 Jul 2019 02:33:13: 25000000 INFO @ Sat, 06 Jul 2019 02:33:14: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:33:20: 26000000 INFO @ Sat, 06 Jul 2019 02:33:21: 26000000 INFO @ Sat, 06 Jul 2019 02:33:21: 24000000 INFO @ Sat, 06 Jul 2019 02:33:26: 27000000 INFO @ Sat, 06 Jul 2019 02:33:28: 27000000 INFO @ Sat, 06 Jul 2019 02:33:29: 25000000 INFO @ Sat, 06 Jul 2019 02:33:32: 28000000 INFO @ Sat, 06 Jul 2019 02:33:36: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:33:36: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:33:36: #1 total tags in treatment: 13804018 INFO @ Sat, 06 Jul 2019 02:33:36: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:33:36: #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 02:33:36: 28000000 INFO @ Sat, 06 Jul 2019 02:33:36: #1 tags after filtering in treatment: 9416219 INFO @ Sat, 06 Jul 2019 02:33:36: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 06 Jul 2019 02:33:36: #1 finished! INFO @ Sat, 06 Jul 2019 02:33:36: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:33:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:33:37: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:33:37: 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 02:33:37: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:33:37: 26000000 INFO @ Sat, 06 Jul 2019 02:33:40: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:33:40: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:33:40: #1 total tags in treatment: 13804018 INFO @ Sat, 06 Jul 2019 02:33:40: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:33:40: #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 02:33:40: #1 tags after filtering in treatment: 9416219 INFO @ Sat, 06 Jul 2019 02:33:40: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 06 Jul 2019 02:33:40: #1 finished! INFO @ Sat, 06 Jul 2019 02:33:40: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:33:40: #2 looking for paired plus/minus strand peaks... cut: /home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.20_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/SRX455438/SRX455438.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:33:41: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:33:41: 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 02:33:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.05_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/SRX455438/SRX455438.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:33:45: 27000000 INFO @ Sat, 06 Jul 2019 02:33:52: 28000000 INFO @ Sat, 06 Jul 2019 02:33:56: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:33:56: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:33:56: #1 total tags in treatment: 13804018 INFO @ Sat, 06 Jul 2019 02:33:56: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:33:56: #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 02:33:57: #1 tags after filtering in treatment: 9416219 INFO @ Sat, 06 Jul 2019 02:33:57: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 06 Jul 2019 02:33:57: #1 finished! INFO @ Sat, 06 Jul 2019 02:33:57: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:33:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:33:57: #2 number of paired peaks: 0 WARNING @ Sat, 06 Jul 2019 02:33:57: 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 02:33:57: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.10_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/SRX455438/SRX455438.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455438/SRX455438.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。