Job ID = 2641239 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 760,053 reads read : 1,520,106 reads written : 1,520,106 spots read : 749,857 reads read : 1,499,714 reads written : 1,499,714 2019-08-24T13:08:06 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 758,477 reads read : 1,516,954 reads written : 1,516,954 spots read : 752,355 reads read : 1,504,710 reads written : 1,504,710 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: 00:01:16 3020742 reads; of these: 3020742 (100.00%) were paired; of these: 1175448 (38.91%) aligned concordantly 0 times 1708097 (56.55%) aligned concordantly exactly 1 time 137197 (4.54%) aligned concordantly >1 times ---- 1175448 pairs aligned concordantly 0 times; of these: 11344 (0.97%) aligned discordantly 1 time ---- 1164104 pairs aligned 0 times concordantly or discordantly; of these: 2328208 mates make up the pairs; of these: 1955869 (84.01%) aligned 0 times 340296 (14.62%) aligned exactly 1 time 32043 (1.38%) aligned >1 times 67.63% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 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] 36960 / 1855953 = 0.0199 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:14:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.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, 24 Aug 2019 22:14:41: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:14:41: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:14:47: 1000000 INFO @ Sat, 24 Aug 2019 22:14:53: 2000000 INFO @ Sat, 24 Aug 2019 22:14:59: 3000000 INFO @ Sat, 24 Aug 2019 22:15:05: 4000000 INFO @ Sat, 24 Aug 2019 22:15:05: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:15:05: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:15:05: #1 total tags in treatment: 1808451 INFO @ Sat, 24 Aug 2019 22:15:05: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:15:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:15:05: #1 tags after filtering in treatment: 1685239 INFO @ Sat, 24 Aug 2019 22:15:05: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 24 Aug 2019 22:15:05: #1 finished! INFO @ Sat, 24 Aug 2019 22:15:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:15:05: #2 number of paired peaks: 7 WARNING @ Sat, 24 Aug 2019 22:15:05: Too few paired peaks (7) 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, 24 Aug 2019 22:15:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.05_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/SRX6403217/SRX6403217.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:15:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.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, 24 Aug 2019 22:15:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:15:11: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:15:17: 1000000 INFO @ Sat, 24 Aug 2019 22:15:22: 2000000 INFO @ Sat, 24 Aug 2019 22:15:28: 3000000 INFO @ Sat, 24 Aug 2019 22:15:34: 4000000 INFO @ Sat, 24 Aug 2019 22:15:34: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:15:34: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:15:34: #1 total tags in treatment: 1808451 INFO @ Sat, 24 Aug 2019 22:15:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:15:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:15:34: #1 tags after filtering in treatment: 1685239 INFO @ Sat, 24 Aug 2019 22:15:34: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 24 Aug 2019 22:15:34: #1 finished! INFO @ Sat, 24 Aug 2019 22:15:34: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:15:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:15:35: #2 number of paired peaks: 7 WARNING @ Sat, 24 Aug 2019 22:15:35: Too few paired peaks (7) 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, 24 Aug 2019 22:15:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.10_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/SRX6403217/SRX6403217.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:15:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.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, 24 Aug 2019 22:15:41: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:15:41: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:15:47: 1000000 INFO @ Sat, 24 Aug 2019 22:15:53: 2000000 INFO @ Sat, 24 Aug 2019 22:15:59: 3000000 INFO @ Sat, 24 Aug 2019 22:16:05: 4000000 INFO @ Sat, 24 Aug 2019 22:16:05: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:16:05: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:16:05: #1 total tags in treatment: 1808451 INFO @ Sat, 24 Aug 2019 22:16:05: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:16:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:16:05: #1 tags after filtering in treatment: 1685239 INFO @ Sat, 24 Aug 2019 22:16:05: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 24 Aug 2019 22:16:05: #1 finished! INFO @ Sat, 24 Aug 2019 22:16:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:16:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:16:05: #2 number of paired peaks: 7 WARNING @ Sat, 24 Aug 2019 22:16:05: Too few paired peaks (7) 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, 24 Aug 2019 22:16:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.20_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/SRX6403217/SRX6403217.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403217/SRX6403217.20_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。