Job ID = 2010672 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,026,667 reads read : 6,053,334 reads written : 6,053,334 rm: cannot remove ‘[DSE]RR*’: 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: 00:02:03 3026667 reads; of these: 3026667 (100.00%) were paired; of these: 1159123 (38.30%) aligned concordantly 0 times 1440847 (47.61%) aligned concordantly exactly 1 time 426697 (14.10%) aligned concordantly >1 times ---- 1159123 pairs aligned concordantly 0 times; of these: 6995 (0.60%) aligned discordantly 1 time ---- 1152128 pairs aligned 0 times concordantly or discordantly; of these: 2304256 mates make up the pairs; of these: 1366666 (59.31%) aligned 0 times 715712 (31.06%) aligned exactly 1 time 221878 (9.63%) aligned >1 times 77.42% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 121655 / 1874127 = 0.0649 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 23:54:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.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 23:54:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:54:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:54:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.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 23:54:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:54:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:54:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.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 23:54:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:54:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:54:47: 1000000 INFO @ Fri, 05 Jul 2019 23:54:48: 1000000 INFO @ Fri, 05 Jul 2019 23:54:48: 1000000 INFO @ Fri, 05 Jul 2019 23:54:53: 2000000 INFO @ Fri, 05 Jul 2019 23:54:54: 2000000 INFO @ Fri, 05 Jul 2019 23:54:54: 2000000 INFO @ Fri, 05 Jul 2019 23:54:58: 3000000 INFO @ Fri, 05 Jul 2019 23:55:00: 3000000 INFO @ Fri, 05 Jul 2019 23:55:00: 3000000 INFO @ Fri, 05 Jul 2019 23:55:04: 4000000 INFO @ Fri, 05 Jul 2019 23:55:06: 4000000 INFO @ Fri, 05 Jul 2019 23:55:06: #1 tag size is determined as 37 bps INFO @ Fri, 05 Jul 2019 23:55:06: #1 tag size = 37 INFO @ Fri, 05 Jul 2019 23:55:06: #1 total tags in treatment: 1745970 INFO @ Fri, 05 Jul 2019 23:55:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:55:06: #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 23:55:06: #1 tags after filtering in treatment: 1237846 INFO @ Fri, 05 Jul 2019 23:55:06: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 23:55:06: #1 finished! INFO @ Fri, 05 Jul 2019 23:55:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:55:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:55:06: #2 number of paired peaks: 35 WARNING @ Fri, 05 Jul 2019 23:55:06: 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 @ Fri, 05 Jul 2019 23:55:06: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:55:06: 4000000 INFO @ Fri, 05 Jul 2019 23:55:08: #1 tag size is determined as 37 bps INFO @ Fri, 05 Jul 2019 23:55:08: #1 tag size = 37 INFO @ Fri, 05 Jul 2019 23:55:08: #1 total tags in treatment: 1745970 INFO @ Fri, 05 Jul 2019 23:55:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:55:08: #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 23:55:09: #1 tags after filtering in treatment: 1237846 INFO @ Fri, 05 Jul 2019 23:55:09: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 23:55:09: #1 finished! INFO @ Fri, 05 Jul 2019 23:55:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:55:09: #2 number of paired peaks: 35 WARNING @ Fri, 05 Jul 2019 23:55:09: 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 @ Fri, 05 Jul 2019 23:55:09: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 23:55:09: #1 tag size is determined as 37 bps INFO @ Fri, 05 Jul 2019 23:55:09: #1 tag size = 37 INFO @ Fri, 05 Jul 2019 23:55:09: #1 total tags in treatment: 1745970 INFO @ Fri, 05 Jul 2019 23:55:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:55:09: #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 23:55:09: #1 tags after filtering in treatment: 1237846 INFO @ Fri, 05 Jul 2019 23:55:09: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 05 Jul 2019 23:55:09: #1 finished! INFO @ Fri, 05 Jul 2019 23:55:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:55:09: #2 number of paired peaks: 35 WARNING @ Fri, 05 Jul 2019 23:55:09: 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 @ Fri, 05 Jul 2019 23:55:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.20_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) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.20_*.xls’needLargeMem: trying to allocate 0 bytes (limit: 17179869184): No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.20_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3865883/SRX3865883.05_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。