Job ID = 2011662 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,522,011 reads read : 21,044,022 reads written : 21,044,022 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1146730.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: 00:06:51 10522011 reads; of these: 10522011 (100.00%) were paired; of these: 2070585 (19.68%) aligned concordantly 0 times 6979115 (66.33%) aligned concordantly exactly 1 time 1472311 (13.99%) aligned concordantly >1 times ---- 2070585 pairs aligned concordantly 0 times; of these: 178477 (8.62%) aligned discordantly 1 time ---- 1892108 pairs aligned 0 times concordantly or discordantly; of these: 3784216 mates make up the pairs; of these: 3490310 (92.23%) aligned 0 times 167893 (4.44%) aligned exactly 1 time 126013 (3.33%) aligned >1 times 83.41% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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 8 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] 2522977 / 8518997 = 0.2962 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 02:06:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.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 02:06:41: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:06:41: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:06:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.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 02:06:42: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:06:42: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.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 02:06:43: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:06:43: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:06:49: 1000000 INFO @ Sat, 06 Jul 2019 02:06:50: 1000000 INFO @ Sat, 06 Jul 2019 02:06:51: 1000000 INFO @ Sat, 06 Jul 2019 02:06:56: 2000000 INFO @ Sat, 06 Jul 2019 02:06:57: 2000000 INFO @ Sat, 06 Jul 2019 02:06:58: 2000000 INFO @ Sat, 06 Jul 2019 02:07:03: 3000000 INFO @ Sat, 06 Jul 2019 02:07:04: 3000000 INFO @ Sat, 06 Jul 2019 02:07:05: 3000000 INFO @ Sat, 06 Jul 2019 02:07:10: 4000000 INFO @ Sat, 06 Jul 2019 02:07:12: 4000000 INFO @ Sat, 06 Jul 2019 02:07:12: 4000000 INFO @ Sat, 06 Jul 2019 02:07:18: 5000000 INFO @ Sat, 06 Jul 2019 02:07:19: 5000000 INFO @ Sat, 06 Jul 2019 02:07:20: 5000000 INFO @ Sat, 06 Jul 2019 02:07:25: 6000000 INFO @ Sat, 06 Jul 2019 02:07:26: 6000000 INFO @ Sat, 06 Jul 2019 02:07:27: 6000000 INFO @ Sat, 06 Jul 2019 02:07:32: 7000000 INFO @ Sat, 06 Jul 2019 02:07:33: 7000000 INFO @ Sat, 06 Jul 2019 02:07:34: 7000000 INFO @ Sat, 06 Jul 2019 02:07:39: 8000000 INFO @ Sat, 06 Jul 2019 02:07:40: 8000000 INFO @ Sat, 06 Jul 2019 02:07:41: 8000000 INFO @ Sat, 06 Jul 2019 02:07:46: 9000000 INFO @ Sat, 06 Jul 2019 02:07:47: 9000000 INFO @ Sat, 06 Jul 2019 02:07:48: 9000000 INFO @ Sat, 06 Jul 2019 02:07:53: 10000000 INFO @ Sat, 06 Jul 2019 02:07:54: 10000000 INFO @ Sat, 06 Jul 2019 02:07:55: 10000000 INFO @ Sat, 06 Jul 2019 02:08:01: 11000000 INFO @ Sat, 06 Jul 2019 02:08:01: 11000000 INFO @ Sat, 06 Jul 2019 02:08:03: 11000000 INFO @ Sat, 06 Jul 2019 02:08:08: 12000000 INFO @ Sat, 06 Jul 2019 02:08:08: 12000000 INFO @ Sat, 06 Jul 2019 02:08:09: 12000000 INFO @ Sat, 06 Jul 2019 02:08:11: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:08:11: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:08:11: #1 total tags in treatment: 5947395 INFO @ Sat, 06 Jul 2019 02:08:11: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:08:11: #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 02:08:11: #1 tags after filtering in treatment: 4596798 INFO @ Sat, 06 Jul 2019 02:08:11: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 02:08:11: #1 finished! INFO @ Sat, 06 Jul 2019 02:08:11: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:08:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:08:12: #2 number of paired peaks: 27 WARNING @ Sat, 06 Jul 2019 02:08:12: Too few paired peaks (27) 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 02:08:12: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:08:12: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:08:12: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:08:12: #1 total tags in treatment: 5947395 INFO @ Sat, 06 Jul 2019 02:08:12: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:08:12: #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 02:08:12: #1 tags after filtering in treatment: 4596798 INFO @ Sat, 06 Jul 2019 02:08:12: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 02:08:12: #1 finished! INFO @ Sat, 06 Jul 2019 02:08:12: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:08:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:08:12: #2 number of paired peaks: 27 WARNING @ Sat, 06 Jul 2019 02:08:12: Too few paired peaks (27) 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 02:08:12: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:08:13: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:08:13: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:08:13: #1 total tags in treatment: 5947395 INFO @ Sat, 06 Jul 2019 02:08:13: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:08:13: #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 02:08:13: #1 tags after filtering in treatment: 4596798 INFO @ Sat, 06 Jul 2019 02:08:13: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 06 Jul 2019 02:08:13: #1 finished! INFO @ Sat, 06 Jul 2019 02:08:13: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:08:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:08:13: #2 number of paired peaks: 27 WARNING @ Sat, 06 Jul 2019 02:08:13: Too few paired peaks (27) 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 02:08:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis pass1 - making usageList (0 chroms): 2 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/SRX455440/SRX455440.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.05_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.10_model.r’CompletedMACS2peakCalling : No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.20_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455440/SRX455440.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。