Job ID = 2011666 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,211,320 reads read : 22,422,640 reads written : 22,422,640 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1146734.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: 00:07:12 11211320 reads; of these: 11211320 (100.00%) were paired; of these: 2349590 (20.96%) aligned concordantly 0 times 7219744 (64.40%) aligned concordantly exactly 1 time 1641986 (14.65%) aligned concordantly >1 times ---- 2349590 pairs aligned concordantly 0 times; of these: 192401 (8.19%) aligned discordantly 1 time ---- 2157189 pairs aligned 0 times concordantly or discordantly; of these: 4314378 mates make up the pairs; of these: 3983917 (92.34%) aligned 0 times 183664 (4.26%) aligned exactly 1 time 146797 (3.40%) aligned >1 times 82.23% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 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] 2830986 / 8937161 = 0.3168 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 02:06:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.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 02:06:57: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:06:57: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:06:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.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 02:06:58: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:06:58: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:07:05: 1000000 INFO @ Sat, 06 Jul 2019 02:07:05: 1000000 INFO @ Sat, 06 Jul 2019 02:07:12: 2000000 INFO @ Sat, 06 Jul 2019 02:07:12: 2000000 INFO @ Sat, 06 Jul 2019 02:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.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 02:07:18: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:07:18: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:07:18: 3000000 INFO @ Sat, 06 Jul 2019 02:07:20: 3000000 INFO @ Sat, 06 Jul 2019 02:07:24: 1000000 INFO @ Sat, 06 Jul 2019 02:07:25: 4000000 INFO @ Sat, 06 Jul 2019 02:07:27: 4000000 INFO @ Sat, 06 Jul 2019 02:07:31: 2000000 INFO @ Sat, 06 Jul 2019 02:07:32: 5000000 INFO @ Sat, 06 Jul 2019 02:07:34: 5000000 INFO @ Sat, 06 Jul 2019 02:07:38: 3000000 INFO @ Sat, 06 Jul 2019 02:07:38: 6000000 INFO @ Sat, 06 Jul 2019 02:07:42: 6000000 INFO @ Sat, 06 Jul 2019 02:07:44: 4000000 INFO @ Sat, 06 Jul 2019 02:07:45: 7000000 INFO @ Sat, 06 Jul 2019 02:07:49: 7000000 INFO @ Sat, 06 Jul 2019 02:07:51: 5000000 INFO @ Sat, 06 Jul 2019 02:07:51: 8000000 INFO @ Sat, 06 Jul 2019 02:07:56: 8000000 INFO @ Sat, 06 Jul 2019 02:07:57: 6000000 INFO @ Sat, 06 Jul 2019 02:07:58: 9000000 INFO @ Sat, 06 Jul 2019 02:08:04: 9000000 INFO @ Sat, 06 Jul 2019 02:08:04: 7000000 INFO @ Sat, 06 Jul 2019 02:08:05: 10000000 INFO @ Sat, 06 Jul 2019 02:08:11: 8000000 INFO @ Sat, 06 Jul 2019 02:08:11: 10000000 INFO @ Sat, 06 Jul 2019 02:08:11: 11000000 INFO @ Sat, 06 Jul 2019 02:08:17: 9000000 INFO @ Sat, 06 Jul 2019 02:08:17: 12000000 INFO @ Sat, 06 Jul 2019 02:08:18: 11000000 INFO @ Sat, 06 Jul 2019 02:08:23: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:08:23: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:08:23: #1 total tags in treatment: 6053170 INFO @ Sat, 06 Jul 2019 02:08:23: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:08:23: #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 02:08:23: #1 tags after filtering in treatment: 4626593 INFO @ Sat, 06 Jul 2019 02:08:23: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 02:08:23: #1 finished! INFO @ Sat, 06 Jul 2019 02:08:23: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:08:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:08:23: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 02:08:23: Too few paired peaks (28) 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 02:08:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.10_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/SRX455444/SRX455444.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:08:24: 10000000 INFO @ Sat, 06 Jul 2019 02:08:25: 12000000 INFO @ Sat, 06 Jul 2019 02:08:30: 11000000 INFO @ Sat, 06 Jul 2019 02:08:31: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:08:31: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:08:31: #1 total tags in treatment: 6053170 INFO @ Sat, 06 Jul 2019 02:08:31: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:08:31: #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 02:08:31: #1 tags after filtering in treatment: 4626593 INFO @ Sat, 06 Jul 2019 02:08:31: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 02:08:31: #1 finished! INFO @ Sat, 06 Jul 2019 02:08:31: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:08:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:08:31: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 02:08:31: Too few paired peaks (28) 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 02:08:31: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.05_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/SRX455444/SRX455444.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:08:37: 12000000 INFO @ Sat, 06 Jul 2019 02:08:42: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:08:42: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:08:42: #1 total tags in treatment: 6053170 INFO @ Sat, 06 Jul 2019 02:08:42: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:08:42: #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 02:08:42: #1 tags after filtering in treatment: 4626593 INFO @ Sat, 06 Jul 2019 02:08:42: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 06 Jul 2019 02:08:42: #1 finished! INFO @ Sat, 06 Jul 2019 02:08:42: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:08:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:08:42: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 02:08:42: Too few paired peaks (28) 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 02:08:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.20_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/SRX455444/SRX455444.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455444/SRX455444.20_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。