Job ID = 2640772 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,489,036 reads read : 18,978,072 reads written : 18,978,072 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: 00:06:42 9489036 reads; of these: 9489036 (100.00%) were paired; of these: 979589 (10.32%) aligned concordantly 0 times 7749484 (81.67%) aligned concordantly exactly 1 time 759963 (8.01%) aligned concordantly >1 times ---- 979589 pairs aligned concordantly 0 times; of these: 13732 (1.40%) aligned discordantly 1 time ---- 965857 pairs aligned 0 times concordantly or discordantly; of these: 1931714 mates make up the pairs; of these: 1876767 (97.16%) aligned 0 times 40816 (2.11%) aligned exactly 1 time 14131 (0.73%) aligned >1 times 90.11% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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] 443701 / 8518496 = 0.0521 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:20:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.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 19:20:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:20:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:20:31: 1000000 INFO @ Sat, 24 Aug 2019 19:20:39: 2000000 INFO @ Sat, 24 Aug 2019 19:20:46: 3000000 INFO @ Sat, 24 Aug 2019 19:20:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.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 19:20:52: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:20:52: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:20:54: 4000000 INFO @ Sat, 24 Aug 2019 19:20:59: 1000000 INFO @ Sat, 24 Aug 2019 19:21:02: 5000000 INFO @ Sat, 24 Aug 2019 19:21:07: 2000000 INFO @ Sat, 24 Aug 2019 19:21:11: 6000000 INFO @ Sat, 24 Aug 2019 19:21:14: 3000000 INFO @ Sat, 24 Aug 2019 19:21:19: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:21:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.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 19:21:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:21:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:21:22: 4000000 INFO @ Sat, 24 Aug 2019 19:21:26: 8000000 INFO @ Sat, 24 Aug 2019 19:21:30: 5000000 INFO @ Sat, 24 Aug 2019 19:21:31: 1000000 INFO @ Sat, 24 Aug 2019 19:21:34: 9000000 INFO @ Sat, 24 Aug 2019 19:21:38: 6000000 INFO @ Sat, 24 Aug 2019 19:21:40: 2000000 INFO @ Sat, 24 Aug 2019 19:21:42: 10000000 INFO @ Sat, 24 Aug 2019 19:21:46: 7000000 INFO @ Sat, 24 Aug 2019 19:21:48: 3000000 INFO @ Sat, 24 Aug 2019 19:21:50: 11000000 INFO @ Sat, 24 Aug 2019 19:21:54: 8000000 INFO @ Sat, 24 Aug 2019 19:21:57: 4000000 INFO @ Sat, 24 Aug 2019 19:21:59: 12000000 INFO @ Sat, 24 Aug 2019 19:22:02: 9000000 INFO @ Sat, 24 Aug 2019 19:22:06: 5000000 INFO @ Sat, 24 Aug 2019 19:22:08: 13000000 INFO @ Sat, 24 Aug 2019 19:22:09: 10000000 INFO @ Sat, 24 Aug 2019 19:22:14: 6000000 INFO @ Sat, 24 Aug 2019 19:22:17: 14000000 INFO @ Sat, 24 Aug 2019 19:22:18: 11000000 INFO @ Sat, 24 Aug 2019 19:22:23: 7000000 INFO @ Sat, 24 Aug 2019 19:22:26: 15000000 INFO @ Sat, 24 Aug 2019 19:22:26: 12000000 INFO @ Sat, 24 Aug 2019 19:22:31: 8000000 INFO @ Sat, 24 Aug 2019 19:22:35: 16000000 INFO @ Sat, 24 Aug 2019 19:22:35: 13000000 INFO @ Sat, 24 Aug 2019 19:22:36: #1 tag size is determined as 38 bps INFO @ Sat, 24 Aug 2019 19:22:36: #1 tag size = 38 INFO @ Sat, 24 Aug 2019 19:22:36: #1 total tags in treatment: 8065923 INFO @ Sat, 24 Aug 2019 19:22:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:22:36: #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 19:22:37: #1 tags after filtering in treatment: 5913512 INFO @ Sat, 24 Aug 2019 19:22:37: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 19:22:37: #1 finished! INFO @ Sat, 24 Aug 2019 19:22:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:22:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:22:37: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:22:37: 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, 24 Aug 2019 19:22:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.05_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/ERX2732457/ERX2732457.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:22:39: 9000000 INFO @ Sat, 24 Aug 2019 19:22:44: 14000000 INFO @ Sat, 24 Aug 2019 19:22:46: 10000000 INFO @ Sat, 24 Aug 2019 19:22:53: 15000000 INFO @ Sat, 24 Aug 2019 19:22:54: 11000000 INFO @ Sat, 24 Aug 2019 19:23:02: 16000000 INFO @ Sat, 24 Aug 2019 19:23:02: 12000000 INFO @ Sat, 24 Aug 2019 19:23:03: #1 tag size is determined as 38 bps INFO @ Sat, 24 Aug 2019 19:23:03: #1 tag size = 38 INFO @ Sat, 24 Aug 2019 19:23:03: #1 total tags in treatment: 8065923 INFO @ Sat, 24 Aug 2019 19:23:03: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:23:03: #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 19:23:04: #1 tags after filtering in treatment: 5913512 INFO @ Sat, 24 Aug 2019 19:23:04: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 19:23:04: #1 finished! INFO @ Sat, 24 Aug 2019 19:23:04: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:23:04: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:23:04: 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, 24 Aug 2019 19:23:04: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.10_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/ERX2732457/ERX2732457.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:23:10: 13000000 INFO @ Sat, 24 Aug 2019 19:23:18: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 19:23:26: 15000000 INFO @ Sat, 24 Aug 2019 19:23:34: 16000000 INFO @ Sat, 24 Aug 2019 19:23:35: #1 tag size is determined as 38 bps INFO @ Sat, 24 Aug 2019 19:23:35: #1 tag size = 38 INFO @ Sat, 24 Aug 2019 19:23:35: #1 total tags in treatment: 8065923 INFO @ Sat, 24 Aug 2019 19:23:35: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:23:35: #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 19:23:35: #1 tags after filtering in treatment: 5913512 INFO @ Sat, 24 Aug 2019 19:23:35: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 24 Aug 2019 19:23:35: #1 finished! INFO @ Sat, 24 Aug 2019 19:23:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:23:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:23:36: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:23:36: 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, 24 Aug 2019 19:23:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.20_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/ERX2732457/ERX2732457.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732457/ERX2732457.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。