Job ID = 2011667 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,856,786 reads read : 13,713,572 reads written : 13,713,572 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1146735.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: 00:05:25 6856786 reads; of these: 6856786 (100.00%) were paired; of these: 936232 (13.65%) aligned concordantly 0 times 4813777 (70.20%) aligned concordantly exactly 1 time 1106777 (16.14%) aligned concordantly >1 times ---- 936232 pairs aligned concordantly 0 times; of these: 245357 (26.21%) aligned discordantly 1 time ---- 690875 pairs aligned 0 times concordantly or discordantly; of these: 1381750 mates make up the pairs; of these: 1061169 (76.80%) aligned 0 times 155593 (11.26%) aligned exactly 1 time 164988 (11.94%) aligned >1 times 92.26% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 964425 / 5999928 = 0.1607 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 02:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.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 02:03:25: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:03:25: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.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 02:03:26: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:03:26: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.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 02:03:27: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:03:27: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:03:33: 1000000 INFO @ Sat, 06 Jul 2019 02:03:37: 1000000 INFO @ Sat, 06 Jul 2019 02:03:38: 1000000 INFO @ Sat, 06 Jul 2019 02:03:41: 2000000 INFO @ Sat, 06 Jul 2019 02:03:47: 2000000 INFO @ Sat, 06 Jul 2019 02:03:48: 2000000 INFO @ Sat, 06 Jul 2019 02:03:49: 3000000 INFO @ Sat, 06 Jul 2019 02:03:57: 3000000 INFO @ Sat, 06 Jul 2019 02:03:57: 4000000 INFO @ Sat, 06 Jul 2019 02:03:57: 3000000 INFO @ Sat, 06 Jul 2019 02:04:05: 5000000 INFO @ Sat, 06 Jul 2019 02:04:07: 4000000 INFO @ Sat, 06 Jul 2019 02:04:07: 4000000 INFO @ Sat, 06 Jul 2019 02:04:13: 6000000 INFO @ Sat, 06 Jul 2019 02:04:16: 5000000 INFO @ Sat, 06 Jul 2019 02:04:17: 5000000 INFO @ Sat, 06 Jul 2019 02:04:21: 7000000 INFO @ Sat, 06 Jul 2019 02:04:26: 6000000 INFO @ Sat, 06 Jul 2019 02:04:27: 6000000 INFO @ Sat, 06 Jul 2019 02:04:29: 8000000 INFO @ Sat, 06 Jul 2019 02:04:36: 7000000 INFO @ Sat, 06 Jul 2019 02:04:37: 9000000 INFO @ Sat, 06 Jul 2019 02:04:37: 7000000 INFO @ Sat, 06 Jul 2019 02:04:45: 10000000 INFO @ Sat, 06 Jul 2019 02:04:46: 8000000 INFO @ Sat, 06 Jul 2019 02:04:47: 8000000 INFO @ Sat, 06 Jul 2019 02:04:50: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:04:50: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:04:50: #1 total tags in treatment: 4969626 INFO @ Sat, 06 Jul 2019 02:04:50: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:04:50: #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 02:04:51: #1 tags after filtering in treatment: 3941971 INFO @ Sat, 06 Jul 2019 02:04:51: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 06 Jul 2019 02:04:51: #1 finished! INFO @ Sat, 06 Jul 2019 02:04:51: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:04:51: #2 number of paired peaks: 27 WARNING @ Sat, 06 Jul 2019 02:04:51: 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 02:04:51: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 02:04:56: 9000000 INFO @ Sat, 06 Jul 2019 02:04:57: 9000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.05_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/SRX455445/SRX455445.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:05:06: 10000000 INFO @ Sat, 06 Jul 2019 02:05:07: 10000000 INFO @ Sat, 06 Jul 2019 02:05:13: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:05:13: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:05:13: #1 total tags in treatment: 4969626 INFO @ Sat, 06 Jul 2019 02:05:13: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:05:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:05:13: #1 tags after filtering in treatment: 3941971 INFO @ Sat, 06 Jul 2019 02:05:13: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 06 Jul 2019 02:05:13: #1 finished! INFO @ Sat, 06 Jul 2019 02:05:13: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:05:14: #2 number of paired peaks: 27 WARNING @ Sat, 06 Jul 2019 02:05:14: 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 02:05:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.10_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/SRX455445/SRX455445.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:05:14: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 02:05:14: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 02:05:14: #1 total tags in treatment: 4969626 INFO @ Sat, 06 Jul 2019 02:05:14: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:05:14: #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 02:05:14: #1 tags after filtering in treatment: 3941971 INFO @ Sat, 06 Jul 2019 02:05:14: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 06 Jul 2019 02:05:14: #1 finished! INFO @ Sat, 06 Jul 2019 02:05:14: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:05:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:05:14: #2 number of paired peaks: 27 WARNING @ Sat, 06 Jul 2019 02:05:14: 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 02:05:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.20_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/SRX455445/SRX455445.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX455445/SRX455445.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。