Job ID = 7115275 SRX = SRX8462227 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2375515 spots for SRR11915686/SRR11915686.sra Written 2375515 spots for SRR11915686/SRR11915686.sra 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: 00:02:08 2375515 reads; of these: 2375515 (100.00%) were paired; of these: 173328 (7.30%) aligned concordantly 0 times 1904448 (80.17%) aligned concordantly exactly 1 time 297739 (12.53%) aligned concordantly >1 times ---- 173328 pairs aligned concordantly 0 times; of these: 15557 (8.98%) aligned discordantly 1 time ---- 157771 pairs aligned 0 times concordantly or discordantly; of these: 315542 mates make up the pairs; of these: 261426 (82.85%) aligned 0 times 41505 (13.15%) aligned exactly 1 time 12611 (4.00%) aligned >1 times 94.50% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 217702 / 2212134 = 0.0984 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 15:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.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 @ Wed, 22 Jul 2020 15:11:20: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:11:20: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:11:27: 1000000 INFO @ Wed, 22 Jul 2020 15:11:33: 2000000 INFO @ Wed, 22 Jul 2020 15:11:39: 3000000 INFO @ Wed, 22 Jul 2020 15:11:45: 4000000 INFO @ Wed, 22 Jul 2020 15:11:46: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:11:46: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:11:46: #1 total tags in treatment: 1984856 INFO @ Wed, 22 Jul 2020 15:11:46: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:11:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 15:11:46: #1 tags after filtering in treatment: 1760872 INFO @ Wed, 22 Jul 2020 15:11:46: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Jul 2020 15:11:46: #1 finished! INFO @ Wed, 22 Jul 2020 15:11:46: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:11:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:11:46: #2 number of paired peaks: 70 WARNING @ Wed, 22 Jul 2020 15:11:46: Too few paired peaks (70) 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 @ Wed, 22 Jul 2020 15:11:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.05_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/SRX8462227/SRX8462227.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 15:11:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.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 @ Wed, 22 Jul 2020 15:11:49: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:11:49: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:11:55: 1000000 INFO @ Wed, 22 Jul 2020 15:12:02: 2000000 INFO @ Wed, 22 Jul 2020 15:12:08: 3000000 INFO @ Wed, 22 Jul 2020 15:12:14: 4000000 INFO @ Wed, 22 Jul 2020 15:12:15: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:12:15: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:12:15: #1 total tags in treatment: 1984856 INFO @ Wed, 22 Jul 2020 15:12:15: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:12:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 15:12:15: #1 tags after filtering in treatment: 1760872 INFO @ Wed, 22 Jul 2020 15:12:15: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Jul 2020 15:12:15: #1 finished! INFO @ Wed, 22 Jul 2020 15:12:15: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:12:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:12:15: #2 number of paired peaks: 70 WARNING @ Wed, 22 Jul 2020 15:12:15: Too few paired peaks (70) 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 @ Wed, 22 Jul 2020 15:12:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.10_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/SRX8462227/SRX8462227.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 15:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.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 @ Wed, 22 Jul 2020 15:12:19: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:12:19: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:12:25: 1000000 INFO @ Wed, 22 Jul 2020 15:12:32: 2000000 INFO @ Wed, 22 Jul 2020 15:12:38: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:12:44: 4000000 INFO @ Wed, 22 Jul 2020 15:12:45: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:12:45: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:12:45: #1 total tags in treatment: 1984856 INFO @ Wed, 22 Jul 2020 15:12:45: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:12:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 15:12:45: #1 tags after filtering in treatment: 1760872 INFO @ Wed, 22 Jul 2020 15:12:45: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Jul 2020 15:12:45: #1 finished! INFO @ Wed, 22 Jul 2020 15:12:45: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:12:45: #2 number of paired peaks: 70 WARNING @ Wed, 22 Jul 2020 15:12:45: Too few paired peaks (70) 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 @ Wed, 22 Jul 2020 15:12:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462227/SRX8462227.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。