Job ID = 14522060 SRX = SRX9067213 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5855211 spots for SRR12580366/SRR12580366.sra Written 5855211 spots for SRR12580366/SRR12580366.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: 00:03:00 5855211 reads; of these: 5855211 (100.00%) were paired; of these: 829991 (14.18%) aligned concordantly 0 times 4204684 (71.81%) aligned concordantly exactly 1 time 820536 (14.01%) aligned concordantly >1 times ---- 829991 pairs aligned concordantly 0 times; of these: 56238 (6.78%) aligned discordantly 1 time ---- 773753 pairs aligned 0 times concordantly or discordantly; of these: 1547506 mates make up the pairs; of these: 1368476 (88.43%) aligned 0 times 131960 (8.53%) aligned exactly 1 time 47070 (3.04%) aligned >1 times 88.31% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 2564974 / 5072638 = 0.5056 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 22:11:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.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, 15 Jan 2022 22:11:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:11:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:11:21: 1000000 INFO @ Sat, 15 Jan 2022 22:11:27: 2000000 INFO @ Sat, 15 Jan 2022 22:11:32: 3000000 INFO @ Sat, 15 Jan 2022 22:11:38: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 22:11:43: 5000000 INFO @ Sat, 15 Jan 2022 22:11:44: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 22:11:44: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 22:11:44: #1 total tags in treatment: 2470101 INFO @ Sat, 15 Jan 2022 22:11:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:11:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 22:11:44: #1 tags after filtering in treatment: 1896151 INFO @ Sat, 15 Jan 2022 22:11:44: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 22:11:44: #1 finished! INFO @ Sat, 15 Jan 2022 22:11:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:11:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:11:44: #2 number of paired peaks: 26 WARNING @ Sat, 15 Jan 2022 22:11:44: Too few paired peaks (26) 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, 15 Jan 2022 22:11:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.05_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/SRX9067213/SRX9067213.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:11:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.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, 15 Jan 2022 22:11:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:11:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:11:51: 1000000 INFO @ Sat, 15 Jan 2022 22:11:56: 2000000 INFO @ Sat, 15 Jan 2022 22:12:01: 3000000 INFO @ Sat, 15 Jan 2022 22:12:07: 4000000 INFO @ Sat, 15 Jan 2022 22:12:12: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 22:12:13: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 22:12:13: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 22:12:13: #1 total tags in treatment: 2470101 INFO @ Sat, 15 Jan 2022 22:12:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:12:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 22:12:13: #1 tags after filtering in treatment: 1896151 INFO @ Sat, 15 Jan 2022 22:12:13: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 22:12:13: #1 finished! INFO @ Sat, 15 Jan 2022 22:12:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:12:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:12:13: #2 number of paired peaks: 26 WARNING @ Sat, 15 Jan 2022 22:12:13: Too few paired peaks (26) 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, 15 Jan 2022 22:12:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.10_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/SRX9067213/SRX9067213.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:12:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.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, 15 Jan 2022 22:12:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:12:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:12:21: 1000000 INFO @ Sat, 15 Jan 2022 22:12:26: 2000000 INFO @ Sat, 15 Jan 2022 22:12:32: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:12:37: 4000000 INFO @ Sat, 15 Jan 2022 22:12:43: 5000000 INFO @ Sat, 15 Jan 2022 22:12:44: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 22:12:44: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 22:12:44: #1 total tags in treatment: 2470101 INFO @ Sat, 15 Jan 2022 22:12:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:12:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 22:12:44: #1 tags after filtering in treatment: 1896151 INFO @ Sat, 15 Jan 2022 22:12:44: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 22:12:44: #1 finished! INFO @ Sat, 15 Jan 2022 22:12:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:12:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:12:44: #2 number of paired peaks: 26 WARNING @ Sat, 15 Jan 2022 22:12:44: Too few paired peaks (26) 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, 15 Jan 2022 22:12:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.20_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/SRX9067213/SRX9067213.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067213/SRX9067213.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。