Job ID = 14521795 SRX = SRX9399066 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4180676 spots for SRR12935347/SRR12935347.sra Written 4180676 spots for SRR12935347/SRR12935347.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: 00:02:34 4180676 reads; of these: 4180676 (100.00%) were paired; of these: 492728 (11.79%) aligned concordantly 0 times 3249044 (77.72%) aligned concordantly exactly 1 time 438904 (10.50%) aligned concordantly >1 times ---- 492728 pairs aligned concordantly 0 times; of these: 97936 (19.88%) aligned discordantly 1 time ---- 394792 pairs aligned 0 times concordantly or discordantly; of these: 789584 mates make up the pairs; of these: 615451 (77.95%) aligned 0 times 131753 (16.69%) aligned exactly 1 time 42380 (5.37%) aligned >1 times 92.64% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 267177 / 3745196 = 0.0713 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 21:41:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.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 21:41:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:41:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:41:19: 1000000 INFO @ Sat, 15 Jan 2022 21:41:24: 2000000 INFO @ Sat, 15 Jan 2022 21:41:29: 3000000 INFO @ Sat, 15 Jan 2022 21:41:33: 4000000 INFO @ Sat, 15 Jan 2022 21:41:38: 5000000 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 21:41:43: 6000000 INFO @ Sat, 15 Jan 2022 21:41:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.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 21:41:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:41:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:41:48: 7000000 INFO @ Sat, 15 Jan 2022 21:41:49: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:41:49: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:41:49: #1 total tags in treatment: 3421953 INFO @ Sat, 15 Jan 2022 21:41:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:41:49: #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 21:41:49: #1 tags after filtering in treatment: 2560291 INFO @ Sat, 15 Jan 2022 21:41:49: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:41:49: #1 finished! INFO @ Sat, 15 Jan 2022 21:41:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:41:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:41:49: #2 number of paired peaks: 4 WARNING @ Sat, 15 Jan 2022 21:41:49: Too few paired peaks (4) 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 21:41:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.05_peaks.narrowPeak: No such file or directory INFO @ Sat, 15 Jan 2022 21:41:50: 1000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:41:54: 2000000 INFO @ Sat, 15 Jan 2022 21:41:59: 3000000 INFO @ Sat, 15 Jan 2022 21:42:04: 4000000 INFO @ Sat, 15 Jan 2022 21:42:08: 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 21:42:13: 6000000 INFO @ Sat, 15 Jan 2022 21:42:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.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 21:42:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:42:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:42:18: 7000000 INFO @ Sat, 15 Jan 2022 21:42:19: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:42:19: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:42:19: #1 total tags in treatment: 3421953 INFO @ Sat, 15 Jan 2022 21:42:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:42:19: #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 21:42:19: #1 tags after filtering in treatment: 2560291 INFO @ Sat, 15 Jan 2022 21:42:19: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:42:19: #1 finished! INFO @ Sat, 15 Jan 2022 21:42:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:42:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:42:19: #2 number of paired peaks: 4 WARNING @ Sat, 15 Jan 2022 21:42:19: Too few paired peaks (4) 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 21:42:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis INFO @ Sat, 15 Jan 2022 21:42:20: 1000000 needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:42:24: 2000000 INFO @ Sat, 15 Jan 2022 21:42:29: 3000000 INFO @ Sat, 15 Jan 2022 21:42:33: 4000000 INFO @ Sat, 15 Jan 2022 21:42:38: 5000000 INFO @ Sat, 15 Jan 2022 21:42:42: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:42:47: 7000000 INFO @ Sat, 15 Jan 2022 21:42:47: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 21:42:47: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 21:42:47: #1 total tags in treatment: 3421953 INFO @ Sat, 15 Jan 2022 21:42:47: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:42:47: #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 21:42:48: #1 tags after filtering in treatment: 2560291 INFO @ Sat, 15 Jan 2022 21:42:48: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:42:48: #1 finished! INFO @ Sat, 15 Jan 2022 21:42:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:42:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:42:48: #2 number of paired peaks: 4 WARNING @ Sat, 15 Jan 2022 21:42:48: Too few paired peaks (4) 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 21:42:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.20_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/SRX9399066/SRX9399066.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399066/SRX9399066.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。