Job ID = 14521592 SRX = SRX9399104 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5095014 spots for SRR12935385/SRR12935385.sra Written 5095014 spots for SRR12935385/SRR12935385.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: 00:02:13 5095014 reads; of these: 5095014 (100.00%) were paired; of these: 495351 (9.72%) aligned concordantly 0 times 3232984 (63.45%) aligned concordantly exactly 1 time 1366679 (26.82%) aligned concordantly >1 times ---- 495351 pairs aligned concordantly 0 times; of these: 31397 (6.34%) aligned discordantly 1 time ---- 463954 pairs aligned 0 times concordantly or discordantly; of these: 927908 mates make up the pairs; of these: 822591 (88.65%) aligned 0 times 62937 (6.78%) aligned exactly 1 time 42380 (4.57%) aligned >1 times 91.93% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 1825846 / 4626666 = 0.3946 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 21:16:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.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 21:16:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:16:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:16:47: 1000000 INFO @ Sat, 15 Jan 2022 21:16:53: 2000000 INFO @ Sat, 15 Jan 2022 21:16:58: 3000000 INFO @ Sat, 15 Jan 2022 21:17:03: 4000000 INFO @ Sat, 15 Jan 2022 21:17:08: 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 21:17:12: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 21:17:12: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 21:17:12: #1 total tags in treatment: 2778714 INFO @ Sat, 15 Jan 2022 21:17:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:17:12: #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 21:17:12: #1 tags after filtering in treatment: 1949870 INFO @ Sat, 15 Jan 2022 21:17:12: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 21:17:12: #1 finished! INFO @ Sat, 15 Jan 2022 21:17:12: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:17:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:17:12: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 21:17:12: Too few paired peaks (31) 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 21:17:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.05_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/SRX9399104/SRX9399104.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:17:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.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 21:17:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:17:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:17:17: 1000000 INFO @ Sat, 15 Jan 2022 21:17:21: 2000000 INFO @ Sat, 15 Jan 2022 21:17:25: 3000000 INFO @ Sat, 15 Jan 2022 21:17:30: 4000000 INFO @ Sat, 15 Jan 2022 21:17:35: 5000000 INFO @ Sat, 15 Jan 2022 21:17:38: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 21:17:38: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 21:17:38: #1 total tags in treatment: 2778714 INFO @ Sat, 15 Jan 2022 21:17:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:17:38: #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 21:17:38: #1 tags after filtering in treatment: 1949870 INFO @ Sat, 15 Jan 2022 21:17:38: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 21:17:38: #1 finished! INFO @ Sat, 15 Jan 2022 21:17:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:17:38: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 21:17:38: Too few paired peaks (31) 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 21:17:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.10_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/SRX9399104/SRX9399104.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 21:17:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.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 21:17:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:17:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:17:48: 1000000 INFO @ Sat, 15 Jan 2022 21:17:53: 2000000 INFO @ Sat, 15 Jan 2022 21:17:57: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:18:02: 4000000 INFO @ Sat, 15 Jan 2022 21:18:07: 5000000 INFO @ Sat, 15 Jan 2022 21:18:11: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 21:18:11: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 21:18:11: #1 total tags in treatment: 2778714 INFO @ Sat, 15 Jan 2022 21:18:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:18:11: #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 21:18:11: #1 tags after filtering in treatment: 1949870 INFO @ Sat, 15 Jan 2022 21:18:11: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 21:18:11: #1 finished! INFO @ Sat, 15 Jan 2022 21:18:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:18:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:18:11: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 21:18:11: Too few paired peaks (31) 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 21:18:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.20_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/SRX9399104/SRX9399104.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399104/SRX9399104.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。