Job ID = 14520233 SRX = SRX8398423 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2220087 spots for SRR11848041/SRR11848041.sra Written 2220087 spots for SRR11848041/SRR11848041.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: 00:01:38 2220087 reads; of these: 2220087 (100.00%) were paired; of these: 277980 (12.52%) aligned concordantly 0 times 1628978 (73.37%) aligned concordantly exactly 1 time 313129 (14.10%) aligned concordantly >1 times ---- 277980 pairs aligned concordantly 0 times; of these: 12252 (4.41%) aligned discordantly 1 time ---- 265728 pairs aligned 0 times concordantly or discordantly; of these: 531456 mates make up the pairs; of these: 518097 (97.49%) aligned 0 times 8322 (1.57%) aligned exactly 1 time 5037 (0.95%) aligned >1 times 88.33% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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] 171983 / 1906756 = 0.0902 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 18:45:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.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 18:45:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:45:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:45:57: 1000000 INFO @ Sat, 15 Jan 2022 18:46:05: 2000000 INFO @ Sat, 15 Jan 2022 18:46:13: 3000000 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 18:46:17: #1 tag size is determined as 49 bps INFO @ Sat, 15 Jan 2022 18:46:17: #1 tag size = 49 INFO @ Sat, 15 Jan 2022 18:46:17: #1 total tags in treatment: 1770421 INFO @ Sat, 15 Jan 2022 18:46:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:46:17: #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 18:46:17: #1 tags after filtering in treatment: 1425344 INFO @ Sat, 15 Jan 2022 18:46:17: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 18:46:17: #1 finished! INFO @ Sat, 15 Jan 2022 18:46:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:46:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:46:17: #2 number of paired peaks: 60 WARNING @ Sat, 15 Jan 2022 18:46:17: Too few paired peaks (60) 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 18:46:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.05_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/SRX8398423/SRX8398423.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:46:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.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 18:46:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:46:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:46:27: 1000000 INFO @ Sat, 15 Jan 2022 18:46:35: 2000000 INFO @ Sat, 15 Jan 2022 18:46:44: 3000000 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 18:46:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.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 18:46:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:46:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:46:49: #1 tag size is determined as 49 bps INFO @ Sat, 15 Jan 2022 18:46:49: #1 tag size = 49 INFO @ Sat, 15 Jan 2022 18:46:49: #1 total tags in treatment: 1770421 INFO @ Sat, 15 Jan 2022 18:46:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:46:49: #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 18:46:49: #1 tags after filtering in treatment: 1425344 INFO @ Sat, 15 Jan 2022 18:46:49: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 18:46:49: #1 finished! INFO @ Sat, 15 Jan 2022 18:46:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:46:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:46:49: #2 number of paired peaks: 60 WARNING @ Sat, 15 Jan 2022 18:46:49: Too few paired peaks (60) 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 18:46:49: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.10_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/SRX8398423/SRX8398423.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:46:57: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:47:05: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:47:13: 3000000 INFO @ Sat, 15 Jan 2022 18:47:18: #1 tag size is determined as 49 bps INFO @ Sat, 15 Jan 2022 18:47:18: #1 tag size = 49 INFO @ Sat, 15 Jan 2022 18:47:18: #1 total tags in treatment: 1770421 INFO @ Sat, 15 Jan 2022 18:47:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:47:18: #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 18:47:18: #1 tags after filtering in treatment: 1425344 INFO @ Sat, 15 Jan 2022 18:47:18: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 18:47:18: #1 finished! INFO @ Sat, 15 Jan 2022 18:47:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:47:18: #2 number of paired peaks: 60 WARNING @ Sat, 15 Jan 2022 18:47:18: Too few paired peaks (60) 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 18:47:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.20_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/SRX8398423/SRX8398423.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8398423/SRX8398423.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling