Job ID = 14521615 SRX = SRX9399007 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4311436 spots for SRR12935289/SRR12935289.sra Written 4311436 spots for SRR12935289/SRR12935289.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: 00:02:18 4311436 reads; of these: 4311436 (100.00%) were paired; of these: 722276 (16.75%) aligned concordantly 0 times 3251080 (75.41%) aligned concordantly exactly 1 time 338080 (7.84%) aligned concordantly >1 times ---- 722276 pairs aligned concordantly 0 times; of these: 172020 (23.82%) aligned discordantly 1 time ---- 550256 pairs aligned 0 times concordantly or discordantly; of these: 1100512 mates make up the pairs; of these: 963677 (87.57%) aligned 0 times 92509 (8.41%) aligned exactly 1 time 44326 (4.03%) aligned >1 times 88.82% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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] 270438 / 3683442 = 0.0734 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 21:22:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.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 21:22:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:22:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:23:00: 1000000 INFO @ Sat, 15 Jan 2022 21:23:04: 2000000 INFO @ Sat, 15 Jan 2022 21:23:08: 3000000 INFO @ Sat, 15 Jan 2022 21:23:12: 4000000 INFO @ Sat, 15 Jan 2022 21:23:16: 5000000 INFO @ Sat, 15 Jan 2022 21:23:20: 6000000 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 21:23:24: 7000000 INFO @ Sat, 15 Jan 2022 21:23:24: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:23:24: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:23:24: #1 total tags in treatment: 3325127 INFO @ Sat, 15 Jan 2022 21:23:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:23:24: #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 21:23:24: #1 tags after filtering in treatment: 2485313 INFO @ Sat, 15 Jan 2022 21:23:24: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:23:24: #1 finished! INFO @ Sat, 15 Jan 2022 21:23:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:23:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:23:25: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:23:25: Too few paired peaks (3) 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 21:23:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.05_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/SRX9399007/SRX9399007.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.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 21:23:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:23:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:23:30: 1000000 INFO @ Sat, 15 Jan 2022 21:23:34: 2000000 INFO @ Sat, 15 Jan 2022 21:23:38: 3000000 INFO @ Sat, 15 Jan 2022 21:23:42: 4000000 INFO @ Sat, 15 Jan 2022 21:23:46: 5000000 INFO @ Sat, 15 Jan 2022 21:23:50: 6000000 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 21:23:54: 7000000 INFO @ Sat, 15 Jan 2022 21:23:55: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:23:55: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:23:55: #1 total tags in treatment: 3325127 INFO @ Sat, 15 Jan 2022 21:23:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:23:55: #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 21:23:55: #1 tags after filtering in treatment: 2485313 INFO @ Sat, 15 Jan 2022 21:23:55: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:23:55: #1 finished! INFO @ Sat, 15 Jan 2022 21:23:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:23:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:23:55: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:23:55: Too few paired peaks (3) 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 21:23:55: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.10_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/SRX9399007/SRX9399007.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:23:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.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 21:23:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:23:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:24:00: 1000000 INFO @ Sat, 15 Jan 2022 21:24:04: 2000000 INFO @ Sat, 15 Jan 2022 21:24:08: 3000000 INFO @ Sat, 15 Jan 2022 21:24:12: 4000000 INFO @ Sat, 15 Jan 2022 21:24:16: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:24:20: 6000000 INFO @ Sat, 15 Jan 2022 21:24:24: 7000000 INFO @ Sat, 15 Jan 2022 21:24:24: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:24:24: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:24:24: #1 total tags in treatment: 3325127 INFO @ Sat, 15 Jan 2022 21:24:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:24:24: #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 21:24:24: #1 tags after filtering in treatment: 2485313 INFO @ Sat, 15 Jan 2022 21:24:24: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 21:24:24: #1 finished! INFO @ Sat, 15 Jan 2022 21:24:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:24:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:24:25: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:24:25: Too few paired peaks (3) 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 21:24:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.20_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/SRX9399007/SRX9399007.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399007/SRX9399007.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。