Job ID = 10224051 SRX = SRX8952608 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13186103 spots for SRR12458278/SRR12458278.sra Written 13186103 spots for SRR12458278/SRR12458278.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: 00:02:20 13186103 reads; of these: 13186103 (100.00%) were paired; of these: 10928094 (82.88%) aligned concordantly 0 times 1961003 (14.87%) aligned concordantly exactly 1 time 297006 (2.25%) aligned concordantly >1 times ---- 10928094 pairs aligned concordantly 0 times; of these: 296714 (2.72%) aligned discordantly 1 time ---- 10631380 pairs aligned 0 times concordantly or discordantly; of these: 21262760 mates make up the pairs; of these: 20327561 (95.60%) aligned 0 times 721766 (3.39%) aligned exactly 1 time 213433 (1.00%) aligned >1 times 22.92% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 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] 546614 / 2500529 = 0.2186 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 09:19:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.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 @ Fri, 16 Oct 2020 09:19:25: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:19:25: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:19:30: 1000000 INFO @ Fri, 16 Oct 2020 09:19:36: 2000000 INFO @ Fri, 16 Oct 2020 09:19:41: 3000000 INFO @ Fri, 16 Oct 2020 09:19:46: 4000000 INFO @ Fri, 16 Oct 2020 09:19:51: #1 tag size is determined as 40 bps INFO @ Fri, 16 Oct 2020 09:19:51: #1 tag size = 40 INFO @ Fri, 16 Oct 2020 09:19:51: #1 total tags in treatment: 1780747 INFO @ Fri, 16 Oct 2020 09:19:51: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:19:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:19:51: #1 tags after filtering in treatment: 1595992 INFO @ Fri, 16 Oct 2020 09:19:51: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Oct 2020 09:19:51: #1 finished! INFO @ Fri, 16 Oct 2020 09:19:51: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:19:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:19:51: #2 number of paired peaks: 55 WARNING @ Fri, 16 Oct 2020 09:19:51: Too few paired peaks (55) 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 @ Fri, 16 Oct 2020 09:19:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.05_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/SRX8952608/SRX8952608.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 09:19:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.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 @ Fri, 16 Oct 2020 09:19:55: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:19:55: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:20:00: 1000000 INFO @ Fri, 16 Oct 2020 09:20:05: 2000000 INFO @ Fri, 16 Oct 2020 09:20:10: 3000000 INFO @ Fri, 16 Oct 2020 09:20:16: 4000000 INFO @ Fri, 16 Oct 2020 09:20:21: #1 tag size is determined as 40 bps INFO @ Fri, 16 Oct 2020 09:20:21: #1 tag size = 40 INFO @ Fri, 16 Oct 2020 09:20:21: #1 total tags in treatment: 1780747 INFO @ Fri, 16 Oct 2020 09:20:21: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:20:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:20:21: #1 tags after filtering in treatment: 1595992 INFO @ Fri, 16 Oct 2020 09:20:21: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Oct 2020 09:20:21: #1 finished! INFO @ Fri, 16 Oct 2020 09:20:21: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:20:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:20:21: #2 number of paired peaks: 55 WARNING @ Fri, 16 Oct 2020 09:20:21: Too few paired peaks (55) 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 @ Fri, 16 Oct 2020 09:20:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.10_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/SRX8952608/SRX8952608.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 09:20:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.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 @ Fri, 16 Oct 2020 09:20:25: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:20:25: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:20:31: 1000000 INFO @ Fri, 16 Oct 2020 09:20:36: 2000000 INFO @ Fri, 16 Oct 2020 09:20:42: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:20:48: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:20:53: #1 tag size is determined as 40 bps INFO @ Fri, 16 Oct 2020 09:20:53: #1 tag size = 40 INFO @ Fri, 16 Oct 2020 09:20:53: #1 total tags in treatment: 1780747 INFO @ Fri, 16 Oct 2020 09:20:53: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:20:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:20:53: #1 tags after filtering in treatment: 1595992 INFO @ Fri, 16 Oct 2020 09:20:53: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Oct 2020 09:20:53: #1 finished! INFO @ Fri, 16 Oct 2020 09:20:53: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:20:53: #2 number of paired peaks: 55 WARNING @ Fri, 16 Oct 2020 09:20:53: Too few paired peaks (55) 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 @ Fri, 16 Oct 2020 09:20:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.20_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/SRX8952608/SRX8952608.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8952608/SRX8952608.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling