Job ID = 14521848 SRX = SRX9399091 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8879908 spots for SRR12935372/SRR12935372.sra Written 8879908 spots for SRR12935372/SRR12935372.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: 00:04:20 8879908 reads; of these: 8879908 (100.00%) were paired; of these: 1817595 (20.47%) aligned concordantly 0 times 5549756 (62.50%) aligned concordantly exactly 1 time 1512557 (17.03%) aligned concordantly >1 times ---- 1817595 pairs aligned concordantly 0 times; of these: 61884 (3.40%) aligned discordantly 1 time ---- 1755711 pairs aligned 0 times concordantly or discordantly; of these: 3511422 mates make up the pairs; of these: 3353203 (95.49%) aligned 0 times 100800 (2.87%) aligned exactly 1 time 57419 (1.64%) aligned >1 times 81.12% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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_sort_core] merging from 8 files... [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] 3138148 / 7111884 = 0.4413 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 21:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.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 21:50:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:50:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:50:12: 1000000 INFO @ Sat, 15 Jan 2022 21:50:17: 2000000 INFO @ Sat, 15 Jan 2022 21:50:21: 3000000 INFO @ Sat, 15 Jan 2022 21:50:26: 4000000 INFO @ Sat, 15 Jan 2022 21:50:30: 5000000 INFO @ Sat, 15 Jan 2022 21:50:35: 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 21:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.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 21:50:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:50:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:50:40: 7000000 INFO @ Sat, 15 Jan 2022 21:50:44: 1000000 INFO @ Sat, 15 Jan 2022 21:50:45: 8000000 INFO @ Sat, 15 Jan 2022 21:50:45: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:50:45: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:50:45: #1 total tags in treatment: 3933993 INFO @ Sat, 15 Jan 2022 21:50:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:50:45: #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 21:50:46: #1 tags after filtering in treatment: 2706858 INFO @ Sat, 15 Jan 2022 21:50:46: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 21:50:46: #1 finished! INFO @ Sat, 15 Jan 2022 21:50:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:50:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:50:46: #2 number of paired peaks: 26 WARNING @ Sat, 15 Jan 2022 21:50:46: Too few paired peaks (26) 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 21:50:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.05_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/SRX9399091/SRX9399091.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:50:49: 2000000 INFO @ Sat, 15 Jan 2022 21:50:55: 3000000 INFO @ Sat, 15 Jan 2022 21:51:01: 4000000 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 21:51:06: 5000000 INFO @ Sat, 15 Jan 2022 21:51:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.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 21:51:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:51:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:51:12: 6000000 INFO @ Sat, 15 Jan 2022 21:51:14: 1000000 INFO @ Sat, 15 Jan 2022 21:51:18: 7000000 INFO @ Sat, 15 Jan 2022 21:51:20: 2000000 INFO @ Sat, 15 Jan 2022 21:51:24: 8000000 INFO @ Sat, 15 Jan 2022 21:51:24: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:51:24: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:51:24: #1 total tags in treatment: 3933993 INFO @ Sat, 15 Jan 2022 21:51:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:51:24: #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 21:51:25: #1 tags after filtering in treatment: 2706858 INFO @ Sat, 15 Jan 2022 21:51:25: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 21:51:25: #1 finished! INFO @ Sat, 15 Jan 2022 21:51:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:51:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:51:25: #2 number of paired peaks: 26 WARNING @ Sat, 15 Jan 2022 21:51:25: Too few paired peaks (26) 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 21:51:25: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.10_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/SRX9399091/SRX9399091.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:51:26: 3000000 INFO @ Sat, 15 Jan 2022 21:51:31: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:51:37: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:51:42: 6000000 INFO @ Sat, 15 Jan 2022 21:51:48: 7000000 INFO @ Sat, 15 Jan 2022 21:51:53: 8000000 INFO @ Sat, 15 Jan 2022 21:51:54: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 21:51:54: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 21:51:54: #1 total tags in treatment: 3933993 INFO @ Sat, 15 Jan 2022 21:51:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:51:54: #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 21:51:54: #1 tags after filtering in treatment: 2706858 INFO @ Sat, 15 Jan 2022 21:51:54: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Jan 2022 21:51:54: #1 finished! INFO @ Sat, 15 Jan 2022 21:51:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:51:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:51:54: #2 number of paired peaks: 26 WARNING @ Sat, 15 Jan 2022 21:51:54: Too few paired peaks (26) 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 21:51:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.20_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/SRX9399091/SRX9399091.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399091/SRX9399091.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling