Job ID = 14521569 SRX = SRX9493772 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4027430 spots for SRR13043894/SRR13043894.sra Written 4027430 spots for SRR13043894/SRR13043894.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: 00:04:14 4027430 reads; of these: 4027430 (100.00%) were paired; of these: 187685 (4.66%) aligned concordantly 0 times 3028014 (75.18%) aligned concordantly exactly 1 time 811731 (20.16%) aligned concordantly >1 times ---- 187685 pairs aligned concordantly 0 times; of these: 38650 (20.59%) aligned discordantly 1 time ---- 149035 pairs aligned 0 times concordantly or discordantly; of these: 298070 mates make up the pairs; of these: 198310 (66.53%) aligned 0 times 62945 (21.12%) aligned exactly 1 time 36815 (12.35%) aligned >1 times 97.54% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 145682 / 3859919 = 0.0377 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 21:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.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 21:20:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:20:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:20:22: 1000000 INFO @ Sat, 15 Jan 2022 21:20:30: 2000000 INFO @ Sat, 15 Jan 2022 21:20:37: 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 21:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.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 21:20:44: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:20:44: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:20:45: 4000000 INFO @ Sat, 15 Jan 2022 21:20:53: 5000000 INFO @ Sat, 15 Jan 2022 21:20:53: 1000000 INFO @ Sat, 15 Jan 2022 21:21:00: 6000000 INFO @ Sat, 15 Jan 2022 21:21:02: 2000000 INFO @ Sat, 15 Jan 2022 21:21:08: 7000000 INFO @ Sat, 15 Jan 2022 21:21:11: 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 21:21:13: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 21:21:13: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 21:21:13: #1 total tags in treatment: 3694474 INFO @ Sat, 15 Jan 2022 21:21:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:21:13: #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 21:21:13: #1 tags after filtering in treatment: 2879175 INFO @ Sat, 15 Jan 2022 21:21:13: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 21:21:13: #1 finished! INFO @ Sat, 15 Jan 2022 21:21:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:21:13: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 21:21:13: 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 21:21:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.05_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/SRX9493772/SRX9493772.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:21:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.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 21:21:14: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:21:14: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:21:20: 4000000 INFO @ Sat, 15 Jan 2022 21:21:23: 1000000 INFO @ Sat, 15 Jan 2022 21:21:28: 5000000 INFO @ Sat, 15 Jan 2022 21:21:31: 2000000 INFO @ Sat, 15 Jan 2022 21:21:37: 6000000 INFO @ Sat, 15 Jan 2022 21:21:39: 3000000 INFO @ Sat, 15 Jan 2022 21:21:46: 7000000 INFO @ Sat, 15 Jan 2022 21:21:47: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:21:50: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 21:21:50: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 21:21:50: #1 total tags in treatment: 3694474 INFO @ Sat, 15 Jan 2022 21:21:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:21:50: #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 21:21:51: #1 tags after filtering in treatment: 2879175 INFO @ Sat, 15 Jan 2022 21:21:51: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 21:21:51: #1 finished! INFO @ Sat, 15 Jan 2022 21:21:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:21:51: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 21:21:51: 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 21:21:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.10_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/SRX9493772/SRX9493772.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:21:55: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:22:03: 6000000 INFO @ Sat, 15 Jan 2022 21:22:11: 7000000 INFO @ Sat, 15 Jan 2022 21:22:15: #1 tag size is determined as 80 bps INFO @ Sat, 15 Jan 2022 21:22:15: #1 tag size = 80 INFO @ Sat, 15 Jan 2022 21:22:15: #1 total tags in treatment: 3694474 INFO @ Sat, 15 Jan 2022 21:22:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:22:15: #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 21:22:15: #1 tags after filtering in treatment: 2879175 INFO @ Sat, 15 Jan 2022 21:22:15: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 21:22:15: #1 finished! INFO @ Sat, 15 Jan 2022 21:22:15: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:22:16: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 21:22:16: 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 21:22:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.20_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/SRX9493772/SRX9493772.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9493772/SRX9493772.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling