Job ID = 14521755 SRX = SRX9399055 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4843818 spots for SRR12935336/SRR12935336.sra Written 4843818 spots for SRR12935336/SRR12935336.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: 00:03:27 4843818 reads; of these: 4843818 (100.00%) were paired; of these: 718011 (14.82%) aligned concordantly 0 times 3639549 (75.14%) aligned concordantly exactly 1 time 486258 (10.04%) aligned concordantly >1 times ---- 718011 pairs aligned concordantly 0 times; of these: 152713 (21.27%) aligned discordantly 1 time ---- 565298 pairs aligned 0 times concordantly or discordantly; of these: 1130596 mates make up the pairs; of these: 859636 (76.03%) aligned 0 times 207096 (18.32%) aligned exactly 1 time 63864 (5.65%) aligned >1 times 91.13% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 303909 / 4220158 = 0.0720 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 21:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.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 21:38:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:38:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:39:03: 1000000 INFO @ Sat, 15 Jan 2022 21:39:10: 2000000 INFO @ Sat, 15 Jan 2022 21:39:17: 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 21:39:24: 4000000 INFO @ Sat, 15 Jan 2022 21:39:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.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 21:39:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:39:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:39:31: 5000000 INFO @ Sat, 15 Jan 2022 21:39:32: 1000000 INFO @ Sat, 15 Jan 2022 21:39:37: 6000000 INFO @ Sat, 15 Jan 2022 21:39:38: 2000000 INFO @ Sat, 15 Jan 2022 21:39:44: 7000000 INFO @ Sat, 15 Jan 2022 21:39:44: 3000000 INFO @ Sat, 15 Jan 2022 21:39:50: 8000000 INFO @ Sat, 15 Jan 2022 21:39:51: 4000000 INFO @ Sat, 15 Jan 2022 21:39:51: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 21:39:51: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 21:39:51: #1 total tags in treatment: 3824539 INFO @ Sat, 15 Jan 2022 21:39:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:39:51: #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 21:39:52: #1 tags after filtering in treatment: 2773417 INFO @ Sat, 15 Jan 2022 21:39:52: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:39:52: #1 finished! INFO @ Sat, 15 Jan 2022 21:39:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:39:52: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:39:52: 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 21:39:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 21:39:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.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 21:39:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:39:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:39:57: 5000000 INFO @ Sat, 15 Jan 2022 21:40:01: 1000000 INFO @ Sat, 15 Jan 2022 21:40:03: 6000000 INFO @ Sat, 15 Jan 2022 21:40:08: 2000000 INFO @ Sat, 15 Jan 2022 21:40:09: 7000000 INFO @ Sat, 15 Jan 2022 21:40:14: 3000000 INFO @ Sat, 15 Jan 2022 21:40:15: 8000000 INFO @ Sat, 15 Jan 2022 21:40:17: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 21:40:17: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 21:40:17: #1 total tags in treatment: 3824539 INFO @ Sat, 15 Jan 2022 21:40:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:40:17: #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 21:40:17: #1 tags after filtering in treatment: 2773417 INFO @ Sat, 15 Jan 2022 21:40:17: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:40:17: #1 finished! INFO @ Sat, 15 Jan 2022 21:40:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:40:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:40:17: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:40:17: 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 21:40:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:40:21: 4000000 INFO @ Sat, 15 Jan 2022 21:40:27: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:40:33: 6000000 INFO @ Sat, 15 Jan 2022 21:40:40: 7000000 INFO @ Sat, 15 Jan 2022 21:40:46: 8000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:40:48: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 21:40:48: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 21:40:48: #1 total tags in treatment: 3824539 INFO @ Sat, 15 Jan 2022 21:40:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:40:48: #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 21:40:48: #1 tags after filtering in treatment: 2773417 INFO @ Sat, 15 Jan 2022 21:40:48: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:40:48: #1 finished! INFO @ Sat, 15 Jan 2022 21:40:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:40:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:40:48: #2 number of paired peaks: 3 WARNING @ Sat, 15 Jan 2022 21:40:48: 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 21:40:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.20_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/SRX9399055/SRX9399055.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9399055/SRX9399055.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling