Job ID = 14522072 SRX = SRX9067223 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5532425 spots for SRR12580376/SRR12580376.sra Written 5532425 spots for SRR12580376/SRR12580376.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: 00:02:40 5532425 reads; of these: 5532425 (100.00%) were paired; of these: 1261543 (22.80%) aligned concordantly 0 times 3582838 (64.76%) aligned concordantly exactly 1 time 688044 (12.44%) aligned concordantly >1 times ---- 1261543 pairs aligned concordantly 0 times; of these: 133984 (10.62%) aligned discordantly 1 time ---- 1127559 pairs aligned 0 times concordantly or discordantly; of these: 2255118 mates make up the pairs; of these: 2068473 (91.72%) aligned 0 times 122034 (5.41%) aligned exactly 1 time 64611 (2.87%) aligned >1 times 81.31% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 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] 746017 / 4358638 = 0.1712 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 22:11:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.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 22:11:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:11:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:11:53: 1000000 INFO @ Sat, 15 Jan 2022 22:11:58: 2000000 INFO @ Sat, 15 Jan 2022 22:12:02: 3000000 INFO @ Sat, 15 Jan 2022 22:12:06: 4000000 INFO @ Sat, 15 Jan 2022 22:12:10: 5000000 INFO @ Sat, 15 Jan 2022 22:12:14: 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 22:12:18: 7000000 INFO @ Sat, 15 Jan 2022 22:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.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 22:12:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:12:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:12:21: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 22:12:21: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 22:12:21: #1 total tags in treatment: 3532810 INFO @ Sat, 15 Jan 2022 22:12:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:12:21: #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 22:12:21: #1 tags after filtering in treatment: 2510156 INFO @ Sat, 15 Jan 2022 22:12:21: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 22:12:21: #1 finished! INFO @ Sat, 15 Jan 2022 22:12:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:12:21: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 22:12:21: 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 22:12:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.05_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/SRX9067223/SRX9067223.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:12:24: 1000000 INFO @ Sat, 15 Jan 2022 22:12:28: 2000000 INFO @ Sat, 15 Jan 2022 22:12:32: 3000000 INFO @ Sat, 15 Jan 2022 22:12:36: 4000000 INFO @ Sat, 15 Jan 2022 22:12:40: 5000000 INFO @ Sat, 15 Jan 2022 22:12:45: 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 22:12:49: 7000000 INFO @ Sat, 15 Jan 2022 22:12:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.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 22:12:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:12:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:12:51: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 22:12:51: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 22:12:51: #1 total tags in treatment: 3532810 INFO @ Sat, 15 Jan 2022 22:12:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:12:51: #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 22:12:51: #1 tags after filtering in treatment: 2510156 INFO @ Sat, 15 Jan 2022 22:12:51: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 22:12:51: #1 finished! INFO @ Sat, 15 Jan 2022 22:12:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:12:51: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 22:12:51: 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 22:12:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.10_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/SRX9067223/SRX9067223.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:12:55: 1000000 INFO @ Sat, 15 Jan 2022 22:13:00: 2000000 INFO @ Sat, 15 Jan 2022 22:13:05: 3000000 INFO @ Sat, 15 Jan 2022 22:13:10: 4000000 INFO @ Sat, 15 Jan 2022 22:13:15: 5000000 INFO @ Sat, 15 Jan 2022 22:13:20: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:13:24: 7000000 INFO @ Sat, 15 Jan 2022 22:13:27: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 22:13:27: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 22:13:27: #1 total tags in treatment: 3532810 INFO @ Sat, 15 Jan 2022 22:13:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:13:27: #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 22:13:27: #1 tags after filtering in treatment: 2510156 INFO @ Sat, 15 Jan 2022 22:13:27: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 22:13:27: #1 finished! INFO @ Sat, 15 Jan 2022 22:13:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:13:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:13:27: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 22:13:27: 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 22:13:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.20_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/SRX9067223/SRX9067223.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067223/SRX9067223.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。