Job ID = 14522140 SRX = SRX9067155 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4273155 spots for SRR12580308/SRR12580308.sra Written 4273155 spots for SRR12580308/SRR12580308.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: 00:02:48 4273155 reads; of these: 4273155 (100.00%) were paired; of these: 769428 (18.01%) aligned concordantly 0 times 3030652 (70.92%) aligned concordantly exactly 1 time 473075 (11.07%) aligned concordantly >1 times ---- 769428 pairs aligned concordantly 0 times; of these: 120829 (15.70%) aligned discordantly 1 time ---- 648599 pairs aligned 0 times concordantly or discordantly; of these: 1297198 mates make up the pairs; of these: 1041184 (80.26%) aligned 0 times 191394 (14.75%) aligned exactly 1 time 64620 (4.98%) aligned >1 times 87.82% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 302711 / 3545303 = 0.0854 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 22:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.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 22:19:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:19:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:19:30: 1000000 INFO @ Sat, 15 Jan 2022 22:19:38: 2000000 INFO @ Sat, 15 Jan 2022 22:19:45: 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 22:19:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.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 22:19:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:19:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:19:53: 4000000 INFO @ Sat, 15 Jan 2022 22:20:01: 5000000 INFO @ Sat, 15 Jan 2022 22:20:02: 1000000 INFO @ Sat, 15 Jan 2022 22:20:09: 6000000 INFO @ Sat, 15 Jan 2022 22:20:13: 2000000 INFO @ Sat, 15 Jan 2022 22:20:15: #1 tag size is determined as 35 bps INFO @ Sat, 15 Jan 2022 22:20:15: #1 tag size = 35 INFO @ Sat, 15 Jan 2022 22:20:15: #1 total tags in treatment: 3201979 INFO @ Sat, 15 Jan 2022 22:20:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:20:15: #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 22:20:16: #1 tags after filtering in treatment: 2384625 INFO @ Sat, 15 Jan 2022 22:20:16: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 22:20:16: #1 finished! INFO @ Sat, 15 Jan 2022 22:20:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:20:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:20:16: #2 number of paired peaks: 25 WARNING @ Sat, 15 Jan 2022 22:20:16: Too few paired peaks (25) 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 22:20:16: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.05_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/SRX9067155/SRX9067155.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.05_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 22:20:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.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 22:20:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:20:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:20:24: 3000000 INFO @ Sat, 15 Jan 2022 22:20:34: 1000000 INFO @ Sat, 15 Jan 2022 22:20:34: 4000000 INFO @ Sat, 15 Jan 2022 22:20:43: 5000000 INFO @ Sat, 15 Jan 2022 22:20:46: 2000000 INFO @ Sat, 15 Jan 2022 22:20:52: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:20:57: 3000000 INFO @ Sat, 15 Jan 2022 22:20:59: #1 tag size is determined as 35 bps INFO @ Sat, 15 Jan 2022 22:20:59: #1 tag size = 35 INFO @ Sat, 15 Jan 2022 22:20:59: #1 total tags in treatment: 3201979 INFO @ Sat, 15 Jan 2022 22:20:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:20:59: #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 22:20:59: #1 tags after filtering in treatment: 2384625 INFO @ Sat, 15 Jan 2022 22:20:59: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 22:20:59: #1 finished! INFO @ Sat, 15 Jan 2022 22:20:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:20:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:21:00: #2 number of paired peaks: 25 WARNING @ Sat, 15 Jan 2022 22:21:00: Too few paired peaks (25) 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 22:21:00: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.10_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/SRX9067155/SRX9067155.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:21:09: 4000000 INFO @ Sat, 15 Jan 2022 22:21:20: 5000000 INFO @ Sat, 15 Jan 2022 22:21:32: 6000000 INFO @ Sat, 15 Jan 2022 22:21:42: #1 tag size is determined as 35 bps INFO @ Sat, 15 Jan 2022 22:21:42: #1 tag size = 35 INFO @ Sat, 15 Jan 2022 22:21:42: #1 total tags in treatment: 3201979 INFO @ Sat, 15 Jan 2022 22:21:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:21:42: #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 22:21:42: #1 tags after filtering in treatment: 2384625 INFO @ Sat, 15 Jan 2022 22:21:42: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 22:21:42: #1 finished! INFO @ Sat, 15 Jan 2022 22:21:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:21:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:21:42: #2 number of paired peaks: 25 WARNING @ Sat, 15 Jan 2022 22:21:42: Too few paired peaks (25) 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 22:21:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.20_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/SRX9067155/SRX9067155.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9067155/SRX9067155.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling