Job ID = 14519804 SRX = SRX9369647 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4290163 spots for SRR12904760/SRR12904760.sra Written 4290163 spots for SRR12904760/SRR12904760.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: 00:03:28 4290163 reads; of these: 4290163 (100.00%) were paired; of these: 878775 (20.48%) aligned concordantly 0 times 2931309 (68.33%) aligned concordantly exactly 1 time 480079 (11.19%) aligned concordantly >1 times ---- 878775 pairs aligned concordantly 0 times; of these: 108758 (12.38%) aligned discordantly 1 time ---- 770017 pairs aligned 0 times concordantly or discordantly; of these: 1540034 mates make up the pairs; of these: 1473944 (95.71%) aligned 0 times 26210 (1.70%) aligned exactly 1 time 39880 (2.59%) aligned >1 times 82.82% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 437632 / 3505716 = 0.1248 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 17:52:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.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 17:52:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:52:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:52:39: 1000000 INFO @ Sat, 15 Jan 2022 17:52:44: 2000000 INFO @ Sat, 15 Jan 2022 17:52:49: 3000000 INFO @ Sat, 15 Jan 2022 17:52:54: 4000000 INFO @ Sat, 15 Jan 2022 17:53:00: 5000000 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 17:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.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 17:53:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:53:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:53:05: 6000000 INFO @ Sat, 15 Jan 2022 17:53:07: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 17:53:07: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 17:53:07: #1 total tags in treatment: 2982086 INFO @ Sat, 15 Jan 2022 17:53:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:53:07: #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 17:53:07: #1 tags after filtering in treatment: 2159926 INFO @ Sat, 15 Jan 2022 17:53:07: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 17:53:07: #1 finished! INFO @ Sat, 15 Jan 2022 17:53:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:53:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:53:07: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 17:53:07: 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 17:53:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.05_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/SRX9369647/SRX9369647.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:53:09: 1000000 INFO @ Sat, 15 Jan 2022 17:53:14: 2000000 INFO @ Sat, 15 Jan 2022 17:53:19: 3000000 INFO @ Sat, 15 Jan 2022 17:53:25: 4000000 INFO @ Sat, 15 Jan 2022 17:53:30: 5000000 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 17:53:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.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 17:53:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:53:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:53:36: 6000000 INFO @ Sat, 15 Jan 2022 17:53:37: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 17:53:37: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 17:53:37: #1 total tags in treatment: 2982086 INFO @ Sat, 15 Jan 2022 17:53:37: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:53:37: #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 17:53:38: #1 tags after filtering in treatment: 2159926 INFO @ Sat, 15 Jan 2022 17:53:38: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 17:53:38: #1 finished! INFO @ Sat, 15 Jan 2022 17:53:38: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:53:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:53:38: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 17:53:38: 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 17:53:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.10_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/SRX9369647/SRX9369647.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:53:39: 1000000 INFO @ Sat, 15 Jan 2022 17:53:44: 2000000 INFO @ Sat, 15 Jan 2022 17:53:50: 3000000 INFO @ Sat, 15 Jan 2022 17:53:55: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:54:00: 5000000 INFO @ Sat, 15 Jan 2022 17:54:06: 6000000 INFO @ Sat, 15 Jan 2022 17:54:07: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 17:54:07: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 17:54:07: #1 total tags in treatment: 2982086 INFO @ Sat, 15 Jan 2022 17:54:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:54:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:54:07: #1 tags after filtering in treatment: 2159926 INFO @ Sat, 15 Jan 2022 17:54:07: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 17:54:07: #1 finished! INFO @ Sat, 15 Jan 2022 17:54:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:54:07: #2 number of paired peaks: 31 WARNING @ Sat, 15 Jan 2022 17:54:07: 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 17:54:07: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.20_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/SRX9369647/SRX9369647.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX9369647/SRX9369647.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling