Job ID = 7117988 SRX = SRX8639564 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T07:02:15 prefetch.2.10.7: 1) Downloading 'SRR12117002'... 2020-07-22T07:02:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T07:04:32 prefetch.2.10.7: HTTPS download succeed 2020-07-22T07:04:32 prefetch.2.10.7: 1) 'SRR12117002' was downloaded successfully 2020-07-22T07:04:32 prefetch.2.10.7: 'SRR12117002' has 0 unresolved dependencies Read 23269868 spots for SRR12117002/SRR12117002.sra Written 23269868 spots for SRR12117002/SRR12117002.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: 00:06:57 23269868 reads; of these: 23269868 (100.00%) were paired; of these: 14495495 (62.29%) aligned concordantly 0 times 7962347 (34.22%) aligned concordantly exactly 1 time 812026 (3.49%) aligned concordantly >1 times ---- 14495495 pairs aligned concordantly 0 times; of these: 245725 (1.70%) aligned discordantly 1 time ---- 14249770 pairs aligned 0 times concordantly or discordantly; of these: 28499540 mates make up the pairs; of these: 28259190 (99.16%) aligned 0 times 167494 (0.59%) aligned exactly 1 time 72856 (0.26%) aligned >1 times 39.28% overall alignment rate Time searching: 00:06:57 Overall time: 00:06:57 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_sort_core] merging from 8 files... [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] 99669 / 8993637 = 0.0111 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 16:17:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.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 @ Wed, 22 Jul 2020 16:17:41: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:17:41: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:17:47: 1000000 INFO @ Wed, 22 Jul 2020 16:17:52: 2000000 INFO @ Wed, 22 Jul 2020 16:17:57: 3000000 INFO @ Wed, 22 Jul 2020 16:18:02: 4000000 INFO @ Wed, 22 Jul 2020 16:18:07: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 16:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.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 @ Wed, 22 Jul 2020 16:18:11: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:18:11: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:18:12: 6000000 INFO @ Wed, 22 Jul 2020 16:18:17: 7000000 INFO @ Wed, 22 Jul 2020 16:18:18: 1000000 INFO @ Wed, 22 Jul 2020 16:18:23: 8000000 INFO @ Wed, 22 Jul 2020 16:18:24: 2000000 INFO @ Wed, 22 Jul 2020 16:18:29: 9000000 INFO @ Wed, 22 Jul 2020 16:18:31: 3000000 INFO @ Wed, 22 Jul 2020 16:18:35: 10000000 INFO @ Wed, 22 Jul 2020 16:18:37: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 16:18:40: 11000000 INFO @ Wed, 22 Jul 2020 16:18:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.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 @ Wed, 22 Jul 2020 16:18:41: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:18:41: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:18:43: 5000000 INFO @ Wed, 22 Jul 2020 16:18:46: 12000000 INFO @ Wed, 22 Jul 2020 16:18:47: 1000000 INFO @ Wed, 22 Jul 2020 16:18:50: 6000000 INFO @ Wed, 22 Jul 2020 16:18:52: 13000000 INFO @ Wed, 22 Jul 2020 16:18:53: 2000000 INFO @ Wed, 22 Jul 2020 16:18:56: 7000000 INFO @ Wed, 22 Jul 2020 16:18:58: 14000000 INFO @ Wed, 22 Jul 2020 16:18:59: 3000000 INFO @ Wed, 22 Jul 2020 16:19:02: 8000000 INFO @ Wed, 22 Jul 2020 16:19:04: 15000000 INFO @ Wed, 22 Jul 2020 16:19:05: 4000000 INFO @ Wed, 22 Jul 2020 16:19:09: 9000000 INFO @ Wed, 22 Jul 2020 16:19:10: 16000000 INFO @ Wed, 22 Jul 2020 16:19:11: 5000000 INFO @ Wed, 22 Jul 2020 16:19:15: 10000000 INFO @ Wed, 22 Jul 2020 16:19:16: 17000000 INFO @ Wed, 22 Jul 2020 16:19:17: 6000000 INFO @ Wed, 22 Jul 2020 16:19:21: 11000000 INFO @ Wed, 22 Jul 2020 16:19:22: 18000000 INFO @ Wed, 22 Jul 2020 16:19:22: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:19:22: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:19:22: #1 total tags in treatment: 8675834 INFO @ Wed, 22 Jul 2020 16:19:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:19:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:19:22: #1 tags after filtering in treatment: 6113114 INFO @ Wed, 22 Jul 2020 16:19:22: #1 Redundant rate of treatment: 0.30 INFO @ Wed, 22 Jul 2020 16:19:22: #1 finished! INFO @ Wed, 22 Jul 2020 16:19:22: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:19:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:19:23: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:19:23: Too few paired peaks (0) 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 @ Wed, 22 Jul 2020 16:19:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.05_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/SRX8639564/SRX8639564.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:19:23: 7000000 INFO @ Wed, 22 Jul 2020 16:19:27: 12000000 INFO @ Wed, 22 Jul 2020 16:19:29: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:19:34: 13000000 INFO @ Wed, 22 Jul 2020 16:19:35: 9000000 INFO @ Wed, 22 Jul 2020 16:19:40: 14000000 INFO @ Wed, 22 Jul 2020 16:19:41: 10000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:19:46: 15000000 INFO @ Wed, 22 Jul 2020 16:19:47: 11000000 INFO @ Wed, 22 Jul 2020 16:19:52: 16000000 INFO @ Wed, 22 Jul 2020 16:19:53: 12000000 INFO @ Wed, 22 Jul 2020 16:19:58: 17000000 INFO @ Wed, 22 Jul 2020 16:19:59: 13000000 INFO @ Wed, 22 Jul 2020 16:20:05: 18000000 INFO @ Wed, 22 Jul 2020 16:20:05: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:20:05: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:20:05: #1 total tags in treatment: 8675834 INFO @ Wed, 22 Jul 2020 16:20:05: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:20:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:20:05: #1 tags after filtering in treatment: 6113114 INFO @ Wed, 22 Jul 2020 16:20:05: #1 Redundant rate of treatment: 0.30 INFO @ Wed, 22 Jul 2020 16:20:05: #1 finished! INFO @ Wed, 22 Jul 2020 16:20:05: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:20:05: 14000000 INFO @ Wed, 22 Jul 2020 16:20:06: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:20:06: Too few paired peaks (0) 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 @ Wed, 22 Jul 2020 16:20:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.10_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/SRX8639564/SRX8639564.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:20:11: 15000000 INFO @ Wed, 22 Jul 2020 16:20:16: 16000000 INFO @ Wed, 22 Jul 2020 16:20:22: 17000000 INFO @ Wed, 22 Jul 2020 16:20:27: 18000000 INFO @ Wed, 22 Jul 2020 16:20:28: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:20:28: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:20:28: #1 total tags in treatment: 8675834 INFO @ Wed, 22 Jul 2020 16:20:28: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:20:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:20:28: #1 tags after filtering in treatment: 6113114 INFO @ Wed, 22 Jul 2020 16:20:28: #1 Redundant rate of treatment: 0.30 INFO @ Wed, 22 Jul 2020 16:20:28: #1 finished! INFO @ Wed, 22 Jul 2020 16:20:28: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:20:28: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:20:28: Too few paired peaks (0) 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 @ Wed, 22 Jul 2020 16:20:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.20_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/SRX8639564/SRX8639564.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639564/SRX8639564.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling