Job ID = 7118078 SRX = SRX8639574 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T07:10:16 prefetch.2.10.7: 1) Downloading 'SRR12117012'... 2020-07-22T07:10:16 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T07:12:13 prefetch.2.10.7: HTTPS download succeed 2020-07-22T07:12:13 prefetch.2.10.7: 1) 'SRR12117012' was downloaded successfully 2020-07-22T07:12:13 prefetch.2.10.7: 'SRR12117012' has 0 unresolved dependencies Read 24097889 spots for SRR12117012/SRR12117012.sra Written 24097889 spots for SRR12117012/SRR12117012.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: 00:05:07 24097889 reads; of these: 24097889 (100.00%) were paired; of these: 18254603 (75.75%) aligned concordantly 0 times 5272662 (21.88%) aligned concordantly exactly 1 time 570624 (2.37%) aligned concordantly >1 times ---- 18254603 pairs aligned concordantly 0 times; of these: 51244 (0.28%) aligned discordantly 1 time ---- 18203359 pairs aligned 0 times concordantly or discordantly; of these: 36406718 mates make up the pairs; of these: 36283015 (99.66%) aligned 0 times 95486 (0.26%) aligned exactly 1 time 28217 (0.08%) aligned >1 times 24.72% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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] 57905 / 5890719 = 0.0098 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 16:22:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.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 16:22:09: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:22:09: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:22:15: 1000000 INFO @ Wed, 22 Jul 2020 16:22:20: 2000000 INFO @ Wed, 22 Jul 2020 16:22:25: 3000000 INFO @ Wed, 22 Jul 2020 16:22:30: 4000000 INFO @ Wed, 22 Jul 2020 16:22:35: 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 16:22:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.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 16:22:39: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:22:39: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:22:40: 6000000 INFO @ Wed, 22 Jul 2020 16:22:46: 1000000 INFO @ Wed, 22 Jul 2020 16:22:46: 7000000 INFO @ Wed, 22 Jul 2020 16:22:52: 2000000 INFO @ Wed, 22 Jul 2020 16:22:52: 8000000 INFO @ Wed, 22 Jul 2020 16:22:58: 3000000 INFO @ Wed, 22 Jul 2020 16:22:58: 9000000 INFO @ Wed, 22 Jul 2020 16:23:04: 4000000 INFO @ Wed, 22 Jul 2020 16:23:04: 10000000 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 16:23:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.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 16:23:09: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:23:09: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:23:10: 5000000 INFO @ Wed, 22 Jul 2020 16:23:10: 11000000 INFO @ Wed, 22 Jul 2020 16:23:15: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:23:15: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:23:15: #1 total tags in treatment: 5785413 INFO @ Wed, 22 Jul 2020 16:23:15: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:23:15: #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 16:23:15: #1 tags after filtering in treatment: 4562274 INFO @ Wed, 22 Jul 2020 16:23:15: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 16:23:15: #1 finished! INFO @ Wed, 22 Jul 2020 16:23:15: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:23:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:23:15: #2 number of paired peaks: 2 WARNING @ Wed, 22 Jul 2020 16:23:15: Too few paired peaks (2) 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 16:23:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.05_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/SRX8639574/SRX8639574.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:23:16: 1000000 INFO @ Wed, 22 Jul 2020 16:23:16: 6000000 INFO @ Wed, 22 Jul 2020 16:23:22: 2000000 INFO @ Wed, 22 Jul 2020 16:23:22: 7000000 INFO @ Wed, 22 Jul 2020 16:23:28: 3000000 INFO @ Wed, 22 Jul 2020 16:23:28: 8000000 INFO @ Wed, 22 Jul 2020 16:23:34: 4000000 INFO @ Wed, 22 Jul 2020 16:23:34: 9000000 INFO @ Wed, 22 Jul 2020 16:23:40: 5000000 INFO @ Wed, 22 Jul 2020 16:23:40: 10000000 INFO @ Wed, 22 Jul 2020 16:23:46: 6000000 INFO @ Wed, 22 Jul 2020 16:23:46: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:23:51: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:23:51: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:23:51: #1 total tags in treatment: 5785413 INFO @ Wed, 22 Jul 2020 16:23:51: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:23:51: #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 16:23:51: #1 tags after filtering in treatment: 4562274 INFO @ Wed, 22 Jul 2020 16:23:51: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 16:23:51: #1 finished! INFO @ Wed, 22 Jul 2020 16:23:51: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:23:51: #2 number of paired peaks: 2 WARNING @ Wed, 22 Jul 2020 16:23:51: Too few paired peaks (2) 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 16:23:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.10_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/SRX8639574/SRX8639574.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:23:52: 7000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:23:57: 8000000 INFO @ Wed, 22 Jul 2020 16:24:03: 9000000 INFO @ Wed, 22 Jul 2020 16:24:08: 10000000 INFO @ Wed, 22 Jul 2020 16:24:14: 11000000 INFO @ Wed, 22 Jul 2020 16:24:18: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:24:18: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:24:18: #1 total tags in treatment: 5785413 INFO @ Wed, 22 Jul 2020 16:24:18: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:24:18: #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 16:24:18: #1 tags after filtering in treatment: 4562274 INFO @ Wed, 22 Jul 2020 16:24:18: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Jul 2020 16:24:18: #1 finished! INFO @ Wed, 22 Jul 2020 16:24:18: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:24:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:24:18: #2 number of paired peaks: 2 WARNING @ Wed, 22 Jul 2020 16:24:18: Too few paired peaks (2) 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 16:24:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.20_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/SRX8639574/SRX8639574.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639574/SRX8639574.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling