Job ID = 7118150 SRX = SRX8639577 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T07:11:04 prefetch.2.10.7: 1) Downloading 'SRR12117015'... 2020-07-22T07:11:04 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T07:12:46 prefetch.2.10.7: HTTPS download succeed 2020-07-22T07:12:46 prefetch.2.10.7: 1) 'SRR12117015' was downloaded successfully 2020-07-22T07:12:46 prefetch.2.10.7: 'SRR12117015' has 0 unresolved dependencies Read 23936357 spots for SRR12117015/SRR12117015.sra Written 23936357 spots for SRR12117015/SRR12117015.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: 00:07:51 23936357 reads; of these: 23936357 (100.00%) were paired; of these: 14175958 (59.22%) aligned concordantly 0 times 8755848 (36.58%) aligned concordantly exactly 1 time 1004551 (4.20%) aligned concordantly >1 times ---- 14175958 pairs aligned concordantly 0 times; of these: 167354 (1.18%) aligned discordantly 1 time ---- 14008604 pairs aligned 0 times concordantly or discordantly; of these: 28017208 mates make up the pairs; of these: 27891941 (99.55%) aligned 0 times 82508 (0.29%) aligned exactly 1 time 42759 (0.15%) aligned >1 times 41.74% overall alignment rate Time searching: 00:07:51 Overall time: 00:07:51 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 12 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] 119865 / 9919907 = 0.0121 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 16:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.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 16:27:03: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:27:03: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:27:11: 1000000 INFO @ Wed, 22 Jul 2020 16:27:18: 2000000 INFO @ Wed, 22 Jul 2020 16:27:25: 3000000 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 16:27:32: 4000000 INFO @ Wed, 22 Jul 2020 16:27:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.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 16:27:33: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:27:33: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:27:39: 1000000 INFO @ Wed, 22 Jul 2020 16:27:40: 5000000 INFO @ Wed, 22 Jul 2020 16:27:45: 2000000 INFO @ Wed, 22 Jul 2020 16:27:47: 6000000 INFO @ Wed, 22 Jul 2020 16:27:51: 3000000 INFO @ Wed, 22 Jul 2020 16:27:53: 7000000 INFO @ Wed, 22 Jul 2020 16:27:57: 4000000 INFO @ Wed, 22 Jul 2020 16:27:59: 8000000 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 16:28:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.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 16:28:03: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:28:03: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:28:03: 5000000 INFO @ Wed, 22 Jul 2020 16:28:05: 9000000 INFO @ Wed, 22 Jul 2020 16:28:09: 1000000 INFO @ Wed, 22 Jul 2020 16:28:09: 6000000 INFO @ Wed, 22 Jul 2020 16:28:11: 10000000 INFO @ Wed, 22 Jul 2020 16:28:15: 2000000 INFO @ Wed, 22 Jul 2020 16:28:15: 7000000 INFO @ Wed, 22 Jul 2020 16:28:18: 11000000 INFO @ Wed, 22 Jul 2020 16:28:21: 3000000 INFO @ Wed, 22 Jul 2020 16:28:22: 8000000 INFO @ Wed, 22 Jul 2020 16:28:26: 12000000 INFO @ Wed, 22 Jul 2020 16:28:27: 4000000 INFO @ Wed, 22 Jul 2020 16:28:28: 9000000 INFO @ Wed, 22 Jul 2020 16:28:33: 13000000 INFO @ Wed, 22 Jul 2020 16:28:34: 5000000 INFO @ Wed, 22 Jul 2020 16:28:34: 10000000 INFO @ Wed, 22 Jul 2020 16:28:40: 6000000 INFO @ Wed, 22 Jul 2020 16:28:40: 11000000 INFO @ Wed, 22 Jul 2020 16:28:41: 14000000 INFO @ Wed, 22 Jul 2020 16:28:46: 7000000 INFO @ Wed, 22 Jul 2020 16:28:47: 12000000 INFO @ Wed, 22 Jul 2020 16:28:48: 15000000 INFO @ Wed, 22 Jul 2020 16:28:52: 8000000 INFO @ Wed, 22 Jul 2020 16:28:53: 13000000 INFO @ Wed, 22 Jul 2020 16:28:55: 16000000 INFO @ Wed, 22 Jul 2020 16:28:58: 9000000 INFO @ Wed, 22 Jul 2020 16:28:59: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:29:02: 17000000 INFO @ Wed, 22 Jul 2020 16:29:05: 10000000 INFO @ Wed, 22 Jul 2020 16:29:05: 15000000 INFO @ Wed, 22 Jul 2020 16:29:09: 18000000 INFO @ Wed, 22 Jul 2020 16:29:11: 11000000 INFO @ Wed, 22 Jul 2020 16:29:11: 16000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:29:16: 19000000 INFO @ Wed, 22 Jul 2020 16:29:17: 12000000 INFO @ Wed, 22 Jul 2020 16:29:17: 17000000 INFO @ Wed, 22 Jul 2020 16:29:21: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:29:21: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:29:21: #1 total tags in treatment: 9640659 INFO @ Wed, 22 Jul 2020 16:29:21: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:29:21: #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 16:29:21: #1 tags after filtering in treatment: 6756718 INFO @ Wed, 22 Jul 2020 16:29:21: #1 Redundant rate of treatment: 0.30 INFO @ Wed, 22 Jul 2020 16:29:21: #1 finished! INFO @ Wed, 22 Jul 2020 16:29:21: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:29:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:29:22: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:29:22: 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 16:29:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.05_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/SRX8639577/SRX8639577.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:29:23: 13000000 INFO @ Wed, 22 Jul 2020 16:29:23: 18000000 INFO @ Wed, 22 Jul 2020 16:29:29: 14000000 INFO @ Wed, 22 Jul 2020 16:29:29: 19000000 INFO @ Wed, 22 Jul 2020 16:29:34: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:29:34: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:29:34: #1 total tags in treatment: 9640659 INFO @ Wed, 22 Jul 2020 16:29:34: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:29:34: #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 16:29:34: #1 tags after filtering in treatment: 6756718 INFO @ Wed, 22 Jul 2020 16:29:34: #1 Redundant rate of treatment: 0.30 INFO @ Wed, 22 Jul 2020 16:29:34: #1 finished! INFO @ Wed, 22 Jul 2020 16:29:34: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:29:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:29:34: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:29:34: 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 16:29:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.10_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/SRX8639577/SRX8639577.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:29:35: 15000000 INFO @ Wed, 22 Jul 2020 16:29:41: 16000000 INFO @ Wed, 22 Jul 2020 16:29:46: 17000000 INFO @ Wed, 22 Jul 2020 16:29:52: 18000000 INFO @ Wed, 22 Jul 2020 16:29:58: 19000000 INFO @ Wed, 22 Jul 2020 16:30:02: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:30:02: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:30:02: #1 total tags in treatment: 9640659 INFO @ Wed, 22 Jul 2020 16:30:02: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:30:02: #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 16:30:02: #1 tags after filtering in treatment: 6756718 INFO @ Wed, 22 Jul 2020 16:30:02: #1 Redundant rate of treatment: 0.30 INFO @ Wed, 22 Jul 2020 16:30:02: #1 finished! INFO @ Wed, 22 Jul 2020 16:30:02: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:30:02: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:30:02: 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 16:30:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.20_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/SRX8639577/SRX8639577.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639577/SRX8639577.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling