Job ID = 7118044 SRX = SRX8639569 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T07:09:16 prefetch.2.10.7: 1) Downloading 'SRR12117007'... 2020-07-22T07:09:16 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T07:11:16 prefetch.2.10.7: HTTPS download succeed 2020-07-22T07:11:16 prefetch.2.10.7: 1) 'SRR12117007' was downloaded successfully 2020-07-22T07:11:16 prefetch.2.10.7: 'SRR12117007' has 0 unresolved dependencies Read 23091706 spots for SRR12117007/SRR12117007.sra Written 23091706 spots for SRR12117007/SRR12117007.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: 00:06:02 23091706 reads; of these: 23091706 (100.00%) were paired; of these: 14707637 (63.69%) aligned concordantly 0 times 7603581 (32.93%) aligned concordantly exactly 1 time 780488 (3.38%) aligned concordantly >1 times ---- 14707637 pairs aligned concordantly 0 times; of these: 45522 (0.31%) aligned discordantly 1 time ---- 14662115 pairs aligned 0 times concordantly or discordantly; of these: 29324230 mates make up the pairs; of these: 29173515 (99.49%) aligned 0 times 122371 (0.42%) aligned exactly 1 time 28344 (0.10%) aligned >1 times 36.83% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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] 100804 / 8423454 = 0.0120 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 16:22:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.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 16:22:52: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:22:52: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:22:59: 1000000 INFO @ Wed, 22 Jul 2020 16:23:05: 2000000 INFO @ Wed, 22 Jul 2020 16:23:11: 3000000 INFO @ Wed, 22 Jul 2020 16:23:18: 4000000 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 16:23:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.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 16:23:22: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:23:22: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:23:24: 5000000 INFO @ Wed, 22 Jul 2020 16:23:29: 1000000 INFO @ Wed, 22 Jul 2020 16:23:31: 6000000 INFO @ Wed, 22 Jul 2020 16:23:35: 2000000 INFO @ Wed, 22 Jul 2020 16:23:38: 7000000 INFO @ Wed, 22 Jul 2020 16:23:42: 3000000 INFO @ Wed, 22 Jul 2020 16:23:45: 8000000 INFO @ Wed, 22 Jul 2020 16:23:48: 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 16:23:52: 9000000 INFO @ Wed, 22 Jul 2020 16:23:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.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 16:23:52: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:23:52: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:23:55: 5000000 INFO @ Wed, 22 Jul 2020 16:23:59: 10000000 INFO @ Wed, 22 Jul 2020 16:23:59: 1000000 INFO @ Wed, 22 Jul 2020 16:24:01: 6000000 INFO @ Wed, 22 Jul 2020 16:24:06: 2000000 INFO @ Wed, 22 Jul 2020 16:24:06: 11000000 INFO @ Wed, 22 Jul 2020 16:24:08: 7000000 INFO @ Wed, 22 Jul 2020 16:24:12: 3000000 INFO @ Wed, 22 Jul 2020 16:24:13: 12000000 INFO @ Wed, 22 Jul 2020 16:24:14: 8000000 INFO @ Wed, 22 Jul 2020 16:24:19: 4000000 INFO @ Wed, 22 Jul 2020 16:24:19: 13000000 INFO @ Wed, 22 Jul 2020 16:24:20: 9000000 INFO @ Wed, 22 Jul 2020 16:24:25: 5000000 INFO @ Wed, 22 Jul 2020 16:24:26: 14000000 INFO @ Wed, 22 Jul 2020 16:24:27: 10000000 INFO @ Wed, 22 Jul 2020 16:24:31: 6000000 INFO @ Wed, 22 Jul 2020 16:24:33: 15000000 INFO @ Wed, 22 Jul 2020 16:24:33: 11000000 INFO @ Wed, 22 Jul 2020 16:24:38: 7000000 INFO @ Wed, 22 Jul 2020 16:24:40: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:24:40: 16000000 INFO @ Wed, 22 Jul 2020 16:24:44: 8000000 INFO @ Wed, 22 Jul 2020 16:24:45: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:24:45: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:24:45: #1 total tags in treatment: 8283305 INFO @ Wed, 22 Jul 2020 16:24:45: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:24:45: #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 16:24:46: #1 tags after filtering in treatment: 5984675 INFO @ Wed, 22 Jul 2020 16:24:46: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Jul 2020 16:24:46: #1 finished! INFO @ Wed, 22 Jul 2020 16:24:46: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:24:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:24:46: 13000000 INFO @ Wed, 22 Jul 2020 16:24:46: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:24:46: 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 16:24:46: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.05_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/SRX8639569/SRX8639569.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:24:50: 9000000 INFO @ Wed, 22 Jul 2020 16:24:52: 14000000 INFO @ Wed, 22 Jul 2020 16:24:56: 10000000 INFO @ Wed, 22 Jul 2020 16:24:58: 15000000 INFO @ Wed, 22 Jul 2020 16:25:03: 11000000 INFO @ Wed, 22 Jul 2020 16:25:04: 16000000 INFO @ Wed, 22 Jul 2020 16:25:09: 12000000 INFO @ Wed, 22 Jul 2020 16:25:09: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:25:09: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:25:09: #1 total tags in treatment: 8283305 INFO @ Wed, 22 Jul 2020 16:25:09: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:25:09: #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 16:25:09: #1 tags after filtering in treatment: 5984675 INFO @ Wed, 22 Jul 2020 16:25:09: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Jul 2020 16:25:09: #1 finished! INFO @ Wed, 22 Jul 2020 16:25:09: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:25:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:25:10: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:25:10: 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 16:25:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.10_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/SRX8639569/SRX8639569.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:25:15: 13000000 INFO @ Wed, 22 Jul 2020 16:25:20: 14000000 INFO @ Wed, 22 Jul 2020 16:25:26: 15000000 INFO @ Wed, 22 Jul 2020 16:25:31: 16000000 INFO @ Wed, 22 Jul 2020 16:25:36: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:25:36: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:25:36: #1 total tags in treatment: 8283305 INFO @ Wed, 22 Jul 2020 16:25:36: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:25:36: #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 16:25:36: #1 tags after filtering in treatment: 5984675 INFO @ Wed, 22 Jul 2020 16:25:36: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Jul 2020 16:25:36: #1 finished! INFO @ Wed, 22 Jul 2020 16:25:36: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:25:36: #2 number of paired peaks: 0 WARNING @ Wed, 22 Jul 2020 16:25:36: 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 16:25:36: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.20_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/SRX8639569/SRX8639569.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8639569/SRX8639569.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling