Job ID = 7114988 SRX = SRX8462219 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:04:06 prefetch.2.10.7: 1) Downloading 'SRR11915678'... 2020-07-22T06:04:06 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:05:24 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:05:25 prefetch.2.10.7: 'SRR11915678' is valid 2020-07-22T06:05:25 prefetch.2.10.7: 1) 'SRR11915678' was downloaded successfully 2020-07-22T06:05:25 prefetch.2.10.7: 'SRR11915678' has 0 unresolved dependencies Read 3054643 spots for SRR11915678/SRR11915678.sra Written 3054643 spots for SRR11915678/SRR11915678.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: 00:02:38 3054643 reads; of these: 3054643 (100.00%) were paired; of these: 172064 (5.63%) aligned concordantly 0 times 2503134 (81.95%) aligned concordantly exactly 1 time 379445 (12.42%) aligned concordantly >1 times ---- 172064 pairs aligned concordantly 0 times; of these: 20962 (12.18%) aligned discordantly 1 time ---- 151102 pairs aligned 0 times concordantly or discordantly; of these: 302204 mates make up the pairs; of these: 230506 (76.27%) aligned 0 times 55559 (18.38%) aligned exactly 1 time 16139 (5.34%) aligned >1 times 96.23% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 378097 / 2897028 = 0.1305 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 15:10:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.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 15:10:48: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:10:48: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:10:55: 1000000 INFO @ Wed, 22 Jul 2020 15:11:03: 2000000 INFO @ Wed, 22 Jul 2020 15:11:10: 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 15:11:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.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 15:11:18: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:11:18: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:11:18: 4000000 INFO @ Wed, 22 Jul 2020 15:11:26: 1000000 INFO @ Wed, 22 Jul 2020 15:11:26: 5000000 INFO @ Wed, 22 Jul 2020 15:11:27: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:11:27: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:11:27: #1 total tags in treatment: 2505199 INFO @ Wed, 22 Jul 2020 15:11:27: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:11:27: #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 15:11:27: #1 tags after filtering in treatment: 2188762 INFO @ Wed, 22 Jul 2020 15:11:27: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Jul 2020 15:11:27: #1 finished! INFO @ Wed, 22 Jul 2020 15:11:27: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:11:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:11:28: #2 number of paired peaks: 58 WARNING @ Wed, 22 Jul 2020 15:11:28: Too few paired peaks (58) 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 15:11:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.05_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/SRX8462219/SRX8462219.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:11:32: 2000000 INFO @ Wed, 22 Jul 2020 15:11:39: 3000000 INFO @ Wed, 22 Jul 2020 15:11:45: 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 15:11:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.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 15:11:48: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:11:48: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:11:52: 5000000 INFO @ Wed, 22 Jul 2020 15:11:53: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:11:53: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:11:53: #1 total tags in treatment: 2505199 INFO @ Wed, 22 Jul 2020 15:11:53: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:11:53: #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 15:11:53: #1 tags after filtering in treatment: 2188762 INFO @ Wed, 22 Jul 2020 15:11:53: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Jul 2020 15:11:53: #1 finished! INFO @ Wed, 22 Jul 2020 15:11:53: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:11:53: #2 number of paired peaks: 58 WARNING @ Wed, 22 Jul 2020 15:11:53: Too few paired peaks (58) 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 15:11:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.10_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/SRX8462219/SRX8462219.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:11:56: 1000000 INFO @ Wed, 22 Jul 2020 15:12:04: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:12:11: 3000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:12:19: 4000000 INFO @ Wed, 22 Jul 2020 15:12:27: 5000000 INFO @ Wed, 22 Jul 2020 15:12:28: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:12:28: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:12:28: #1 total tags in treatment: 2505199 INFO @ Wed, 22 Jul 2020 15:12:28: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:12:28: #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 15:12:28: #1 tags after filtering in treatment: 2188762 INFO @ Wed, 22 Jul 2020 15:12:28: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Jul 2020 15:12:28: #1 finished! INFO @ Wed, 22 Jul 2020 15:12:28: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:12:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:12:28: #2 number of paired peaks: 58 WARNING @ Wed, 22 Jul 2020 15:12:28: Too few paired peaks (58) 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 15:12:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.20_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/SRX8462219/SRX8462219.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462219/SRX8462219.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling