Job ID = 7115143 SRX = SRX8462224 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T06:06:18 prefetch.2.10.7: 1) Downloading 'SRR11915683'... 2020-07-22T06:06:18 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T06:07:08 prefetch.2.10.7: HTTPS download succeed 2020-07-22T06:07:08 prefetch.2.10.7: 'SRR11915683' is valid 2020-07-22T06:07:08 prefetch.2.10.7: 1) 'SRR11915683' was downloaded successfully 2020-07-22T06:07:08 prefetch.2.10.7: 'SRR11915683' has 0 unresolved dependencies Read 2996571 spots for SRR11915683/SRR11915683.sra Written 2996571 spots for SRR11915683/SRR11915683.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: 00:02:56 2996571 reads; of these: 2996571 (100.00%) were paired; of these: 211000 (7.04%) aligned concordantly 0 times 2406074 (80.29%) aligned concordantly exactly 1 time 379497 (12.66%) aligned concordantly >1 times ---- 211000 pairs aligned concordantly 0 times; of these: 13470 (6.38%) aligned discordantly 1 time ---- 197530 pairs aligned 0 times concordantly or discordantly; of these: 395060 mates make up the pairs; of these: 327097 (82.80%) aligned 0 times 53820 (13.62%) aligned exactly 1 time 14143 (3.58%) aligned >1 times 94.54% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 321375 / 2791343 = 0.1151 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 15:12:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.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 15:12:48: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:12:48: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:12:55: 1000000 INFO @ Wed, 22 Jul 2020 15:13:01: 2000000 INFO @ Wed, 22 Jul 2020 15:13:07: 3000000 INFO @ Wed, 22 Jul 2020 15:13:14: 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 15:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.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 15:13:18: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:13:18: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:13:20: 5000000 INFO @ Wed, 22 Jul 2020 15:13:20: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:13:20: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:13:20: #1 total tags in treatment: 2464541 INFO @ Wed, 22 Jul 2020 15:13:20: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:13:20: #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 15:13:20: #1 tags after filtering in treatment: 2142426 INFO @ Wed, 22 Jul 2020 15:13:20: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Jul 2020 15:13:20: #1 finished! INFO @ Wed, 22 Jul 2020 15:13:20: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:13:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:13:21: #2 number of paired peaks: 78 WARNING @ Wed, 22 Jul 2020 15:13:21: Too few paired peaks (78) 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 15:13:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.05_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/SRX8462224/SRX8462224.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:13:25: 1000000 INFO @ Wed, 22 Jul 2020 15:13:31: 2000000 INFO @ Wed, 22 Jul 2020 15:13:38: 3000000 INFO @ Wed, 22 Jul 2020 15:13:44: 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 15:13:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.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 15:13:48: #1 read tag files... INFO @ Wed, 22 Jul 2020 15:13:48: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 15:13:51: 5000000 INFO @ Wed, 22 Jul 2020 15:13:51: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:13:51: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:13:51: #1 total tags in treatment: 2464541 INFO @ Wed, 22 Jul 2020 15:13:51: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:13:51: #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 15:13:51: #1 tags after filtering in treatment: 2142426 INFO @ Wed, 22 Jul 2020 15:13:51: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Jul 2020 15:13:51: #1 finished! INFO @ Wed, 22 Jul 2020 15:13:51: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:13:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:13:51: #2 number of paired peaks: 78 WARNING @ Wed, 22 Jul 2020 15:13:51: Too few paired peaks (78) 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 15:13:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.10_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/SRX8462224/SRX8462224.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 15:13:55: 1000000 INFO @ Wed, 22 Jul 2020 15:14:02: 2000000 INFO @ Wed, 22 Jul 2020 15:14:08: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 15:14:15: 4000000 BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 15:14:21: 5000000 INFO @ Wed, 22 Jul 2020 15:14:22: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 15:14:22: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 15:14:22: #1 total tags in treatment: 2464541 INFO @ Wed, 22 Jul 2020 15:14:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 15:14:22: #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 15:14:22: #1 tags after filtering in treatment: 2142426 INFO @ Wed, 22 Jul 2020 15:14:22: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Jul 2020 15:14:22: #1 finished! INFO @ Wed, 22 Jul 2020 15:14:22: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 15:14:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 15:14:22: #2 number of paired peaks: 78 WARNING @ Wed, 22 Jul 2020 15:14:22: Too few paired peaks (78) 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 15:14:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.20_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/SRX8462224/SRX8462224.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX8462224/SRX8462224.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling