Job ID = 5791013 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,338,252 reads read : 20,676,504 reads written : 20,676,504 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:05:13 10338252 reads; of these: 10338252 (100.00%) were paired; of these: 307554 (2.97%) aligned concordantly 0 times 8755834 (84.69%) aligned concordantly exactly 1 time 1274864 (12.33%) aligned concordantly >1 times ---- 307554 pairs aligned concordantly 0 times; of these: 5025 (1.63%) aligned discordantly 1 time ---- 302529 pairs aligned 0 times concordantly or discordantly; of these: 605058 mates make up the pairs; of these: 525873 (86.91%) aligned 0 times 60965 (10.08%) aligned exactly 1 time 18220 (3.01%) aligned >1 times 97.46% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 1210031 / 10033133 = 0.1206 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 Apr 2020 08:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.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 Apr 2020 08:29:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:29:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:29:13: 1000000 INFO @ Wed, 22 Apr 2020 08:29:17: 2000000 INFO @ Wed, 22 Apr 2020 08:29:21: 3000000 INFO @ Wed, 22 Apr 2020 08:29:26: 4000000 INFO @ Wed, 22 Apr 2020 08:29:30: 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 Apr 2020 08:29:34: 6000000 INFO @ Wed, 22 Apr 2020 08:29:39: 7000000 INFO @ Wed, 22 Apr 2020 08:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.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 Apr 2020 08:29:39: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:29:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:29:44: 8000000 INFO @ Wed, 22 Apr 2020 08:29:46: 1000000 INFO @ Wed, 22 Apr 2020 08:29:49: 9000000 INFO @ Wed, 22 Apr 2020 08:29:51: 2000000 INFO @ Wed, 22 Apr 2020 08:29:54: 10000000 INFO @ Wed, 22 Apr 2020 08:29:57: 3000000 INFO @ Wed, 22 Apr 2020 08:29:59: 11000000 INFO @ Wed, 22 Apr 2020 08:30:03: 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 Apr 2020 08:30:04: 12000000 INFO @ Wed, 22 Apr 2020 08:30:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.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 Apr 2020 08:30:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:30:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:30:09: 5000000 INFO @ Wed, 22 Apr 2020 08:30:09: 13000000 INFO @ Wed, 22 Apr 2020 08:30:12: 1000000 INFO @ Wed, 22 Apr 2020 08:30:14: 14000000 INFO @ Wed, 22 Apr 2020 08:30:14: 6000000 INFO @ Wed, 22 Apr 2020 08:30:17: 2000000 INFO @ Wed, 22 Apr 2020 08:30:19: 15000000 INFO @ Wed, 22 Apr 2020 08:30:20: 7000000 INFO @ Wed, 22 Apr 2020 08:30:22: 3000000 INFO @ Wed, 22 Apr 2020 08:30:24: 16000000 INFO @ Wed, 22 Apr 2020 08:30:26: 8000000 INFO @ Wed, 22 Apr 2020 08:30:27: 4000000 INFO @ Wed, 22 Apr 2020 08:30:29: 17000000 INFO @ Wed, 22 Apr 2020 08:30:31: 9000000 INFO @ Wed, 22 Apr 2020 08:30:32: 5000000 INFO @ Wed, 22 Apr 2020 08:30:33: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:30:33: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:30:33: #1 total tags in treatment: 8821065 INFO @ Wed, 22 Apr 2020 08:30:33: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:30:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:30:33: #1 tags after filtering in treatment: 6696407 INFO @ Wed, 22 Apr 2020 08:30:33: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 08:30:33: #1 finished! INFO @ Wed, 22 Apr 2020 08:30:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:30:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:30:33: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:30:33: 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 Apr 2020 08:30:33: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 08:30:37: 10000000 INFO @ Wed, 22 Apr 2020 08:30:37: 6000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.05_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/SRX5874509/SRX5874509.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:30:42: 7000000 INFO @ Wed, 22 Apr 2020 08:30:43: 11000000 INFO @ Wed, 22 Apr 2020 08:30:48: 8000000 INFO @ Wed, 22 Apr 2020 08:30:48: 12000000 INFO @ Wed, 22 Apr 2020 08:30:53: 9000000 INFO @ Wed, 22 Apr 2020 08:30:54: 13000000 INFO @ Wed, 22 Apr 2020 08:30:58: 10000000 INFO @ Wed, 22 Apr 2020 08:30:59: 14000000 INFO @ Wed, 22 Apr 2020 08:31:03: 11000000 INFO @ Wed, 22 Apr 2020 08:31:05: 15000000 INFO @ Wed, 22 Apr 2020 08:31:08: 12000000 INFO @ Wed, 22 Apr 2020 08:31:11: 16000000 INFO @ Wed, 22 Apr 2020 08:31:13: 13000000 INFO @ Wed, 22 Apr 2020 08:31:17: 17000000 INFO @ Wed, 22 Apr 2020 08:31:18: 14000000 INFO @ Wed, 22 Apr 2020 08:31:22: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:31:22: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:31:22: #1 total tags in treatment: 8821065 INFO @ Wed, 22 Apr 2020 08:31:22: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:31:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:31:22: #1 tags after filtering in treatment: 6696407 INFO @ Wed, 22 Apr 2020 08:31:22: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 08:31:22: #1 finished! INFO @ Wed, 22 Apr 2020 08:31:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:31:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:31:22: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:31:22: 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 Apr 2020 08:31:22: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 08:31:23: 15000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.10_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/SRX5874509/SRX5874509.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:31:28: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:31:33: 17000000 INFO @ Wed, 22 Apr 2020 08:31:36: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:31:36: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:31:36: #1 total tags in treatment: 8821065 INFO @ Wed, 22 Apr 2020 08:31:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:31:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:31:37: #1 tags after filtering in treatment: 6696407 INFO @ Wed, 22 Apr 2020 08:31:37: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 08:31:37: #1 finished! INFO @ Wed, 22 Apr 2020 08:31:37: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:31:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:31:37: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:31:37: 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 Apr 2020 08:31:37: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874509/SRX5874509.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。