Job ID = 5791284 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 29,798,091 reads read : 59,596,182 reads written : 59,596,182 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: 00:10:58 29798091 reads; of these: 29798091 (100.00%) were paired; of these: 9954445 (33.41%) aligned concordantly 0 times 17881660 (60.01%) aligned concordantly exactly 1 time 1961986 (6.58%) aligned concordantly >1 times ---- 9954445 pairs aligned concordantly 0 times; of these: 59747 (0.60%) aligned discordantly 1 time ---- 9894698 pairs aligned 0 times concordantly or discordantly; of these: 19789396 mates make up the pairs; of these: 19362390 (97.84%) aligned 0 times 368021 (1.86%) aligned exactly 1 time 58985 (0.30%) aligned >1 times 67.51% overall alignment rate Time searching: 00:10:58 Overall time: 00:10:58 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 20 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] 9421035 / 19856995 = 0.4744 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 09:57:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.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 09:57:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:57:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:57:11: 1000000 INFO @ Wed, 22 Apr 2020 09:57:17: 2000000 INFO @ Wed, 22 Apr 2020 09:57:23: 3000000 INFO @ Wed, 22 Apr 2020 09:57:28: 4000000 INFO @ Wed, 22 Apr 2020 09:57:33: 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 09:57:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.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 09:57:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:57:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:57:39: 6000000 INFO @ Wed, 22 Apr 2020 09:57:41: 1000000 INFO @ Wed, 22 Apr 2020 09:57:45: 7000000 INFO @ Wed, 22 Apr 2020 09:57:48: 2000000 INFO @ Wed, 22 Apr 2020 09:57:51: 8000000 INFO @ Wed, 22 Apr 2020 09:57:55: 3000000 INFO @ Wed, 22 Apr 2020 09:57:57: 9000000 INFO @ Wed, 22 Apr 2020 09:58:02: 4000000 BedGraph に変換中... INFO @ Wed, 22 Apr 2020 09:58:03: 10000000 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 09:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.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 09:58:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:58:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:58:08: 5000000 INFO @ Wed, 22 Apr 2020 09:58:09: 11000000 INFO @ Wed, 22 Apr 2020 09:58:11: 1000000 INFO @ Wed, 22 Apr 2020 09:58:15: 6000000 INFO @ Wed, 22 Apr 2020 09:58:15: 12000000 INFO @ Wed, 22 Apr 2020 09:58:17: 2000000 INFO @ Wed, 22 Apr 2020 09:58:21: 13000000 INFO @ Wed, 22 Apr 2020 09:58:22: 7000000 INFO @ Wed, 22 Apr 2020 09:58:23: 3000000 INFO @ Wed, 22 Apr 2020 09:58:28: 14000000 INFO @ Wed, 22 Apr 2020 09:58:28: 8000000 INFO @ Wed, 22 Apr 2020 09:58:30: 4000000 INFO @ Wed, 22 Apr 2020 09:58:34: 15000000 INFO @ Wed, 22 Apr 2020 09:58:35: 9000000 INFO @ Wed, 22 Apr 2020 09:58:36: 5000000 INFO @ Wed, 22 Apr 2020 09:58:40: 16000000 INFO @ Wed, 22 Apr 2020 09:58:42: 6000000 INFO @ Wed, 22 Apr 2020 09:58:42: 10000000 INFO @ Wed, 22 Apr 2020 09:58:46: 17000000 INFO @ Wed, 22 Apr 2020 09:58:48: 7000000 INFO @ Wed, 22 Apr 2020 09:58:49: 11000000 INFO @ Wed, 22 Apr 2020 09:58:52: 18000000 INFO @ Wed, 22 Apr 2020 09:58:54: 8000000 INFO @ Wed, 22 Apr 2020 09:58:55: 12000000 INFO @ Wed, 22 Apr 2020 09:58:58: 19000000 INFO @ Wed, 22 Apr 2020 09:59:00: 9000000 INFO @ Wed, 22 Apr 2020 09:59:02: 13000000 INFO @ Wed, 22 Apr 2020 09:59:04: 20000000 INFO @ Wed, 22 Apr 2020 09:59:06: 10000000 INFO @ Wed, 22 Apr 2020 09:59:09: 14000000 INFO @ Wed, 22 Apr 2020 09:59:10: 21000000 INFO @ Wed, 22 Apr 2020 09:59:12: 11000000 INFO @ Wed, 22 Apr 2020 09:59:13: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 09:59:13: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 09:59:13: #1 total tags in treatment: 10426267 INFO @ Wed, 22 Apr 2020 09:59:13: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:59:13: #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 09:59:13: #1 tags after filtering in treatment: 7939978 INFO @ Wed, 22 Apr 2020 09:59:13: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 09:59:13: #1 finished! INFO @ Wed, 22 Apr 2020 09:59:13: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:59:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:59:13: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:59:13: 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 09:59:13: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.05_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/SRX7409543/SRX7409543.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:59:17: 15000000 INFO @ Wed, 22 Apr 2020 09:59:19: 12000000 INFO @ Wed, 22 Apr 2020 09:59:23: 16000000 INFO @ Wed, 22 Apr 2020 09:59:25: 13000000 INFO @ Wed, 22 Apr 2020 09:59:30: 17000000 INFO @ Wed, 22 Apr 2020 09:59:31: 14000000 INFO @ Wed, 22 Apr 2020 09:59:36: 18000000 INFO @ Wed, 22 Apr 2020 09:59:37: 15000000 INFO @ Wed, 22 Apr 2020 09:59:43: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:59:44: 16000000 INFO @ Wed, 22 Apr 2020 09:59:49: 20000000 INFO @ Wed, 22 Apr 2020 09:59:50: 17000000 INFO @ Wed, 22 Apr 2020 09:59:56: 21000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:59:57: 18000000 INFO @ Wed, 22 Apr 2020 09:59:58: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 09:59:58: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 09:59:58: #1 total tags in treatment: 10426267 INFO @ Wed, 22 Apr 2020 09:59:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:59:58: #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 09:59:58: #1 tags after filtering in treatment: 7939978 INFO @ Wed, 22 Apr 2020 09:59:58: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 09:59:58: #1 finished! INFO @ Wed, 22 Apr 2020 09:59:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:59:59: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:59:59: 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 09:59:59: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.10_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/SRX7409543/SRX7409543.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:00:02: 19000000 INFO @ Wed, 22 Apr 2020 10:00:13: 20000000 INFO @ Wed, 22 Apr 2020 10:00:19: 21000000 INFO @ Wed, 22 Apr 2020 10:00:21: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:00:21: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:00:21: #1 total tags in treatment: 10426267 INFO @ Wed, 22 Apr 2020 10:00:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:00:21: #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 10:00:21: #1 tags after filtering in treatment: 7939978 INFO @ Wed, 22 Apr 2020 10:00:21: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 22 Apr 2020 10:00:21: #1 finished! INFO @ Wed, 22 Apr 2020 10:00:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:00:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:00:21: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:00:21: 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 10:00:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.20_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/SRX7409543/SRX7409543.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409543/SRX7409543.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling