Job ID = 5791127 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,930,811 reads read : 11,861,622 reads written : 11,861,622 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: 00:02:29 5930811 reads; of these: 5930811 (100.00%) were paired; of these: 150852 (2.54%) aligned concordantly 0 times 4930879 (83.14%) aligned concordantly exactly 1 time 849080 (14.32%) aligned concordantly >1 times ---- 150852 pairs aligned concordantly 0 times; of these: 1725 (1.14%) aligned discordantly 1 time ---- 149127 pairs aligned 0 times concordantly or discordantly; of these: 298254 mates make up the pairs; of these: 275098 (92.24%) aligned 0 times 16132 (5.41%) aligned exactly 1 time 7024 (2.36%) aligned >1 times 97.68% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 400807 / 5779855 = 0.0693 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 08:40:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.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 08:40:21: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:40:21: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:40:25: 1000000 INFO @ Wed, 22 Apr 2020 08:40:30: 2000000 INFO @ Wed, 22 Apr 2020 08:40:34: 3000000 INFO @ Wed, 22 Apr 2020 08:40:39: 4000000 INFO @ Wed, 22 Apr 2020 08:40:43: 5000000 INFO @ Wed, 22 Apr 2020 08:40:48: 6000000 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 08:40:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.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 08:40:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:40:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:40:52: 7000000 INFO @ Wed, 22 Apr 2020 08:40:55: 1000000 INFO @ Wed, 22 Apr 2020 08:40:57: 8000000 INFO @ Wed, 22 Apr 2020 08:41:00: 2000000 INFO @ Wed, 22 Apr 2020 08:41:02: 9000000 INFO @ Wed, 22 Apr 2020 08:41:04: 3000000 INFO @ Wed, 22 Apr 2020 08:41:06: 10000000 INFO @ Wed, 22 Apr 2020 08:41:09: 4000000 INFO @ Wed, 22 Apr 2020 08:41:10: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 08:41:10: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 08:41:10: #1 total tags in treatment: 5379158 INFO @ Wed, 22 Apr 2020 08:41:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:41:10: #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 08:41:10: #1 tags after filtering in treatment: 3547303 INFO @ Wed, 22 Apr 2020 08:41:10: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Apr 2020 08:41:10: #1 finished! INFO @ Wed, 22 Apr 2020 08:41:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:41:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:41:10: #2 number of paired peaks: 16 WARNING @ Wed, 22 Apr 2020 08:41:10: Too few paired peaks (16) 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 08:41:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.05_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/SRX6614923/SRX6614923.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:41:14: 5000000 INFO @ Wed, 22 Apr 2020 08:41:18: 6000000 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 08:41:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.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 08:41:21: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:41:21: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:41:23: 7000000 INFO @ Wed, 22 Apr 2020 08:41:26: 1000000 INFO @ Wed, 22 Apr 2020 08:41:28: 8000000 INFO @ Wed, 22 Apr 2020 08:41:31: 2000000 INFO @ Wed, 22 Apr 2020 08:41:32: 9000000 INFO @ Wed, 22 Apr 2020 08:41:36: 3000000 INFO @ Wed, 22 Apr 2020 08:41:37: 10000000 INFO @ Wed, 22 Apr 2020 08:41:41: 4000000 INFO @ Wed, 22 Apr 2020 08:41:41: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 08:41:41: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 08:41:41: #1 total tags in treatment: 5379158 INFO @ Wed, 22 Apr 2020 08:41:41: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:41:41: #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 08:41:41: #1 tags after filtering in treatment: 3547303 INFO @ Wed, 22 Apr 2020 08:41:41: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Apr 2020 08:41:41: #1 finished! INFO @ Wed, 22 Apr 2020 08:41:41: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:41:41: #2 number of paired peaks: 16 WARNING @ Wed, 22 Apr 2020 08:41:41: Too few paired peaks (16) 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 08:41:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.10_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/SRX6614923/SRX6614923.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:41:45: 5000000 INFO @ Wed, 22 Apr 2020 08:41:49: 6000000 INFO @ Wed, 22 Apr 2020 08:41:53: 7000000 INFO @ Wed, 22 Apr 2020 08:41:58: 8000000 INFO @ Wed, 22 Apr 2020 08:42:02: 9000000 INFO @ Wed, 22 Apr 2020 08:42:06: 10000000 INFO @ Wed, 22 Apr 2020 08:42:10: #1 tag size is determined as 37 bps INFO @ Wed, 22 Apr 2020 08:42:10: #1 tag size = 37 INFO @ Wed, 22 Apr 2020 08:42:10: #1 total tags in treatment: 5379158 INFO @ Wed, 22 Apr 2020 08:42:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:42:10: #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 08:42:10: #1 tags after filtering in treatment: 3547303 INFO @ Wed, 22 Apr 2020 08:42:10: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Apr 2020 08:42:10: #1 finished! INFO @ Wed, 22 Apr 2020 08:42:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:42:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:42:10: #2 number of paired peaks: 16 WARNING @ Wed, 22 Apr 2020 08:42:10: Too few paired peaks (16) 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 08:42:10: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.20_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/SRX6614923/SRX6614923.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614923/SRX6614923.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。