Job ID = 5790978 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,217,476 reads read : 4,434,952 reads written : 4,434,952 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: 00:01:27 2217476 reads; of these: 2217476 (100.00%) were paired; of these: 195337 (8.81%) aligned concordantly 0 times 1792347 (80.83%) aligned concordantly exactly 1 time 229792 (10.36%) aligned concordantly >1 times ---- 195337 pairs aligned concordantly 0 times; of these: 9631 (4.93%) aligned discordantly 1 time ---- 185706 pairs aligned 0 times concordantly or discordantly; of these: 371412 mates make up the pairs; of these: 351338 (94.60%) aligned 0 times 14589 (3.93%) aligned exactly 1 time 5485 (1.48%) aligned >1 times 92.08% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 14915 / 1970411 = 0.0076 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 08:12:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.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 08:12:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:12:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:12:27: 1000000 INFO @ Wed, 22 Apr 2020 08:12:32: 2000000 INFO @ Wed, 22 Apr 2020 08:12:36: 3000000 INFO @ Wed, 22 Apr 2020 08:12:41: 4000000 INFO @ Wed, 22 Apr 2020 08:12:41: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:12:41: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:12:41: #1 total tags in treatment: 2007233 INFO @ Wed, 22 Apr 2020 08:12:41: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:12:41: #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 08:12:41: #1 tags after filtering in treatment: 1877034 INFO @ Wed, 22 Apr 2020 08:12:41: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 22 Apr 2020 08:12:41: #1 finished! INFO @ Wed, 22 Apr 2020 08:12:41: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:12:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:12:41: #2 number of paired peaks: 34 WARNING @ Wed, 22 Apr 2020 08:12:41: Too few paired peaks (34) 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 08:12:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.05_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/SRX5874481/SRX5874481.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 08:12:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.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 08:12:52: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:12:52: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:12:57: 1000000 INFO @ Wed, 22 Apr 2020 08:13:02: 2000000 INFO @ Wed, 22 Apr 2020 08:13:06: 3000000 INFO @ Wed, 22 Apr 2020 08:13:11: 4000000 INFO @ Wed, 22 Apr 2020 08:13:11: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:13:11: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:13:11: #1 total tags in treatment: 2007233 INFO @ Wed, 22 Apr 2020 08:13:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:11: #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 08:13:11: #1 tags after filtering in treatment: 1877034 INFO @ Wed, 22 Apr 2020 08:13:11: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 22 Apr 2020 08:13:11: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:11: #2 number of paired peaks: 34 WARNING @ Wed, 22 Apr 2020 08:13:11: Too few paired peaks (34) 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 08:13:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.10_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/SRX5874481/SRX5874481.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling 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 08:13:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.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 08:13:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:27: 1000000 INFO @ Wed, 22 Apr 2020 08:13:32: 2000000 INFO @ Wed, 22 Apr 2020 08:13:36: 3000000 INFO @ Wed, 22 Apr 2020 08:13:41: 4000000 INFO @ Wed, 22 Apr 2020 08:13:41: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:13:41: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:13:41: #1 total tags in treatment: 2007233 INFO @ Wed, 22 Apr 2020 08:13:41: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:41: #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 08:13:41: #1 tags after filtering in treatment: 1877034 INFO @ Wed, 22 Apr 2020 08:13:41: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 22 Apr 2020 08:13:41: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:41: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:41: #2 number of paired peaks: 34 WARNING @ Wed, 22 Apr 2020 08:13:41: Too few paired peaks (34) 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 08:13:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.20_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/SRX5874481/SRX5874481.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874481/SRX5874481.20_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。