Job ID = 14521444 SRX = SRX11788628 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 2268788 READS because READLEN < 1 Read 9795135 spots for SRR15488912/SRR15488912.sra Written 9795135 spots for SRR15488912/SRR15488912.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: 00:00:01 Time loading mirror index: 00:00:00 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) 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] 15 unmatched pairs [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] 11 unmatched pairs [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] 3 unmatched pairs [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] 1 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] 1 unmatched pairs [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] 3239192 / 6985096 = 0.4637 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:12:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.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 @ Sat, 15 Jan 2022 21:12:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:12:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:12:14: 1000000 INFO @ Sat, 15 Jan 2022 21:12:21: 2000000 INFO @ Sat, 15 Jan 2022 21:12:27: 3000000 INFO @ Sat, 15 Jan 2022 21:12:34: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:12:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.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 @ Sat, 15 Jan 2022 21:12:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:12:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:12:40: 5000000 INFO @ Sat, 15 Jan 2022 21:12:43: 1000000 INFO @ Sat, 15 Jan 2022 21:12:47: 6000000 INFO @ Sat, 15 Jan 2022 21:12:49: 2000000 INFO @ Sat, 15 Jan 2022 21:12:53: 7000000 INFO @ Sat, 15 Jan 2022 21:12:55: 3000000 INFO @ Sat, 15 Jan 2022 21:13:00: 8000000 INFO @ Sat, 15 Jan 2022 21:13:01: 4000000 INFO @ Sat, 15 Jan 2022 21:13:02: #1 tag size is determined as 26 bps INFO @ Sat, 15 Jan 2022 21:13:02: #1 tag size = 26 INFO @ Sat, 15 Jan 2022 21:13:02: #1 total tags in treatment: 3740890 INFO @ Sat, 15 Jan 2022 21:13:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:13:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:13:02: #1 tags after filtering in treatment: 2702195 INFO @ Sat, 15 Jan 2022 21:13:02: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 21:13:02: #1 finished! INFO @ Sat, 15 Jan 2022 21:13:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:13:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:13:02: #2 number of paired peaks: 44 WARNING @ Sat, 15 Jan 2022 21:13:02: Too few paired peaks (44) 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 @ Sat, 15 Jan 2022 21:13:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.05_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/SRX11788628/SRX11788628.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:13:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.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 @ Sat, 15 Jan 2022 21:13:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:13:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:13:07: 5000000 INFO @ Sat, 15 Jan 2022 21:13:13: 6000000 INFO @ Sat, 15 Jan 2022 21:13:14: 1000000 INFO @ Sat, 15 Jan 2022 21:13:19: 7000000 INFO @ Sat, 15 Jan 2022 21:13:21: 2000000 INFO @ Sat, 15 Jan 2022 21:13:25: 8000000 INFO @ Sat, 15 Jan 2022 21:13:27: #1 tag size is determined as 26 bps INFO @ Sat, 15 Jan 2022 21:13:27: #1 tag size = 26 INFO @ Sat, 15 Jan 2022 21:13:27: #1 total tags in treatment: 3740890 INFO @ Sat, 15 Jan 2022 21:13:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:13:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:13:27: #1 tags after filtering in treatment: 2702195 INFO @ Sat, 15 Jan 2022 21:13:27: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 21:13:27: #1 finished! INFO @ Sat, 15 Jan 2022 21:13:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:13:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:13:27: 3000000 INFO @ Sat, 15 Jan 2022 21:13:27: #2 number of paired peaks: 44 WARNING @ Sat, 15 Jan 2022 21:13:27: Too few paired peaks (44) 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 @ Sat, 15 Jan 2022 21:13:27: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.10_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/SRX11788628/SRX11788628.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:13:33: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:13:38: 5000000 INFO @ Sat, 15 Jan 2022 21:13:44: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:13:49: 7000000 INFO @ Sat, 15 Jan 2022 21:13:54: 8000000 INFO @ Sat, 15 Jan 2022 21:13:56: #1 tag size is determined as 26 bps INFO @ Sat, 15 Jan 2022 21:13:56: #1 tag size = 26 INFO @ Sat, 15 Jan 2022 21:13:56: #1 total tags in treatment: 3740890 INFO @ Sat, 15 Jan 2022 21:13:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:13:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:13:56: #1 tags after filtering in treatment: 2702195 INFO @ Sat, 15 Jan 2022 21:13:56: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 21:13:56: #1 finished! INFO @ Sat, 15 Jan 2022 21:13:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:13:56: #2 number of paired peaks: 44 WARNING @ Sat, 15 Jan 2022 21:13:56: Too few paired peaks (44) 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 @ Sat, 15 Jan 2022 21:13:56: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.20_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/SRX11788628/SRX11788628.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX11788628/SRX11788628.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling