Open jonwright99 opened 4 years ago
To reproduce;
1) Make a PE datastore sdg-datastore make -1 PE_R1.fastq -2 PE_R2.fastq -t paired -d 1 -n pe -o pe.ds
sdg-datastore make -1 PE_R1.fastq -2 PE_R2.fastq -t paired -d 1 -n pe -o pe.ds
2) Make a PacBio datastore sdg-datastore make -L pb_reads.fastq -t long -n pacbio -o pacbio.ds
sdg-datastore make -L pb_reads.fastq -t long -n pacbio -o pacbio.ds
3) Make ws with PE reads only sdg-workspace make -g k200.contigs_raw.gfa -p pe.ds.prseq -o pe_ws ** runs fine
sdg-workspace make -g k200.contigs_raw.gfa -p pe.ds.prseq -o pe_ws
4) Make a ws with PE and PB reads sdg-workspace make -g k200.contigs_raw.gfa -L pacbio.ds.loseq -p pe.ds.prseq -o pe_pb_ws
sdg-workspace make -g k200.contigs_raw.gfa -L pacbio.ds.loseq -p pe.ds.prseq -o pe_pb_ws
Step 4 gives a segfault although stdout suggests the ws has been built correctly;
/hpc-home/wrightj/github/bioinfologics/sdg/build/sdg-workspace make -g k200.contigs_raw.gfa -L pacbio.ds.loseq -p pe.ds.prseq -o pb_pe_ws 2020-05-29 08:10:24: Graph fasta filesname: k200.contigs_raw.fasta 2020-05-29 08:10:24: Loading sequences from k200.contigs_raw.fasta 2020-05-29 08:10:28: 1024254 nodes loaded (246228 canonised). 2020-05-29 08:10:34: 1024254 nodes after connecting with 1348742 links. 2020-05-29 08:10:34: PairedReadsDatastore open: pe.ds.prseq max read length: 251 Total reads: 168907918 2020-05-29 08:10:34: LongReadsDatastore open: pacbio.ds.loseq Total reads: 10000000 2020-05-29 08:10:34: Dumping workspace to pe_pb_ws.sdgws 2020-05-29 08:10:36: Dumping long read mappings 2020-05-29 08:10:36: Done!
To reproduce;
1) Make a PE datastore
sdg-datastore make -1 PE_R1.fastq -2 PE_R2.fastq -t paired -d 1 -n pe -o pe.ds2) Make a PacBio datastore
sdg-datastore make -L pb_reads.fastq -t long -n pacbio -o pacbio.ds3) Make ws with PE reads only
sdg-workspace make -g k200.contigs_raw.gfa -p pe.ds.prseq -o pe_ws** runs fine4) Make a ws with PE and PB reads
sdg-workspace make -g k200.contigs_raw.gfa -L pacbio.ds.loseq -p pe.ds.prseq -o pe_pb_wsStep 4 gives a segfault although stdout suggests the ws has been built correctly;