Using unitig-caller 1.3.0 to count unitigs in a set of draft genome assemblies for GWAS, I'm unable to produce any output and get the error "Error "CompactedDBG::construct(): Could not create tmp directory. Abort." It might be I'm just not running it correctly but I thought I'd report the issue in case this is a bug.
Thanks in advance for any advice and here's a record of my exact command with some troubleshooting that may help to diagnose/reproduce:
(pyseer) JPegorino@lnx-0001:~/shared/data/M_Project/GWAS$ unitig-caller --version
unitig-caller 1.3.0
(pyseer) JPegorino@lnx-0001:~/shared/data/M_Project/GWAS$ cut -f2 Data_records/unitig_counter_infile.txt | head -3
/home/shared/data/M_Project/GWAS/genomes/8422_AR828.fasta
/home/shared/data/M_Project/GWAS/genomes/8423_AR829.fasta
/home/shared/data/M_Project/GWAS/genomes/8428_AR834.fasta
(pyseer) JPegorino@lnx-0001:~/shared/data/M_Project/GWAS$ ls /home/shared/data/M_Project/GWAS/genomes/8422_AR828_Bov_AR_ST1.fasta
/home/shared/data/M_Project/GWAS/genomes/8422_AR828_Bov_AR_ST1.fasta
(pyseer) JPegorino@lnx-0001:~/shared/data/M_Project/GWAS$ unitig-caller --call --refs <(cut -f2 Data_records/unitig_counter_infile.txt)
Building a DBG and calling unitigs within...
Building coloured compacted DBG...
CompactedDBG::construct(): Could not create tmp directory. Abort.
ColoredCDBG::buildColors(): Graph is invalid (maybe not built yet?) and colors cannot be mapped.
ColoredCDBG::getColorNames(): Graph is invalid or colors are not yet mapped to unitigs.
Calling unitigs within population...
Generating pyseer file...
(pyseer) JPegorino@lnx-0001:~/shared/data/M_Project/GWAS$ find /home/$(whoami)/.conda/envs/pyseer/ -name "*.py" | xargs -I{} readlink -m {} | grep 'CompactedDBG'
(pyseer) JPegorino@lnx-0001:~/shared/data/M_Project/GWAS$ wc -l unitig_caller.pyseer
0 unitig_caller.pyseer
Using unitig-caller 1.3.0 to count unitigs in a set of draft genome assemblies for GWAS, I'm unable to produce any output and get the error "Error "CompactedDBG::construct(): Could not create tmp directory. Abort." It might be I'm just not running it correctly but I thought I'd report the issue in case this is a bug.
Thanks in advance for any advice and here's a record of my exact command with some troubleshooting that may help to diagnose/reproduce: