millironx/cowcalf-rumen-metagenomic-pipeline
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Fixed find and xargs to actually work together

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This commit is contained in:
Thomas Allen Christensen II 2019-05-24 11:21:45 -06:00
parent ff276e74fa
commit 52ddd10d57
1 changed files with 3 additions and 3 deletions
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6
main.sh
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@ -23,8 +23,8 @@ module load r
# Metaxa2 uses 4 cpus, we need to make sure that each instance has
# enough cpus to run
echo "--^-- X: Reading FASTQ sequences..."
find . -maxdepth 1 -0 -name "*R1_001.fastq.gz" | \
xargs -L1 -P"$SLURM_NTASKS" srun -n1 -N1 --exclusive ./fastq-to-taxonomy.sh
find . -maxdepth 1 -print0 -name "*R1_001.fastq.gz" | \
xargs -0 -L1 -P"$SLURM_NTASKS" srun -n1 -N1 --exclusive ./fastq-to-taxonomy.sh
echo "--^-- X: Reading FASTQ sequences...Done!"
# Compile those pesky individual taxonomic tables into a single
@ -188,4 +188,4 @@ xargs -a catcols.txt -P"$SLURM_NTASKS" -L1 srun -n1 -N1 --exclusive \
xargs -a numcols.txt -P"$SLURM_NTASKS" -L1 srun -n1 -N1 --exclusive \
./sample-regression.sh
echo "--^-- X: All Done!"
echo "--^-- X: All Done!"