daligner: Track 'dust' annotation file is junk

[mictadlo]

Hi,

I got many daligner: Track 'dust' annotation file is junk with the following commands

DBsplit -x500 -s200 DB
DBdust DB 
HPC.daligner DB -T8 -mdust -H6973 

I wrote the following script to submit each command from test.01.OVL parallel.

#!/bin/bash

while IFS='' read -r line || [[ -n "$line" ]]; do
  cmd=$line 

  #cat <<EOF
  qsub <<EOF
#!/bin/bash -l

#PBS -N HPCdaligner
#PBS -l walltime=48:00:00
#PBS -j oe
#PBS -l mem=80G
#PBS -l ncpus=4
#PBS -M m.lorenc@qut.edu.au
###PBS -m bea

cd \$PBS_O_WORKDIR

$cmd

EOF

done < "$1"

The script gets executed as following way sh HPC.daligner_pbs.sh test.01.OVL

Did I miss anything?

Thank you in advance.

Michal

[thegenemyers]

Hmm, I ran exactly your sequence on a small E.Coli data base and did not encounter a problem. Your more recent issue e-mail about the daligner itself suggests you got passed this issue, please advise? (And if you did figure out what the problem is could you let me know.) -- Gene

On 12/26/17, 10:17 PM, Michał T. Lorenc wrote:

Hi,

I got many |daligner: Track 'dust' annotation file is junk| with the following commands

DBsplit -x500 -s200 DB DBdust DB HPC.daligner DB -T8 -mdust -H6973	bash -v

Did I miss anything?

Thank you in advance.

Michal

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[mictadlo]

I think I have forgotten to do Catrack -v DB dust