phyluce_probe_run_multiple_lastzs_sqlite --probefile

[Jami5on]

**Hello!

I am receiving the following error:**

EOFError: EOF when reading a line /var/spool/slurm/slurmd/job9943744/slurm_script: line 27: --probefile: command not found

with the following script:

module load anaconda3

conda activate phyluce-1.7.3

cd /scratch/jr4253

run the search

phyluce_probe_run_multiple_lastzs_sqlite \ --db Manticora_mygaloides_genome.sqlite \ --output Manticora_mygaloides_genome_lastz \ --scaffoldlist Manticora_mygaloides_genome \ --genome-base-path ./Manticora_mygaloides_genome \ # Update this line --probefile /scratch/jr4253/Adephaga_2Kv2_final_probe_set_full.fasta \ --cores 12

My scratch is my working area with my probe set and genome files accessible. I have also tried this with the genome fatsa from tutorial 3 and am getting the same error.

Any ideas?

Thanks

[brantfaircloth]

There is likely an error in how you are calling phyluce_probe_run_multiple_lastzs_sqlite. How this is formatted is hard to discern, given what is pasted above, but my guess is that the \ # Update this line on the line before --probefile is part of what is causing your issue.

Generally speaking, multiline commands also need to have \ after each line. You can see an example of this in the tutorial.