Description
Hi, thank you for this great tool. My rnaQUAST job appears to be hanging with no progress for >36 hours. Nothing has been written to the rnaQUAST database (Saccharomyces_cerevisiae.R64-1-1.108.db
) in >36 hours as well. I am running rnaQUAST with 285 assembly fastas; please see the attached rnaQUAST.log
for system details and other details.
In short, I called rnaQUAST as follows:
rnaQUAST.py \
-t "${SLURM_CPUS_ON_NODE}" \
--labels ${n_GG[*]} \
--transcripts ${f_GG[*]} \
--reference "${p_ref}/${f_ref}" \
--gtf "${p_gtf}/${f_gtf}" \
--gmap_index "${p_gmap}/${d_gmap}" \
--strand_specific \
--left_reads "fastqs/merged_Q_IP_UTK_R1.fq.gz" \
--right_reads "fastqs/merged_Q_IP_UTK_R3.fq.gz" \
--output_dir "outfiles_rnaQUAST-test_Trinity-GG_Q-N/" \
--busco_lineage "BUSCO/saccharomycetes_odb10.2020-08-05.tar.gz" \
--gene_mark \
--disable_infer_genes \
--disable_infer_transcripts
...where "${SLURM_CPUS_ON_NODE}"
is 32 and arrays ${n_GG[*]}
and ${f_GG[*]}
are composed of 285 elements each.
In checking the log, the job has been hanging at this step for >36 hours:
2023-02-18 17:55:33
Getting database coverage by reads...
Can you tell me if there is anything wrong with my invocation of rnaQUAST (e.g., perhaps I need to decompress the BUSCO database?), or is this lengthy amount of time with no apparent progress to be expected given the large number of assembly fastas?
Any feedback will be greatly appreciated. Thanks,
Kris
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