Genemark errors: OSError: [Errno 20] Not a directory

[maysonlin]

Greeting, I have received this error message while running funannotate prediction, it seems there is something wrong with Genemark:

Running GeneMark-ES on assembly Traceback (most recent call last): File "/funannotate/bin/funannotate", line 713, in <module> main() File "/funannotate/bin/funannotate", line 703, in main mod.main(arguments) File "/funannotate/lib/python2.7/site-packages/funannotate/predict.py", line 1094, in main args.soft_mask, args.cpus, os.path.join(args.out, 'predict_misc'), GeneMarkGFF3, args.organism) File "/funannotate/lib/python2.7/site-packages/funannotate/library.py", line 5909, in RunGeneMarkES runSubprocess3(cmd, outdir, log) File "/funannotate/lib/python2.7/site-packages/funannotate/library.py", line 698, in runSubprocess3 proc = subprocess.Popen(cmd, cwd=dir, stdout=FNULL, stderr=subprocess.PIPE) File "/funannotate/lib/python2.7/subprocess.py", line 394, in __init__ errread, errwrite) File "/funannotate/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 20] Not a directory

Here is my funannotate script: singularity exec --env-file /home/slin023/funannotate.txt /home/slurmsample/singularity/funannotate_1.8.3.sif funannotate predict -i /home/slin023/funannotate/masked.fasta --species "Phormia regina" --transcript_evidence /scratch/mdegenna/slin023/Transannotation/Trinity-GG.fasta --rna_bam /home/data/FLAG/PhormiaMaggotAging/aging/TrimMapping/trimSorted.out.bam -o funannotateout

To trace back to my "funannotate.txt" for path. Here is the content of funannotate.txt": export GENEMARK_PATH=/home/slin023/gmes_linux_64_4/gmhmme3

export PATH=/home/slin023/signalp-4.1/:/funannotate/bin:$PATH

export EGGNOG_DATA_DIR=/scratch/mdegenna/slin023/eggnog

export FUNANNOTATE_DB=/scratch/mdegenna/slin023/funannotate

export AUGUSTUS_CONFIG_PATH=/funannotate/config

export EVM_HOME=/funannotate/opt/evidencemodeler-1.1.1/

export TRINITYHOME=/funannotate/opt/trinity-2.8.5

export PASAHOME=/funannotate/opt/pasa-2.4.1

Here is the Genemark site I downloaded Genemark (GeneMark-ES/ET/EP ver 4.69_lic,LINUX 64 kernel 4 - 5) and using gmhmme3 since it's eukaryotes species. I am running Genemark on HPC slurm (LINUX 64), so I am not sure if I downloaded the wrong package. The message indicates it has to be a file , not a directory. If you have any suggestion or feedback, please let me know. Thank you! Best,