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EBI-Metagenomics / EukCC

Tool to estimate genome quality of microbial eukaryotes
GNU General Public License v3.0
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Issues when running eukcc in test genome #3

Closed leosouliotis closed 4 years ago

leosouliotis commented 4 years ago

I am trying to run EukCC example as explained in the docs. Running the following command on the test genome (downloaded as wget -O testgenome.fa.gz ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/251/995/GCF_002251995.1_ASM225199v2/GCF_002251995.1_ASM225199v2_genomic.fna.gz ):

eukcc --db ~/leo/Databases/eukcc_db_20191023_1/ --ncores 4 --outdir eukcc_testgenome testgenome.fa

with the following result.

02/14/2020 14:50:15: Starting EukCC 02/14/2020 14:50:15: Running GeneMark-ES 02/14/2020 14:50:29: GeneMark-ES failed on this bin

While this is not informative, I am leaving here the contents of runGMES.log

check before run
create directories
commit input data
data report
commit training data
training data report
prepare initial model
get GC of sequence
GC 48
build initial ES model
running step ES_A
running gm.hmm on local multi-core system
17 contigs in training
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_2.out  /m
nt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_2
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_1.out  /m
nt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_1
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_3.out  /m
nt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_3
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_4.out  /m
nt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_4
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_8.out  /m
nt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_8
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_5.out  /m
nt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_5
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_7.out  /m
nt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_7
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_6.out  /m
nt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_6
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_11.out  /
mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_11
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_12.out  /
mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_12
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_10.out  /
mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_10
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_9.out  /m
nt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_9
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_15.out  /
mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_15
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_14.out  /
mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_14
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_13.out  /
mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_13
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_17.out  /
mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_17
warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_16.out  /
mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_16
concatenate predictions: /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1
training level ES_A: /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1
error, file not found /mnt/gpfs/leo/bin/gm_et_linux_64/parse_set.pl: set.out
error on call: /mnt/gpfs/leo/bin/gm_et_linux_64/parse_set.pl --section ES_A --cfg  /mnt/gpfs/leo/bin/EukCC/eukcc_testge
nome/workfiles/gmes/run.cfg  --v
openpaul commented 4 years ago

Thank you, can you also upload the content of the file runGMES.log? Most often this is caused by missing the license key of GeneMark-ES or having it placed under the wrong file name. Make sure you have a valid license in the file ~/.gm_key

openpaul commented 4 years ago

With version 0.1.2 I now check for the license to be present and give a warning if it is not found. The commit for this is: https://github.com/Finn-Lab/EukCC/commit/663a33fc4df24bbeb4931212092bf882040ebb94

leosouliotis commented 4 years ago

Thanks for the response. I don't see that error somewhere, and I just checked again and the key is copied as ~/./gm_key so I suppose it shouldn't mess it up.

I copied the contents of the runGMES.log in my initial message; did I miss-understood and you need additional information too?

openpaul commented 4 years ago

Sorry my mistake. I meant the gmes.log file. You mentioned you have the key in the location ~/./gm_key but it should be in ~/.gm_key. I am unsure if the extra slash was a typo or not

leosouliotis commented 4 years ago

Yeap, that was a typo; the actual path is ~/.gm_key . Here is the gmes.log file:

/home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:13 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild - -reformat_fasta --uppercase --allow_x --letters_per_line 60 --out data/dna.fna --label _dna --trace info/dna.trace --in /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/input.fna /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:14 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --stat info/dna.general --details /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:15 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --stat_fasta info/dna.multi_fasta /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:15 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:13 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --reformat_fasta --uppercase --allow_x --letters_per_line 60 --out data/dna.fna --label _dna --trace info/dna.trace --in /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/input.fna /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:14 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --stat info/dna.general --details /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:15 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --stat_fasta info/dna.multi_fasta /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:15 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --substring_n_distr info/dna.gap_distr /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:16 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/gc_distr.pl --in data/dna.fna --out info/dna.gc.csv --w 1000,8000 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:17 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/dna.fna --split dna.fa --max_contig 5000000 --min_contig 5000 --letters_per_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n --trace ../../info/training.trace /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:18 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/training.fna --stat info/training.general --allow_x --GC_PRECISION 0 --details /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:18 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/build_mod.pl --cfg /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run.cfg --section ES_ini --def /mnt/gpfs/leo/bin/gm_et_linux_64/heu_dir/heu_05_gcode_1_gc_48.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:18 2020] ln -sf /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod run/ini.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:18 2020] 17 contigs in training /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:19 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_4.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_4 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:19 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_3.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_3 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:19 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_2.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_2 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:20 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_5.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_5 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:20 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_6.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_6 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:21 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_9.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_9 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:19 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_1.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_1 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:21 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_7.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_7 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:22 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_10.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_10 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_12.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_12 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_11.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_11 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:21 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_8.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_8 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_13.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_13 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:24 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_14.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_14 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:24 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_15.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_15 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:25 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_16.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_16 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:25 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_17.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_17 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:25 2020] ln -sf /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/prev.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:26 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/parse_set.pl --section ES_A --cfg /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run.cfg --v /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:26 2020] error /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:17 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --reformat_fasta --uppercase --allow_x --letters_per_line 60 --out data/dna.fna --label _dna --trace info/dna.trace --in /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/input.fna /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:18 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --stat info/dna.general --details /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:18 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --stat_fasta info/dna.multi_fasta /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:18 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --substring_n_distr info/dna.gap_distr /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:19 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/gc_distr.pl --in data/dna.fna --out info/dna.gc.csv --w 1000,8000 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:21 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/dna.fna --split dna.fa --max_contig 5000000 --min_contig 5000 --letters_per_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n --trace ../../info/training.trace /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:21 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/training.fna --stat info/training.general --allow_x --GC_PRECISION 0 --details /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:22 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/build_mod.pl --cfg /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run.cfg --section ES_ini --def /mnt/gpfs/leo/bin/gm_et_linux_64/heu_dir/heu_05_gcode_1_gc_48.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:22 2020] ln -sf /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod run/ini.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:22 2020] 17 contigs in training /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:22 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_2.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_2 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:22 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_1.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_1 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_3.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_3 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_4.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_4 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_8.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_8 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_5.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_5 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_7.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_7 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:24 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_6.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_6 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:25 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_11.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_11 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:25 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_12.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_12 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:25 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_10.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_10 --seq data/dna.fna --allow_x --substring_n_distr info/dna.gap_distr /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:16 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/gc_distr.p l --in data/dna.fna --out info/dna.gc.csv --w 1000,8000 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:17 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/dna.fna --split dna.fa --max_contig 5000000 --min_ contig 5000 --letters_per_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n --trace ../../info/training. trace /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:18 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild - -seq data/training.fna --stat info/training.general --allow_x --GC_PRECISION 0 --details /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:18 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/build_mod. pl --cfg /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run.cfg --section ES_ini --def /mnt/gpfs/leo/bin/gm_e t_linux_64/heu_dir/heu_05_gcode_1_gc_48.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:18 2020] ln -sf /mnt/gpfs/leo/bin/EukCC/eukcc_testg enome/workfiles/gmes/run/ES_ini/es_ini.mod run/ini.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:18 2020] 17 contigs in training /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:19 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_4.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_4 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:19 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ (base) leo@ww-hmem02:~/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes$ cat gmes.log | pbcopy No command 'pbcopy' found, did you mean: Command 'bcopy' from package 'bareos-tools' (universe) Command 'bcopy' from package 'bacula-sd-sqlite3' (universe) Command 'bcopy' from package 'bacula-sd-pgsql' (universe) Command 'bcopy' from package 'bacula-sd-mysql' (universe) pbcopy: command not found (base) leo@ww-hmem02:~/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes$ less gmes.log (base) leo@ww-hmem02:~/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes$ more gmes.log /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:13 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild - -reformat_fasta --uppercase --allow_x --letters_per_line 60 --out data/dna.fna --label _dna --trace info/dna.trace --in /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/input.fna /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:14 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --stat info/dna.general --details /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:15 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --stat_fasta info/dna.multi_fasta /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:15 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --substring_n_distr info/dna.gap_distr /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:16 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/gc_distr.p l --in data/dna.fna --out info/dna.gc.csv --w 1000,8000 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:17 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/dna.fna --split dna.fa --max_contig 5000000 --min_ contig 5000 --letters_per_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n --trace ../../info/training. trace /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:18 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild - -seq data/training.fna --stat info/training.general --allow_x --GC_PRECISION 0 --details /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:18 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/build_mod. pl --cfg /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run.cfg --section ES_ini --def /mnt/gpfs/leo/bin/gm_e t_linux_64/heu_dir/heu_05_gcode_1_gc_48.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:18 2020] ln -sf /mnt/gpfs/leo/bin/EukCC/eukcc_testg enome/workfiles/gmes/run/ES_ini/es_ini.mod run/ini.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:18 2020] 17 contigs in training /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:19 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_4.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_4 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:19 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_3.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_3 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:19 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_2.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_2 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:20 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_5.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_5 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:20 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_6.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_6 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:21 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_9.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_9 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:19 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_1.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_1 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:21 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_7.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_7 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:22 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_10.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_10 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_12.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_12 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_11.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_11 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:21 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_8.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_8 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_13.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_13 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:24 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_14.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_14 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:24 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_15.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_15 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:25 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_16.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_16 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:25 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_17.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_17 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:25 2020] ln -sf /mnt/gpfs/leo/bin/EukCC/eukcc_testge nome/workfiles/gmes/run/ES_ini/es_ini.mod /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/prev.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:26 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/parse_set. pl --section ES_A --cfg /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run.cfg --v /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:33:26 2020] error /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:17 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild - -reformat_fasta --uppercase --allow_x --letters_per_line 60 --out data/dna.fna --label _dna --trace info/dna.trace --in /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/input.fna /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:18 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --stat info/dna.general --details /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:18 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --stat_fasta info/dna.multi_fasta /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:18 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq data/dna.fna --allow_x --substring_n_distr info/dna.gap_distr /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:19 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/gc_distr.p l --in data/dna.fna --out info/dna.gc.csv --w 1000,8000 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:21 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild --seq /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/dna.fna --split dna.fa --max_contig 5000000 --min_ contig 5000 --letters_per_line 100 --split_at_n 5000 --split_at_x 5000 --allow_x --x_to_n --trace ../../info/training. trace /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:21 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/probuild - -seq data/training.fna --stat info/training.general --allow_x --GC_PRECISION 0 --details /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:22 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/build_mod. pl --cfg /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run.cfg --section ES_ini --def /mnt/gpfs/leo/bin/gm_e t_linux_64/heu_dir/heu_05_gcode_1_gc_48.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:22 2020] ln -sf /mnt/gpfs/leo/bin/EukCC/eukcc_testg enome/workfiles/gmes/run/ES_ini/es_ini.mod run/ini.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:22 2020] 17 contigs in training /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:22 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_2.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_2 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:22 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_1.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_1 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_3.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_3 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_4.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_4 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_8.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_8 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_5.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_5 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:23 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_7.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_7 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:24 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_6.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_6 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:25 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_11.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_11 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:25 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_12.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_12 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:25 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_10.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_10 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:26 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_15.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_15 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:25 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_9.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/work files/gmes/data/training/dna.fa_9 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:26 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_14.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_14 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:26 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_13.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_13 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:27 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_17.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_17 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:27 2020] warning on: /mnt/gpfs/leo/bin/gm_et_linux_6 4/gmhmme3 -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_ini/es_ini.mod -f tr -o /mnt/gpfs/leo/ bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_16.out /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/wor kfiles/gmes/data/training/dna.fa_16 /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:28 2020] ln -sf /mnt/gpfs/leo/bin/EukCC/eukcc_testge nome/workfiles/gmes/run/ES_ini/es_ini.mod /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/prev.mod /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:29 2020] /mnt/gpfs/leo/bin/gm_et_linux_64/parse_set. pl --section ES_A --cfg /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run.cfg --v /home/leo/leo/bin/gm_et_linux_64/gmes_petap.pl : [Fri Feb 14 14:50:29 2020] error

openpaul commented 4 years ago

Ok, seems like the license is not the issue, but GeneMark-ES seems to be the problem.

As I did not develop GeneMark-ES my support will be limited to what I know, but I recognise this should be fixable. If you want I can help troubleshooting this, also to maybe document the process.

First we checked if GeneMark-ES complains about the license, but this seems to not be the case. Second we can debug the process by stepping manually trough the process of GeneMark-ES and try steps individually. Lucky for us Gmes reports what it did, when it failed.

In your case we can see it had a warning on running

/mnt/gpfs/leo/bin/gm_et_linux_64/gmhmme3  -m /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES
_ini/es_ini.mod   -f tr   -o /mnt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/run/ES_A_1/hmmout/dna.fa_2.out  /m
nt/gpfs/leo/bin/EukCC/eukcc_testgenome/workfiles/gmes/data/training/dna.fa_2

Can you copy paste this and report what the warning actually was? I suspect a segfault. A bug I noticed once before but then was not reproducible for me at the time, but I suspect it has something to do, with missing libraries, maybe.

leosouliotis commented 4 years ago

I just copied and pasted this command to the terminal and this is what I got:

Segmentation fault (core dumped)

openpaul commented 4 years ago

Ok, this is unfortunate as this tells us very little about the issue GeneMark-ES, or in this case the binary gmhmme3 has. I would assume that the binary was build using an older kernel or is linked against other libraries. What operating system are you using?

Can you test it on another linux install? We have been running on RedHat linux 7.4, which worked well. I would assume CentOS to be also fine.

leosouliotis commented 4 years ago

I am using Ubuntu 16.04.6 LTS, I have another linux machine with the same operating system, I could give it a shot there and see

openpaul commented 4 years ago

It might be related to the kernel. I am running 5.3.0-3-amd64 and I get the same error now on my debian machine. On our work machines, they run a kernel version 3.10 it works well. I know it worked with kernel 4.19 (or 4.12, cant remember exactly). So it might be related to the new 5.0 kernel.

I am currently building a VM to verify this. I will update this in the tutorial as soon as we narrowed this down. And if you want feel free to email the people from GeneMark-ES for support.

openpaul commented 4 years ago

Hello, so on my machine with kernel 5.4 I was not able to get the 64 bit version running again, which is running fine on Red Hat 7.4 with kernel 3.10 I can however use the 32 bit version. Remember that you need a different license key for the 32 bit version. So I assume you could try giving that a go.

openpaul commented 4 years ago

Closing for now, as its been weeks since the last comment

MrOlm commented 3 years ago

Hello,

I'm hitting this error as well and am wondering which 32 bit version you used? At the download site (http://exon.gatech.edu/GeneMark/license_download.cgi) GeneMark-ES appears to only be available in 64-bit version.

Thanks, Matt

Screen Shot 2020-10-15 at 1 26 04 PM
openpaul commented 3 years ago

I think they got rid of the 32 bit version, seems like GeneMark-ES causes issues. I can only recommend either emailing the people from GeneMark-ES or using a different gene caller.

I also had some success setting up a singulairty container:

I used a combination of two scripts for it:

build.sh


N="eukcc"
# Installing GenemarkES
tar xzvf gmes_linux_64.tar.gz
# build container as sandbox
sudo singularity build --sandbox $N $N.conf
# rm unzipped data
rm -rf gmes_linux_64

sudo singularity build $N.sif $N

With the config file looking like this:

Bootstrap: docker
From: conda/miniconda3

%files
    gmes_linux_64 /usr/

%post
    apt update
    apt upgrade -y
    apt dist-upgrade
    apt install -y cpanminus make gcc  dialog  procps bwa zip git less
    cpanm inc::Module::Install::DSL Hash::Merge MCE::Mutex FindBin Test::Pod Logger::Simple  Parallel::ForkManager.pm YAML

    #conda update --all
    conda install -c bioconda  -c conda-forge eukcc pygmes pplacer hmmer
    pip install --upgrade pygmes

%environment
    export LC_ALL=C     
    export PATH=/usr/gmes_linux_64/:$PATH

This worked out for me, but obviously requires singularity.

MrOlm commented 3 years ago

Hi Paul,

Interesting and thanks for the reply. I haven't used singularity before, but I do use Docker (a Docker container is how I'm running EukCC now as well). I see that the syntax of the config file looks like Docker but is a bit different. You don't happen to have a working Docker image as well, do you?

From my work with eukaryotes before I just can't believe how complicated gene calling is as compared to prokaryotes. It's also bizarre that GeneMark requires all of this license stuff, which complicates conda / Docker installs, and is such a difficult program to work with in my experience. That fact that EukCC handles all that stuff is great and the major reason I'm into it as a tool. It's too bad GeneMark doesn't play nice.

Thanks again, Matt

openpaul commented 3 years ago

Hey Matt, yeah GeneMark is a mayor issue. Singularity is pretty similar to docker, you can probably convert one recipe quite fast into another.

I am not super familiar with docker though, so I don't have a docker container, no. Sorry :/ If you come up with one feel free to share. I could add it to the documentation.

For our sake lets hope there will be progress in the eukaryotic gene predictors :)

Cheers