GLnexus , error while combining gvcf files

[DineshRavindraRaju]

Hi All,

I have 40 gvcfs file generated from deepvariant and was combining them using GLnexus

here is my sbatch file

#SBATCH -J GLnexus
#SBATCH -p normal
#SBATCH -N 5
#SBATCH -n 11
#SBATCH -o GLnexus.o%j
#SBATCH -e GLnexus.e%j
#SBATCH -t 00:08:00
#SBATCH --mail-type=ALL
#SBATCH --qos=maxjobs100

<------ Account String ----->
<--- (Use this ONLY if you have MULTIPLE accounts) --->
#SBATCH -A MCB21061
#------------------------------------------------------

module load tacc-apptainer
module load parallel-netcdf/4.6.2

cd /scratch/09505/s223885/deepvariant_test/test/gl_test/

apptainer exec /home1/09505/s223885/GLnexus/glnexus_v1.4.1.sif glnexus_cli --config DeepVariantWES /scratch/09505/s223885/deepvariant_test/test/gl_vcf_small/*.g.vcf.gz > /scratch/09505/s223885/deepvariant_test/test/gl_test/ALL_40.bcf

ERROR

[3252169] [2023-11-05 15:49:18.682] [GLnexus] [info] contigs: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y MT GL000207.1 GL000226.1 GL000229.1 GL000231.1 GL000210.1 GL000239.1 GL000235.1 GL000201.1 GL000247.1 GL000245.1 GL000197.1 GL000203.1 GL000246.1 GL000249.1 GL000196.1 GL000248.1 GL000244.1 GL000238.1 GL000202.1 GL000234.1 GL000232.1 GL000206.1 GL000240.1 GL000236.1 GL000241.1 GL000243.1 GL000242.1 GL000230.1 GL000237.1 GL000233.1 GL000204.1 GL000198.1 GL000208.1 GL000191.1 GL000227.1 GL000228.1 GL000214.1 GL000221.1 GL000209.1 GL000218.1 GL000220.1 GL000213.1 GL000211.1 GL000199.1 GL000217.1 GL000216.1 GL000215.1 GL000205.1 GL000219.1 GL000224.1 GL000223.1 GL000195.1 GL000212.1 GL000222.1 GL000200.1 GL000193.1 GL000194.1 GL000225.1 GL000192.1 NC_007605 hs37d5
[3252169] [2023-11-05 15:49:19.066] [GLnexus] [info] db_get_contigs GLnexus.DB
[3252169] [2023-11-05 15:49:19.590] [GLnexus] [info] Beginning bulk load with no range filter.
[3252169] [2023-11-05 15:50:54.588] [GLnexus] [info] Loaded 40 datasets with 40 samples; 116674418800 bytes in 1318363541 BCF records (310 duplicate) in 3821600 buckets. Bucket max 357928 bytes, 3920 records. 0 BCF records skipped due to caller-specific exceptions
[3252169] [2023-11-05 15:50:54.589] [GLnexus] [info] Created sample set *@40
[3252169] [2023-11-05 15:50:54.590] [GLnexus] [info] Flushing database...
[3252169] [2023-11-05 15:52:43.895] [GLnexus] [info] Bulk load complete!
[3252169] [2023-11-05 15:52:44.589] [GLnexus] [warning] Processing full length of 86 contigs, as no --bed was provided. Providing a BED file with regions of interest, if applicable, can speed this up.
[3252169] [2023-11-05 15:52:44.600] [GLnexus] [info] found sample set *@40
[3252169] [2023-11-05 15:52:44.601] [GLnexus] [info] discovering alleles in 86 range(s) on 126 threads
[3252169] [2023-11-05 15:54:23.937] [GLnexus] [info] discovered 11655338 alleles

terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc

/var/spool/slurmd/job1297083/slurm_script: line 38: 3252143 Aborted (core dumped) apptainer exec
/home1/09505/s223885/GLnexus/glnexus_v1.4.1.sif glnexus_cli --config DeepVariantWES /scratch/09505/s223885/deepvariant_test/test/gl_vcf_small/*.g.vcf.gz > /scratch/09505/s223885/deepvariant_test/test/gl_test/ALL_24.bcf

[DineshRavindraRaju]

Hi All,

Could you guys help me fix the above error .@mlin @VorontsovIE @cmclean @geetduggal

Thankyou

[VorontsovIE]

Is the file actually named .g.vcf.gz ? (in /scratch/09505/s223885/deepvariant_test/test/gl_vcf_small/.g.vcf.gz)

[DineshRavindraRaju]

Sorry that was a typo it's written as "*.g.vcf.gz" @VorontsovIE