"fail to open FASTA index" during running database_annotation.pl !

[BiodeB]

Hi, First and foremost, I'd like to thank you for designing such wonderful program. However, during running database_annotation.pl, I'm getting some error like, fail to open FASTA index and final reformatting ...sh: line 1: 205531 Segmentation fault Please let me know where I'm doing wrong and how resolve this issue.

annotating input file with ANNOVAR ...NOTICE: Output files are written to cfDNA1_snp_anno_ISOWN.vcf.temp.annovar.vcf.temp.convert2annovar.variant_function, cfDNA1_snp_anno_ISOWN.vcf.temp.annovar.vcf.temp.convert2annovar.exonic_variant_function
NOTICE: Reading gene annotation from /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_tools/annovar/humandb/hg38_refGene.txt ... Done with 88819 transcripts (including 21511 without coding sequence annotation) for 28307 unique genes
NOTICE: Processing next batch with 3895568 unique variants in 3895568 input lines
NOTICE: Finished analyzing 1000000 query variants
NOTICE: Finished analyzing 2000000 query variants
NOTICE: Finished analyzing 3000000 query variants
NOTICE: Reading FASTA sequences from /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_tools/annovar/humandb/hg38_refGeneMrna.fa ... Done with 37514 sequences
WARNING: A total of 606 sequences will be ignored due to lack of correct ORF annotation

annotating input file with dbSNP ...

/projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline tabix -m 2020 -d /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/dbSNP/dbSNP_00-All.modified.vcf.gz -A -E -p dbSNP_00-All -i cfDNA1_snp_anno_ISOWN.vcf.temp.annovar.vcf  -f /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/HG/GRCh38_ch.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.dbSNP.vcfsh: line 1: 205513 Segmentation fault      /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline tabix -m 2020 -d /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/dbSNP/dbSNP_00-All.modified.vcf.gz -A -E -p dbSNP_00-All -i cfDNA1_snp_anno_ISOWN.vcf.temp.annovar.vcf -f /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/HG/GRCh38_ch.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.dbSNP.vcf

annotating input file with COSMIC ...

/projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline tabix -m 2020 -d /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/COSMIC_dat/CosmicCodNonCodVariants.vcf.gz -A -E -p COSMIC_96 -i cfDNA1_snp_anno_ISOWN.vcf.temp.dbSNP.vcf  -f /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/HG/GRCh38_ch.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.cosmic.vcfsh: line 1: 205517 Segmentation fault      /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline tabix -m 2020 -d /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/COSMIC_dat/CosmicCodNonCodVariants.vcf.gz -A -E -p COSMIC_96 -i cfDNA1_snp_anno_ISOWN.vcf.temp.dbSNP.vcf -f /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/HG/GRCh38_ch.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.cosmic.vcf

annotating input file with ExAC ...

/projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline tabix -m 2020 -d /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/ExAC/ExAC.r1.database.vcf.gz -A -E -p ExAC.r1.database -i cfDNA1_snp_anno_ISOWN.vcf.temp.cosmic.vcf  -f /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/HG/GRCh38_ch.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.exac.vcfsh: line 1: 205520 Segmentation fault      /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline tabix -m 2020 -d /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/ExAC/ExAC.r1.database.vcf.gz -A -E -p ExAC.r1.database -i cfDNA1_snp_anno_ISOWN.vcf.temp.cosmic.vcf -f /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/HG/GRCh38_ch.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.exac.vcf

annotating input file with MutationAccessor ...

/projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline tabix -m 2020 -d /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/mut_assessor/mut_assessor_r3_hg38.vcf.gz -A -E -p mut_assessor_r3_hg38 -i cfDNA1_snp_anno_ISOWN.vcf.temp.exac.vcf  -f /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/HG/GRCh38_ch.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.ma.vcfsh: line 1: 205523 Segmentation fault      /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline tabix -m 2020 -d /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/mut_assessor/mut_assessor_r3_hg38.vcf.gz -A -E -p mut_assessor_r3_hg38 -i cfDNA1_snp_anno_ISOWN.vcf.temp.exac.vcf -f /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/HG/GRCh38_ch.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.ma.vcf

annotating input file with PolyPhen ...

annotating input file with sequence context ...[fai_load] build FASTA index.
open: No such file or directory
[_razf_open] fail to open /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/HG/GRCh38_ch.fa
[fai_build] fail to open the FASTA file /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/HG/GRCh38_ch.fa
[fai_load] fail to open FASTA index.

calculating flanking region ...sh: line 1: 205529 Segmentation fault      /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline_internal tabix -m 9555 -i cfDNA1_snp_anno_ISOWN.vcf.temp.sequence.context.vcf -f /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/../external_databases/HG/GRCh38_ch.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.flanking.vcf

final reformatting ...sh: line 1: 205531 Segmentation fault      /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline_internal tabix -m 9503 -i cfDNA1_snp_anno_ISOWN.vcf.temp.flanking.vcf > cfDNA1_snp_anno_ISOWN.vcf.temp.flanking.vcf.temp.final.vcf

cleanup: deleting temporary files ( cfDNA1_snp_anno_ISOWN.vcf*.temp.* ) ...

real    7m2.150s
user    6m42.663s
sys 0m8.288s