Getting "qpipeline: Permission denied" while running database_annotation.pl

[BiodeB]

Hi, First and foremost, I'd like to thank you for designing such wonderful program. Nevertheless, when I run database_annotation.pl, I receive the error ISOWN/bin/qpipeline: Permission denied. This is my first ISOWN run's output log file.

Please let me know where I'm doing wrong.

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/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/external_databases/GRCh38_chr.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.dbSNP.vcfsh: /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline: Permission denied

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/external_databases/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/external_databases/GRCh38_chr.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.cosmic.vcfsh: /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline: Permission denied

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/external_databases/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/external_databases/GRCh38_chr.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.exac.vcfsh: /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline: Permission denied

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/external_databases/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/external_databases/GRCh38_chr.fa > cfDNA1_snp_anno_ISOWN.vcf.temp.ma.vcfsh: /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline: Permission denied

annotating input file with PolyPhen ...sh: /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline: Permission denied

annotating input file with sequence context ...sh: /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline: Permission denied

calculating flanking region ...sh: /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline_internal: Permission denied

final reformatting ...sh: /projects/foran/SDLab/DK/data/MAP/VarRefDB/ISOWN/bin/qpipeline_internal: Permission denied

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

real    7m1.906s
user    6m42.055s
sys 0m8.200s

[BiodeB]

The issue is solved after using chmod +x on qpipeline and qpipeline_internal.