error opening fasta file: ref/hg38.fasta: no fai for fasta

[dridk]

I ran the following command :

docker run -it -v ${PWD}:/input -v /mnt/R60/bioinformatique/hg38/:/ref brentp/smoove smoove call -x --name test --exclude /ref/exclude.cnvnator_100bp.GRCh38.20170403.bed --fasta ref/hg38.fasta -p 10 --genotype /input/OneSegHumanFemale1.dedup.bam /input/OneSegHumanFemale2.dedup.bam /input/OneSegHumanFemale3.dedup.bam /input/OneSegHumanFemale4.dedup.bam /input/SGT152803pur1.dedup.bam /input/SGT152803pur2.dedup.bam /input/SGT153103nonpur1.dedup.bam /input/SGT153103nonpur2.dedup.bam

I get this error :

[smoove] 2021/05/06 16:15:32 starting lumpy
[smoove] 2021/05/06 16:15:32 wrote lumpy command to .//test-lumpy-cmd.sh
[smoove] 2021/05/06 16:15:32 writing sorted, indexed file to test-smoove.genotyped.vcf.gz
[smoove] 2021/05/06 16:15:32 excluding variants with all unknown or homozygous reference genotypes
[smoove] 2021/05/06 16:15:32 > gsort version 0.0.6
[smoove] 2021/05/06 16:15:32 chr1       1000000
panic: error opening fasta file: ref/hg38.fasta: no fai for fasta

goroutine 196547 [running]:
github.com/brentp/smoove/lumpy.check(...)
        /home/brentp/go/go/src/github.com/brentp/smoove/lumpy/lumpy.go:54
github.com/brentp/smoove/lumpy.writeContigs(0xc000147dc0, 0x7ffec56c4db3, 0xe)
        /home/brentp/go/go/src/github.com/brentp/smoove/lumpy/lumpy.go:223 +0x558
github.com/brentp/smoove/lumpy.bndFilter.func1(0xc0057462e8, 0xc000147dc0, 0xc00d579500, 0xc008fe3aea, 0x7ffec56c4db3, 0xe, 0xc000db1260, 0x6)
        /home/brentp/go/go/src/github.com/brentp/smoove/lumpy/lumpy.go:275 +0x1e9
created by github.com/brentp/smoove/lumpy.bndFilter
        /home/brentp/go/go/src/github.com/brentp/smoove/lumpy/lumpy.go:266 +0x29f

But I am sure I have the FAI file ( generated with samtools faidx )

(gatk) ➜  output ls /mnt/R60/bioinformatique/hg38/hg38.fasta*
/mnt/R60/bioinformatique/hg38/hg38.fasta      /mnt/R60/bioinformatique/hg38/hg38.fasta.ann  /mnt/R60/bioinformatique/hg38/hg38.fasta.fai  /mnt/R60/bioinformatique/hg38/hg38.fasta.sa
/mnt/R60/bioinformatique/hg38/hg38.fasta.amb  /mnt/R60/bioinformatique/hg38/hg38.fasta.bwt  /mnt/R60/bioinformatique/hg38/hg38.fasta.pac

I have no idea... which file name it is looking for ?

[brentp]

Error is this: panic: error opening fasta file: ref/hg38.fasta: no fai for fasta you missed the / before your ref directory.

[yqlan]

Error is this: panic: error opening fasta file: ref/hg38.fasta: no fai for fasta you missed the / before your ref directory.

Hi, i have .fai file and i got same error:

'panic: error opening fasta file: /project2/araman/yqlan/yeastAdaptation_seqData/yeast_reference_genome-genes/sacCer3_WGS_idx/sacCer3.fa: no fai for fasta'

command: ` genome_idx=/project2/araman/yqlan/yeastAdaptation_seqData/yeast_reference_genome-genes/sacCer3_WGS_idx/sacCer3.fa smoove_sig=/project2/araman/yqlan/software/smoove.sif module load singularity/3.4.0 cd /project2/araman/yqlan/yeastAdaptation_seqData/wholeGenomeSeq_results/20240131_LH00315_0080_B22H3W5LT3-AR-Lan-8s

singularity exec $smoove_sig smoove call --outdir ./smoove_output/ --name AR-Lan-8s --fasta $genome_idx --support 100 -p 2 --genotype ./gatk_dataPreprocess/AR-YL-8s-*_recal.bam `

do you have any suggestions? Thanks.