[loadChr] Error loading fasta info from chr

[dlema82]

Hello, I am trying to get some Fst stats,
I've been all over google and github and sourceforge and biostars and etc. I cannot find a solution. Please help me find a workaround, or explain what I am doing wrong. What am I missing here????

I keep getting this error:

[loadChr] Error loading fasta info from chr:'KP202265.1_Panthera_pardus'
-> Problem with length of fastafile vs length of chr in BAM header
-> Chromosome name: 'KP202265.1_Panthera_pardus' length from BAM header:24850 length from fai file:0
Trying to access fasta efter end of chromsome+200:KP202265.1_Panthera_pardus/KP202265.1_Panthera_pardus pos=250 ref_len=0
Trying to access fasta efter end of chromsome+200:KP202265.1_Panthera_pardus/KP202265.1_Panthera_pardus pos=433 ref_len=0

I have tried using the -checkBamHeaders flag, but I get the error regardless. I've also tried samtools reheader to try to make them compatible, but it doesn't work either, I still get the error.

This is for haploid mitochondrial data. Here is my ref fai:
KP202265.1_Panthera_pardus 24850 28 70 71

And the header for the ref fasta:

KP202265.1_Panthera_pardus

And here is the head of my bam files called with:
samtools view 2469_mtgenome.mapped.srt.dedup.KP.bam | head -n 2
A00312:75:HLLFVDSXX:4:1215:13810:31923 163 KP202265.1_Panthera_pardus 160 4M1I145M = 170 330 CGATGGGTTAATGACTAATCAGCCCATGATCACACATAACTGTGGTGTCATGCATTTGGTATCTTTAATTTTTAGGGGGTCGAACTTGCTATGACTCAGCTATGACCTAAAGGTCCTGACTCAGTCAAATATAATGTAGCTGGACTTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFF,FFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFF:FFF MC:Z:96M8D43M3D11M MD:Z:9G2G30A17T87 PG:Z:MarkDuplicates NM:i:5 AS:i:126 XS:i:0
A00312:75:HLLFVDSXX:4:2351:6253:11318 145 KP202265.1_Panthera_pardus 160 4M1I145M = 16482 16334 CGATGGGTTAATGACTAATCAGCCCATGATCACACATAACTGTGGTGTCATGCATTTGGTATCTTTAATTTTTAGGGGGTCGAACTTGCTATGACTCAGCTATGACCTAAAGGTCCTGACTCAGTCAAATATAATGTAGCTGGACTTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF MC:Z:150M MD:Z:9G2G30A17T87 PG:Z:MarkDuplicates NM:i:5 AS:i:126 XS:i:0

Here is my prompt:
ANGSD="/nas3/dlema/angsd/angsd"
REAL="/nas3/dlema/angsd/misc/realSFS"
ANC="/nas3/dlema/NC028302.1_Pleo_mtgenome.fasta"
REF="/nas3/dlema/Ppardus_mtgenome_li_etal_plateau.fa"
FILTERS="-minMapQ 30 -minQ 20"
OPT=" -dosaf 1 -gl 1" ##I have tried with and without -checkBamHeaders and I get the error regardless

$ANGSD -b africa.filelist -anc $ANC -out total_africa $FILTERS $OPT -ref $REF
$ANGSD -b east.filelist -anc $ANC -out east $FILTERS $OPT -ref $REF
$ANGSD -b west.filelist -anc $ANC -out west $FILTERS $OPT -ref $REF
$ANGSD -b west1.filelist -anc $ANC -out west1 $FILTERS $OPT -ref $REF
$ANGSD -b northeast.filelist -anc $ANC -out northeast $FILTERS $OPT -ref $REF
$ANGSD -b south.filelist -anc $ANC -out south $FILTERS $OPT -ref $REF
$ANGSD -b east1.filelist -anc $ANC -out east1 $FILTERS $OPT -ref $REF
$ANGSD -b east2.filelist -anc $ANC -out east2 $FILTERS $OPT -ref $REF

$REAL total_africa.saf.idx > total_africa.sfs
$REAL east.saf.idx > east.sfs
$REAL west.saf.idx > west.sfs
$REAL west1.saf.idx > west1.sfs
$REAL northeast.saf.idx > northeast.sfs
$REAL south.saf.idx > south.sfs
$REAL east1.saf.idx > east1.sfs
$REAL east2.saf.idx > east2.sfs

$REAL east.saf.idx west.saf.idx > east_west.ml
$REAL east.saf.idx west1.saf.idx > east_west1.ml
$REAL east.saf.idx northeast.saf.idx > east_northeast.ml
$REAL east.saf.idx south.saf.idx > east_south.ml
$REAL east1.saf.idx east2.saf.idx > east1_east2.ml
$REAL west.saf.idx west1.saf.idx > west_west1.ml
$REAL west.saf.idx northeast.saf.idx > west_northeast.ml
$REAL west.saf.idx south.saf.idx > west_south.ml
$REAL west1.saf.idx northeast.saf.idx > west1_northeast.ml
$REAL west1.saf.idx south.saf.idx > west1_south.ml
$REAL northeast.saf.idx south.saf.idx > northeast_south.ml

$REAL fst index east.saf.idx west.saf.idx -sfs east_west.ml -fstout east.west
$REAL fst index east.saf.idx west1.saf.idx -sfs east_west1.ml -fstout east.west1
$REAL fst index east.saf.idx northeast.saf.idx -sfs east_northeast.ml -fstout east.northeast
$REAL fst index east.saf.idx south.saf.idx -sfs east_south.ml -fstout east.south
$REAL fst index east1.saf.idx east2.saf.idx -sfs east1_east2.ml -fstout east1.east2
$REAL fst index west.saf.idx west1.saf.idx -sfs west_west1.ml -fstout west.west1
$REAL fst index west.saf.idx northeast.saf.idx -sfs west_northeast.ml -fstout west.northeast
$REAL fst index west.saf.idx south.saf.idx -sfs west_south.ml -fstout west.south
$REAL fst index west1.saf.idx northeast.saf.idx -sfs west1_northeast.ml -fstout west1.northeast
$REAL fst index west1.saf.idx south.saf.idx -sfs west1_south.ml -fstout west1.south
$REAL fst index northeast.saf.idx south.saf.idx -sfs northeast_south.ml -fstout northeast.south

Thank you!!