Question: Unable to find FASTA index entry for 'unitig_2993_pilon error.
gravatar for tmrhyd
16 months ago by
tmrhyd0 wrote:

Hey all,

I have a sorted and indexed .bam file, and I am running it through freebayes, with the script : "freebayes -f /path/to/reference.fasta Bamfile.bam > NewVCF_file.vcf" I have in the directory I am running this script from, and in the directory that the reference file is in the index files for the reference, the .fai and .dict files. Every time I run this script I get the "Unable to find FASTA index entry for 'unitig_2993_pilon error. " Even know I have the index files.

I have gone back and used Picard tools to remake the .dict file and used the samtools faidx command to make the .fai reference file.

Is there something I'm not doing? I have the correct Bam file and index files and it just continually throws the indexing error. What could be the problem here?

ADD COMMENTlink modified 16 months ago • written 16 months ago by tmrhyd0


a dict file isn't needed for freebayes. What is the output of:

$ grep unitig_2993_pilon /path/to/reference.fasta


$ grep unitig_2993_pilon /path/to/reference.fasta.fai

fin swimmer

ADD REPLYlink written 16 months ago by finswimmer13k

Nothing happened for either? the command didn't run a error, but didn't return any input either.

ADD REPLYlink written 16 months ago by tmrhyd0

Hello again,

grep should print out lines that contain unitig_2993_pilon. If you're not getting any output, there are no such lines.

I would guess you're using a different reference for freebayes, than for the one used to generate the bam file. Let's check:

grep "^>" /path/to/reference.fasta


samtools view -H Bamfile.bam

Please use the formatting bar (especially the code option) to present the output.


ADD REPLYlink written 16 months ago by finswimmer13k

The reference fasta that I used to generate the bam file is the same one I am trying to read with freebayes now. And I ran grep "^>" /path/to/reference.fasta on the fasta file, and got no output from it.

I ran samtools view -H Bamfile.bam and got the following output

@HD VN:1.6  SO:coordinate
@SQ SN:unitig_2993_pilon    LN:2917948
@SQ SN:unitig_1070_pilon    LN:2422025
@SQ SN:unitig_3212_pilon    LN:2333870
@SQ SN:unitig_2610_pilon    LN:2172154
@SQ SN:unitig_1181_pilon    LN:2129517
@SQ SN:unitig_106_pilon LN:1838231
@SQ SN:unitig_1277_pilon    LN:1743889
@SQ SN:unitig_1021_pilon    LN:1663658
@SQ SN:unitig_3042_pilon    LN:1649263
@SQ SN:unitig_3279_pilon    LN:1527568
@SQ SN:unitig_2120_pilon    LN:1509310
@SQ SN:unitig_115_pilon LN:1444814
@SQ SN:unitig_379_pilon LN:1425260
@SQ SN:unitig_1029_pilon    LN:1373247
@SQ SN:unitig_252_pilon LN:1370713
@SQ SN:unitig_3261_pilon    LN:1337604
@SQ SN:unitig_1037_pilon    LN:1313761
@SQ SN:unitig_1269_pilon    LN:1299244
@SQ SN:unitig_1238_pilon    LN:1281759
@SQ SN:unitig_160_pilon LN:1281741
@SQ SN:unitig_301_pilon LN:1278989
@SQ SN:unitig_1087_pilon    LN:1271292
@SQ SN:unitig_210_pilon LN:1246260
@SQ SN:unitig_2504_pilon    LN:1246197
@SQ SN:unitig_172_pilon LN:1235266
@SQ SN:unitig_10_pilon  LN:1173389
@SQ SN:unitig_238_pilon LN:1162262
@SQ SN:unitig_497_pilon LN:1159025
@SQ SN:NODE_3240_length_10782_cov_174.486_ID_44076566_pilon LN:10785
@SQ SN:NODE_3312_length_10157_cov_4.82738_ID_39130478_pilon LN:10157
@SQ SN:NODE_3460_length_9131_cov_1843.18_ID_44734617_pilon  LN:9149
@RG ID:rgID LB:lib1 PL:ILLUMINA SM: PU:unit1    
@PG ID:bwa  PN:bwa  CL:bwa mem -M -t 8 -R @RG\tID:rgID\tLB:lib1\tPL:ILLUMINA\tSM:Sequence\tPU:unit1\tPI:252 /path/to/ref.fasta /path/to/trimmed.fastq /path/to/trimmed.fastq
@PG ID:SAMBLASTER   CL:samblaster -i stdin -o stdout
ADD REPLYlink modified 16 months ago • written 16 months ago by tmrhyd0
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