Error in matching of headers in FASTA and BAM

[jotech]

I'm having problems when creating the coverage file. After creating a mapping with bbmap I tried to use it with blobtools but get the error:

blobtools map2cov -i JUb134_2a/JUb134.contigs.fasta -b JUb134_mapping_sorted.bam
[+] Parsing FASTA - JUb134_2a/JUb134.contigs.fasta
[+] Parsing bam0 - /work_beegfs/sukem066/cembio/raw/assemblies/JUb134_mapping_sorted.bam
[X] Headers in FASTA and BAM don't seem to match

But the header seem to be fine:

cat JUb134_2a/JUb134.contigs.fasta | grep ">"
>tig00000001 len=3421598 reads=6559 covStat=2111.80 gappedBases=no class=contig suggestRepeat=no suggestCircular=yes
>tig00000088 len=189412 reads=99 covStat=264.14 gappedBases=no class=contig suggestRepeat=no suggestCircular=yes
>tig00000093 len=76753 reads=32 covStat=94.92 gappedBases=no class=contig suggestRepeat=no suggestCircular=yes
>tig00000099 len=15682 reads=6 covStat=-3.34 gappedBases=no class=contig suggestRepeat=no suggestCircular=no
>tig00001073 len=430451 reads=423 covStat=520.69 gappedBases=no class=contig suggestRepeat=no suggestCircular=no
>tig00001074 len=20212 reads=1 covStat=0.00 gappedBases=no class=contig suggestRepeat=no suggestCircular=no

samtools view -H JUb134_mapping_sorted.bam
@HD     VN:1.4  SO:coordinate
@SQ     SN:tig00000001 len=3421598 reads=6559 covStat=2111.80 gappedBases=no class=contig suggestRepeat=no suggestCircular=yes  LN:3421598
@SQ     SN:tig00000088 len=189412 reads=99 covStat=264.14 gappedBases=no class=contig suggestRepeat=no suggestCircular=yes      LN:189412
@SQ     SN:tig00000093 len=76753 reads=32 covStat=94.92 gappedBases=no class=contig suggestRepeat=no suggestCircular=yes        LN:76753
@SQ     SN:tig00000099 len=15682 reads=6 covStat=-3.34 gappedBases=no class=contig suggestRepeat=no suggestCircular=no  LN:15682
@SQ     SN:tig00001073 len=430451 reads=423 covStat=520.69 gappedBases=no class=contig suggestRepeat=no suggestCircular=no      LN:430451
@SQ     SN:tig00001074 len=20212 reads=1 covStat=0.00 gappedBases=no class=contig suggestRepeat=no suggestCircular=no   LN:20212
@PG     ID:BBMap        PN:BBMap        VN:38.69        CL:java -ea -Xmx172515m -Xms172515m align2.BBMap build=1 overwrite=true fastareadlen=500 ref=JUb134_2a/JUb134.contigs.fasta in=H07478-L1_S6_L001_R1_001_filtered.fastq in2=H07478-L1_S6_L001_R2_001_filtered.fastq out=JUb134_mapping.sam bamscript=bs.sh

I appreciate any help.

[DRL]

Hi jotech,

Blobtools will split headers on the first whitespace (see readme)

I did not know that bbmap did not do that. Easiest/fastest solution is probably to remap with bwa mem

cheers,

dom

[jotech]

ok this worked thanks!