Graphmap 0.3.0 results in many unaligned seqs

[andreas-wilm]

See also isovic/graphmap#28

See e.g. AHS182

cd /mnt/projects/wilma/16s/S16_V2/bugs/AHS182

source /mnt/software/etc/gis.bashrc
source activate py3k
snakemake -s snake.make --configfile conf.json -p -T --dryrun --force


new:

samtools view graphmap-0.3.0-1d16f07.ident.bam | head -n 1
82|ACCG02000012.525518.527039   0   742595  281 1   477M1D249M  *   0   0   <removed>   *   MD:Z:3C473^G246T2   NM:i:3  AS:i:3604   H0:i:4  ZE:f:0  ZF:f:0.334728   ZQ:i:726    ZR:i:1382   Xi:f:99.6

samtools view greengenes-hits-graphmap.bam | grep '821|AF414833.1.1363'
821|AF414833.1.1363 4   *   0   255 *   *   0   0   <removed> * NM:i:-1 AS:i:-731   H0:i:0  ZE:f:inf    ZF:f:0  ZQ:i:731    ZR:i:0  Xi:f:0

/mnt/projects/wilma/16s/S16_V2_inst/f714a48/classify_hits.py -f -q emirge_outprimer_trimmed.fa -i graphmap-0.3.0-1d16f07.ident.bam -t /mnt/genomeDB/misc/greengenes.secondgenome.com/downloads/13_5/gg_13_5_otus/taxonomy/99_otu_taxonomy.txt -o -
82|ACCG02000012.525518.527039   0.290834    742595  99.6    k:Bacteria  p:Actinobacteria    c:Actinobacteria    o:Bifidobacteriales f:Bifidobacteriaceae    g:Bifidobacterium   s:breve
821|AF414833.1.1363 0.127213    *   0   k:  p:  c:  o:  f:  g:  s:

old:

samtools view graphmap-0.2.2-dev-604a386.ident.bam | head -n 1
82|ACCG02000012.525518.527039   0   484303  338 1   726M    *   0   0   <removed>   *   NM:i:2  AS:i:3612   H0:i:1  ZE:f:0  ZF:f:0.334728   ZQ:i:726    ZR:i:1535   Xi:f:99.7
821|AF414833.1.1363 0   4480544 347 0   731M    *   0   0   <removed> * NM:i:5  AS:i:3610   H0:i:1  ZE:f:0  ZF:f:0.335099   ZQ:i:731    ZR:i:1536   Xi:f:99.3

/mnt/projects/wilma/16s/S16_V2_inst/f714a48/classify_hits.py -f -q emirge_outprimer_trimmed.fa -i graphmap-0.2.2-dev-604a386.ident.bam -t /mnt/genomeDB/misc/greengenes.secondgenome.com/downloads/13_5/gg_13_5_otus/taxonomy/99_otu_taxonomy.txt -o -
82|ACCG02000012.525518.527039   0.290834    484303  99.7    k:Bacteria  p:Actinobacteria    c:Actinobacteria    o:Bifidobacteriales f:Bifidobacteriaceae    g:Bifidobacterium   s:breve
821|AF414833.1.1363 0.127213    4480544 99.3    k:Bacteria  p:Bacteroidetes c:Bacteroidia   o:Bacteroidales f:Prevotellaceae    g:Prevotella    s:nigrescens