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hyattpd / Prodigal

Prodigal Gene Prediction Software
GNU General Public License v3.0
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Prodigal still processes gzip'ed files with no error #72

Open nick-youngblut opened 4 years ago

nick-youngblut commented 4 years ago

I didn't know that prodigal can't handle gzip'ed files, so I ran some genomes through it, and prodigal finished successfully (no errors or warnings). However, the output was:

><B2>LZ^S^_<B7>2<A6>^P<ED><D8>Rݪ^P`<EE>E<A5>6@>^Te~<B9>^Lʟ<98>_1 # 2 # 2425 # -1 # ID=1_1;partial=10;start_type=GTG;rbs_motif=CCTCC;rbs_spacer=15bp;gc_cont=0.923
MXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXQXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXVXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXX
>z<85>^S<B9><B7>d^Y<C3>1<CF>U^Ej5<B2>Nm<9D><DA>L^DA<C5><EA><89>Z^U<DE>|!d<F3><F0>^Cw^\~B<E9><F5>$τ^Vl<CA><DD><EF><BA>&l<AD>6[<C5>v<FD>I<A6><B8><F3>q^D^P^Q*<83><A5><96><EB><FF>7^X暟<F0>oެ<C6><C9>}<C3>>^P[<B7><E4>^H<C8><F3>(g<85>sd<9A><AF>~<83>gn<C5>>+̷(N^ZaJu<A2>^H蓪;<F3>B<DF>/}^
<C3>?^RA<82>L<FA>G!k<B9>d<EC>{<9C>.̭}<A4>!H<EC><9F>$<FD>R<A7><93>xϒއs^DnS<8F>^N<F4>^FB:(0I'<ED><8F>hz♒(<87><FE>t^F?<EC>ܥC<AA>'S<FE><ED><95><E7>O<D9><DE>q_1 # 1 # 2988 # -1 # ID=2_1;partial=10;start_type=ATG;rbs_motif=CCC;rbs_spacer=12bp;gc_cont=0.934
MXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXHXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
[etc.]

It would be good if prodigal provided an error if gzip'ed files are used. Better yet, it would be great if prodigal just handled gzip'ed files.

tseemann commented 4 years ago

Prodigal does support .gz files, but only on the github HEAD version, not the most recent "release".

alanorth commented 4 years ago

Prodigal does support .gz files, but only on the github HEAD version, not the most recent "release".

On that note, could you tag a new release? I'm currently deploying this to my cluster with version git-004218fb. :\

tseemann commented 4 years ago

I am not the author. Can you just use prodigal -i <(gunzip -c file.fasta.gz) ?