Prodigal still processes gzip'ed files with no error
Opened this issue · 3 comments
nick-youngblut commented
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
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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
Prodigal does support .gz files, but only on the github HEAD version, not the most recent "release".
alanorth commented
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
I am not the author.
Can you just use prodigal -i <(gunzip -c file.fasta.gz) ?