Stringtie --merge error "Warning: invalid start coordinate at line"

Question

[drajangirija]

Hi I am getting an error while running stringtie --merge

stringtie --merge -G /home/ec2-user/environment/nextflow-tutorial/data/exp-3/Homo_sapiens_GRCH38.96.gtf.gz -o merged.gtf *.gtf

The error is

```**Warning: invalid start coordinate at line:

:aG"VAm".VVLkg!"ܳpDÀ

                s|&]"`ʯ
                       AVoҮp9NwgՉk)ϭLjv"UrJ  H       s(2|)iJ sQH     u(f(0t),"˒q[ʏ,ReFL      uQ      u\d     !
                                                                                                             ń:r3(Ą:ౄTgbBܸDbBBZɋbBDbBXBy٬1NG"1]SLM'|vgjf

Warning: invalid start coordinate at line: h4TanC`=5fj=veHǴO _OOUP?dc|cչOaZK̽Q1k% {20JіPG(%kFwOFF WHHX3Ϯb[5"ȩq7V) 'l+\<hG %l:qwtE WL-yg֗'˸u niK_)kCE՜&BMc5U;U9e泐1wO 4qGO!/K GDx30<9"\<"DpOq]Zi\:{]KeLf4OO5CAo!^]G/,~;8!_Կߒ:D-V<gCmUǐh$9&a^,G<1,CIzgH/G<3 %iIij2! Warning: unexpected tab character in last column, line truncated:

Ru):F%YJ@8XBdY#GrYZ{Ycl|僰Ge鄊5!j)BDȍ@V9+~y\sʲƪ`ͲV

                                               Z\1c(8
                                                            du!u,K#S$FԲ4S,D#,k-K+D2,b!L9OAֳe}Y*GOe隹;tORpғz_
                                                                                                           ZVɑ\NiNjIȲ|dQ#GzYڨU5V$dYl        qde֜     ˧W3!G&YZ^j%'l      Y2ɲFQgYoS5V$dY$9Α9T     Y/'82Ebk.Ks:$!yK#,k/5g$!GMlett  FCzT:zp8ɑ\YŹVC8r$o>{R   ]cZe-   pde螼ee}-(U82ɲF

**```

Answer 1

[Pierre Lindenbaum]

it looks like this tool is not able to decode gzipped-files. Try again after gunzipping Homo_sapiens_GRCH38.96.gtf.gz

[drajangirija]

Thanks..It worked