#1 error with own gtf file

[Anonymous]

htseq-count HTSeq-0.5.3p9 with python 2.6.6 on Scientific Linux 6.3 (=RHEL 6.3) - which works flawless with other SAMs (e.g. RUM mapped) and ensembl GTF files.

problem (see http://seqanswers.com/forums/showthread.php?t=25897\):
i have a sorted sam file from stampy (paired end) mapped against all viral sequences (multiFA-file) looking like this:
_____________________________
>AC_000001.1
CATCATCAATAATAT...
>AC_000002.1
CATCATCAATAATCT...
...
_____________________________

stampy command:
--- code ---
$stampy/stampy.py --substitutionrate=0.01 -t 20 --sensitive --xcigar -g $index/viruses -h $index/viruses -o out.sam \
-M $fq1 $fq2
---------------

and made an own gtf file from the multiFA like this:
____________________________________________________________
AC_000001.1 virus genome 1 33034 . . . gene_id "AC_000001.1";
AC_000002.1 virus genome 1 34446 . . . gene_id "AC_000002.1";
AC_000003.1 virus genome 1 30536 . . . gene_id "AC_000003.1";
____________________________________________________________

now I want count all mapped read-pairs, which map both to one virus genome (i.e. multiFA-entry):

-- code --
htseq-count -m union -s no -t genome -i gene_id $sam $gff > ${name}.count
-------------

why do i get this error:

--- error ---
Error occured in line 1 of file /home/ws/Data/Oncotest/fa/viral_genome_sorted.fa/viral_genome.GFF.
Error: [Errno 20] Not a directory: '/home/ws/Data/Oncotest/fa/viral_genome_sorted.fa/viral_genome.GFF'
[Exception type: IOError, raised in __init__.py:45]
---------------

[Simon Anders]

My guess is that something went wrong with your shell code expansions. The file name given in the error message, "'/home/ws/Data/Oncotest/fa/viral_genome_sorted.fa/viral_genome.GFF", seems to be two file names with the separating space missing.

Put an "echo" in front of your "htseq-count ..." line to see precisely what the shell variables $sam and $gff expand to.

[Anonymous]

embarrassing, toe-curling embarrassing - i should have looked simply at the error - the path was wrong, as you supposed...