Question: HTseq error: Too few arguements
0
gravatar for Ambika
21 months ago by
Ambika30
United States/Auburn/Auburn University
Ambika30 wrote:

Hi everyone,

I tried to run Htseq with my sorted bam files using the following argument but I am getting too few arguments error

My command looks like:

htseq-count -m union -f bam -r name -t  accepted_hits_sorted_1.bam /home/aubayp/augustus_Fov891A_65.gff > output_htseq_1.sam

Please help.

Thank you Ambika

rna-seq htseq • 1.6k views
ADD COMMENTlink modified 21 months ago by genomax70k • written 21 months ago by Ambika30

Do you have "_" at the beginning and end of the command or is that just the side effect of you trying to make the command bold? Way to format code is to enclose it in single tick marks (symbol next to number key 1) on either end of the command. They it shows up the way word code does in sentence before this one.

You are using a > (redirect output) command before the sam file name. Remove that and redirect the counts to a new file like htseq-count -m union -f bam -r name -t accepted_hits_sorted_1.bam /home/aubayp/augustus_Fov891A_65.gff > counts.file

ADD REPLYlink modified 21 months ago • written 21 months ago by genomax70k

"_" sign is the sign I used to make my commands bold. I tried the way you said and it is giving me same error.

ADD REPLYlink written 21 months ago by Ambika30
2

htseq-count -m union -f bam -r name accepted_hits_sorted_1.bam /home/aubayp/augustus_Fov891A_65.gff > counts.file

You have an extra -t in there without saying what you want to use for feature. If you remove that (or add -t exon) the command will work provided you have the right gff file.

Take a look at featureCounts otherwise. It is easy to use and fast.

ADD REPLYlink modified 21 months ago • written 21 months ago by genomax70k

Thank you genomax, that error is solved, However I am getting the error for gff file now .


Error occured when processing GFF file (line 19 of file /home/aubayp/augustus_Fov891A_65.gff): Failure parsing GFF attribute line [Exception type: ValueError, raised in __init__.py:164]


Does this mean my gff file is not in correct format or do I need to specify some additional features?

ADD REPLYlink written 21 months ago by Ambika30

Can you show lines 18, 19 and 20 of your gff?

ADD REPLYlink written 21 months ago by WouterDeCoster40k

That can be done using sed -n 18,20p /home/aubayp/augustus_Fov891A_65.gff

ADD REPLYlink written 21 months ago by genomax70k
tig00000038     AUGUSTUS        gene    1332    2596    0.83    -       .       g1
tig00000038     AUGUSTUS        transcript      1332    2596    0.83    -       .       g1.t1
tig00000038     AUGUSTUS        stop_codon      1332    1334    .       -       0       transcript_id "g1.t1"; gene_id "g1";

It looks like this

ADD REPLYlink modified 21 months ago by WouterDeCoster40k • written 21 months ago by Ambika30

Your gff looks weird. Where did you get it?

ADD REPLYlink written 21 months ago by WouterDeCoster40k

My labmate made this, using augustus I guess. Does the format needs to be changed?

ADD REPLYlink written 21 months ago by Ambika30

Have a look at the GFF specifications

ADD REPLYlink written 21 months ago by WouterDeCoster40k

Thank you WouterDeCoster will look into that.

ADD REPLYlink written 21 months ago by Ambika30
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