EvidenceModeler # Error, cannot write

Question

[ashaneev07]

Hiii....

I've been trying to run Evidence modeler using gene predictions from Augustus and snap. But i'm getting the following error. Can anyone please help me out of this? Thank you in advance....

writing /home/Documents/EVM/inputs/genes.final.gff3 for  scf7180000642636
Error, cannot write to  scf7180000642636/genes.final.gff3 at partition_EVM_inputs.pl line 270, <$fh> line 1.

[lieven.sterck]

did you check if you have write permission in the directory you are writing to? Or that there is still sufficient storage available in that location?

[ashaneev07]

I've checked it with the snap file only but, that seems running smoothly and creates output files in the same directory. by adding the augustus result it shows the same error.

[lieven.sterck]

did you check if you did not fill up the disk space in the meanwhile?

perhaps also provide the full cmdline you are trying to execute.

[ashaneev07]

disc has more than1 tb available. The following command was used

perl EvmUtils/partition_EVM_inputs.pl --genome /home/Documents/data/P6125_Assembly.fasta.masked      --gene_predictions /home/Documents/EVM/inputs/genes.final.gff3 --protein_alignments /home/Documents/EVM/inputs/final.gff3      --transcript_alignments /home/Documents/EVM/inputs/gmap.spliced_alignments.gff3      --segmentSize 100000 --overlapSize 10000 --partition_listing partitions_list.out &

[lieven.sterck]

thanks.

and it's not because the disk is a 1Tb one it can't be full, or there could be user specified quota active on that disk.

[ashaneev07]

hmm... i've even run with augustus result only but that shows the same error. Is there any problem with augustus file? here is the file.

 scf7180000642636   AUGUSTUS    CDS 1880    1995    0.36    +   2   ID=g1.t1.cds;Parent=g1.t1
 scf7180000642636   AUGUSTUS    exon    1880    2262    .   +   .   Parent=g1.t1
 scf7180000642636   AUGUSTUS    stop_codon  1993    1995    .   +   0   Parent=g1.t1
 scf7180000642636   AUGUSTUS    transcription_end_site  2262    2262    .   +   .   Parent=g1.t1
 scf7180000642636   AUGUSTUS    gene    29106   29841   0.29    +   .   ID=g2
 scf7180000642636   AUGUSTUS    transcript  29106   29841   0.29    +   .   ID=g2.t1;Parent=g2
 scf7180000642636   AUGUSTUS    transcription_start_site    29106   29106   .   +   .   Parent=g2.t1
 scf7180000642636   AUGUSTUS    exon    29106   29841   .   +   .   Parent=g2.t1
 scf7180000642636   AUGUSTUS    start_codon 29146   29148   .   +   0   Parent=g2.t1

[lieven.sterck]

not at first sight no.

Perhaps you can compare this augustus gff file with one that does work? (or do none of them work?)

if you know a little bit of PERL language you could also have a look at what is going on on that specified line n the perl script.