Can't use an undefined value as a symbol reference

[hungweichen0327]

Dear developer:

When I ran this software, I encountered an error.

This is the content of the config file (FS003_diploid_config.txt):

Project:
-----------------------
Project name          = FS003_diploid
Assembly length       = WG
Genome size           = 
Ploidy                = 2
Circular              =
Threads               = 32
Output path           = /home/hwc/nas2_hwc/CPL_Cladosporium/assembly/FS003/NOVOLoci/diploid/
TMP path              = /home/hwc/nas2_hwc/CPL_Cladosporium/assembly/FS003/NOVOLoci/diploid_tmp/

Nanopore reads:
-----------------------
Nanopore reads        = /home/hwc/nas2_hwc/CPL_Cladosporium/ONT_data/merged_barcode06.fastq.gz
Local DB and NP reads =
Sequencing depth NP   = 13 
R10                   = yes
Min read length NP    = 1000

PacBio reads:
-----------------------
PacBio reads          =                  
Local DB and PB reads =
Sequencing depth PB   =
Min read length PB    = 

When I ran the NOVOLoci with the script:
nohup novoloci -c FS003_diploid_config.txt 1> novoloci_FS003_diploid.out 2> novoloci_FS003_diploid.err &

The novoloci_FS003_diploid.err shows:

nohup: ignoring input
Can't use an undefined value as a symbol reference at /home/hwc/mambaforge/envs/novoloci/bin/novoloci line 25353.
Finished with active child processes [1866182.0.main] (1)

The content of lines 25343 to 25363 is:

	$contig_length{$id} = length($read);
}

$circular = "";

END1:
#close OUTPUT18;
if ($seed_id2 ne "")
{
	close $filehandle{$seed_id2};
	close $filehandle3{$seed_id2};
	close $filehandle4{$seed_id2};
}
#print $id." ID_CURRENT\n";
#print length($read)." ID_CURRENT_LENGTH\n";

if ($first_back_assembly eq "yes" && length($read) < 1500)
{
	unlink $output_file5;
	unlink $output_file13;
	foreach my $seed_id_tmp (keys %seed)

and the last a few lines of the novoloci_FS003_diploid.out shows:

Nanopore reads
--------------
Total count             : 111960
Total length            : 550608480 bp
N50                     : 14093 bp
Average read length     : 4917 bp
Max read length         : 1494702 bp
Min read length         : 5 bp
Reads below min length  : 39611
Total removed bp        : 15296643 bp

Reduced sequencing depth: 13


Prepare seeds......OK

I installed the NOVOLoci using the conda.
How do I fix this problem? Thank you for the help.

[hungweichen0327]

Dear @ndierckx,

Do you have any suggestions how to solve this problem?
Thank you!

[ndierckx]

Hi, Sorry for the late reply, was moving countries, only got wifi today, never had to change to test conda installation, will do it now and get back to you..

[hungweichen0327]

Thank you for the kind help. Look forward to hearing from you soon.

[ndierckx]

Sorry for the delay, didn't had much time this week, but I fixed the problem, will upload a new version tomorrow.
But isn't Cladosporium haploid, because you put ploidy 2?

[hungweichen0327]

Thank you for fixing the problem.
Based on the README contents "Give the ploidy of the sample. If it is a very heterozygous diploid species (>2%), you can give ploidy 1", I would like to compare the results using ploidy = 1 and 2.