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Can't call method "length" on an undefined value at /home/metaerg/bin/output_reports.pl line 316. #35

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roshanzhc opened this issue Dec 31, 2020 · 3 comments

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@roshanzhc
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[Thu Dec 31 12:50:05 2020] Running: /home/phixgen/MinPath/MinPath.py -any jk_2/data/cds.gene2ec.mapping.txt -map ec2path -report jk_2/data/cds.gene2ec.minpath -details jk_2/data/cds.gene2ec.minpath.details > /dev/null 2>&1;
[Thu Dec 31 12:50:11 2020] Writing tabular format summary output to jk_2/data/
[Thu Dec 31 12:50:36 2020] Writing tbl output to jk_2/data/
[Thu Dec 31 12:51:01 2020] Generating annotation statistics file
Can't call method "length" on an undefined value at /home/phixgen/metaerg/bin/output_reports.pl line 316.
[Thu Dec 31 12:52:19 2020] Could not run command:/media/phixgen/HDD2/miniconda3/bin/perl /home/phixgen/metaerg/bin/output_reports.pl -g jk_2/data/all.gff -o jk_2 -f jk_2/metaerg.pl_12312020.fna,

@roshanzhc
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$p->desc("$desc len=$len cid=$sid") if defined $p;
$ffn_fh->write_seq($p);

	my $aa_seq = $cds_aa_seqs->{TAG($f, 'ID')};
	$aa_seq->desc("$desc len=" . $aa_seq->length . " cid=$sid");           (Line 316)

@roshanzhc
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Please help us in correcting this final error. Thank you in advance.

@tsa4a12
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tsa4a12 commented Aug 3, 2021

Program runs fine when I deal with assembled contigs,
yet I also encountered similar problem when the input is already ORFs. (under the section #Add locus_tags and protein_id[CDS only] (and Parent genes if asked))

......
[Tue Aug 3 07:21:39 2021] ******Finish annotate cds

[Tue Aug 3 07:21:44 2021] Adding /locus_tag identifiers
Can't call method "length" on an undefined value at /home/tom/tools/metaerg/bin/metaerg.pl line 143, line 39137.

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