oneSeq not working
cagescudero opened this issue · comments
Hello,
I followed the example provided in the README but I get the following error:
~/tools/HaMStR$ ./bin/oneSeq.pl -seqFile=data/infile.fa -seqid=P83876 -refspec=HUMAN@9606@1 -minDist=genus -maxDist=kingdom -coreOrth=5 -cleanup -global
Use of uninitialized value $force in numeric eq (==) at ./bin/oneSeq.pl line 1459.
MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDYSTKYRY
Your sequence was named: nlTazcr
No FAS filter for core-orthologs set.
Annotation tools found in /home/ubuntu/annotation_fas!
#########################
--> Running annoFAS.pl
--> acquiring sequence lengths
...done: sequence lengths are calculated for input file.
--> starting: cast
--> starting: decodeanhmm
decodeanhmm 1.1f
Copyright (C) 1998 by Anders Krogh
Tue Feb 11 15:42:51 2020
Model in file "/home/ubuntu/annotation_fas/TMHMM/TMHMM2.0.model" parsed successfully.
--> starting: COILS2
1 sequences 142 aas 0 in coil
--> starting: signalp.pl
--> starting: seg
--> starting: pfam_scan.pl
Starting hmmscan now...
hmmscan finished.
Creating output file...
finished.
Deleting temporary output file...
--> starting: smart_scan_v4.pl
Starting hmmscan now...
hmmscan finished.
Creating output file...
finished.
Deleting temporary output file...
--> annotation finished.
tool start: 11/02/2020 15:42:51:0
tool end : 11/02/2020 15:42:54:0
#####################
Building up the taxonomy tree. Start 1581435774
--------------------- WARNING ---------------------
MSG: Could not merge the lineage of 40276 with the rest of the tree
---------------------------------------------------
Can't call method "add_Descendent" on an undefined value at /home/ubuntu/anaconda3/envs/hamstr/lib/site_perl/5.26.2/Bio/Tree/TreeFunctionsI.pm line 529.
Best,
Cata
Hi,
could you please completely re-create a new conda env and install hamstr again? The warning message
Use of uninitialized value $force in numeric eq (==) at ./bin/oneSeq.pl line 1459.
indicates that you are not using the latest version. You should not see this any more with the new version.
About the error with the method add_Descendent, can you check the folder HaMStR/taxonomy and show me the files there?
Many thanks!
Hi,
I installed everything from zero and the example worked.
Thanks for the help!
Cata