Problems running the script nentferner.pl

[Jose Maria Martin-Duran]

Hi,

I'm trying to run HaMStR on my computer (Linux server). I installed HaMStR with ./configure --noublast and everything seemed to go OK, since the tests could run successfully. However, when I'm trying to run HaMStR on my dataset, I got a FATAL error, apparently with the nentferner.pl script. My protein fasta file has the following format (no break lines within sequences):

comp124034c0::comp124034c0seq1::g.18969::m.18969
TYRERWRKMLPFNVGKGREIAKAVKDLRTFGKQVIADRLKLIQSGSTNVPEDMLTFILKEAQLLSSGILLTYRERWRKMLPFNVGKGREIAKAVKDLRTFGKQVIADRLKLIQSGSTNVPEDMLTFILKEAQLLSSGIL
comp13277c0::comp13277c0seq1::g.6::m.6
FSHFDKDGQNNISLNEFLDSLRPPIDEKREQMIFQAFNAVDKDYDGVITINDFKGSYSMKRHPKYQTGEWTEEQCFADYLSKFDTENNPDNKITYEEFLNYYAAVSDRVRDDRAFKRSLPNAYDL
comp13307c0::comp13307c0seq1::g.9::m.9
KIDDTDEKSTDTSRPEDVETVVEEKEHSNRSVGRLAVGENVTENGILNLPPRRSQLVDQFFPEKSTDTSRPEDVETVVEEKEHSNRSVGRLAVGENVTENGILNLPPRRSQLVDQFFPAVVQPNMKKQ*

When I run this command:

hamstr -sequence_file=Austrognathia.noline.fasta -hmmset=lophotrochozoa_hmmer3 -refspec=schma_370 -taxon=Austrognathia -cleartmp -protein -cpu 4 -representative

I got the following output

removing newlines from the infile Austrognathia.noline.fasta such that a sequence forms a consecutive string
could not open >/Austrognathia.noline.fasta.mod
Checking for sequence type
Checking for the blast program succeeded
Checking for hmmsearch succeeded
Checking for genewise succeeded
checking for presence of the hmm files: succeeded
checking for presence of the core-ortholog file: succeeded
testing whether the taxon has been determined: succeeded
Checking for reference species and blast-dbs succeeded
checking for blast-dbs: succeeded
checking for low complexity filter setting: succeeded

There was an error running HaMStR v.13.2.6

VERSION: HaMStR v.13.2.6

HOSTNAME fritzen.sars.no

USER DEFINED PARAMTERS (inc. default values)

 -append:   not set
 -blastpath:    /sysdev/s9/chema/src/hamstr.v13.2.6/blast_dir
 -checkCoorthologsRef:  not set
 -cleartmp: 1
 -concat:   not set
 -est:  not set
 -eval_blast:   10
 -eval_hmmer:   1
 -filter:   T
 -hit_limit:    not set
 -hmm:  not set
 -hmmpath:  /sysdev/s9/chema/src/hamstr.v13.2.6/core_orthologs
 -hmmset:   lophotrochozoa_hmmer3
 -intron:   k
 -longhead: not set
 -nonoverlapping_cos:   not set
 -outpath:  .
 -protein:  1
 -rbh:  not set
 -refspec:  schma_370
 -relaxed:  not set
 -representative:   1
 -reuse:    not set
 -sequence_file:    Austrognathia.noline.fasta
 -show_hmmsets: not set
 -sort_global_align:    not set
 -strict:   not set
 -taxon:    Austrognathia
 -ublast:   0

INFILE PROCESSING

Removing line breaks from ./Austrognathia.noline.fasta.

FATAL: Problems running the script nentferner.pl

CHECKING FOR PROGRAMS

check for blastp succeeded
check for hmmsearch succeeded

CHECKING FOR HMMs

running HaMStR with all hmms in /sysdev/s9/chema/src/hamstr.v13.2.6/core_orthologs/lophotrochozoa_hmmer3/hmm_dir
check for /sysdev/s9/chema/src/hamstr.v13.2.6/core_orthologs/lophotrochozoa_hmmer3/lophotrochozoa_hmmer3.fa succeeded

CHECKING TAXON NAME

using default taxon Austrognathia for all sequences

CHECKING FOR REFERENCE TAXON

 Reference species for the re-blast: schma_370

CHECKING FOR BLAST DATABASES

check for /sysdev/s9/chema/src/hamstr.v13.2.6/blast_dir/schma_370/schma_370_prot succeeded

PROGRAM OPTIONS

hmmsearch will run with an e-value limit of 1
re-blast hit_limit: none applied
Blast will run with an evalue limit of 10

check for low complexity filter setting succeeded. Chosen value is T
HaMStR will run with the -representative option

However, the script worked well with the test datasets, and the perl modules are installed.

It's probably something quite stupid, but I cannot figure it out. Any help with issue will be welcome.

Thanks!

Chema

[Ingo Ebersberger]

Hi Chema,
please try adding the flag -central to the hamstr call and let me know how it goes.
Best,

Ingo