InParanoid ERROR : "Blast output file A->B is missing", No sqltable output file is produced

Question

[hlb580]

Hi, I am trying to run 6 Fasta Files(100 seq each) in Inparanoid to obtain the sqltables in order to use them later on on QuickParanoid, however some of the runs: 'perl inparanoid.pl Fastasequence_1 Fastasequence_2' output the following 'error' and do not provide a sqltable file like the other runs, I have no clue what is going on and how to fix it, Thank you very much in advance for your help

100 sequences in file Octopeteuthis 100 sequences in file Sdofleini Trying to run BLAST now - this may take several hours ... or days in worst case! Formatting BLAST databases Done formatting Starting BLAST searches...

Starting first BLAST pass for Octopeteuthis - Octopeteuthis on Tue May 16 13:49:54 CEST 2017 [blastall] WARNING: the -C 3 argument is currently experimental

Starting second BLAST pass for Octopeteuthis - Octopeteuthis on Tue May 16 13:49:55 CEST 2017

Starting first BLAST pass for Octopeteuthis - Sdofleini on Tue May 16 13:50:01 CEST 2017 [blastall] WARNING: the -C 3 argument is currently experimental

Starting second BLAST pass for Octopeteuthis - Sdofleini on Tue May 16 13:50:01 CEST 2017

Starting first BLAST pass for Sdofleini - Octopeteuthis on Tue May 16 13:50:01 CEST 2017 [blastall] WARNING: the -C 3 argument is currently experimental

Starting second BLAST pass for Sdofleini - Octopeteuthis on Tue May 16 13:50:01 CEST 2017

Starting first BLAST pass for Sdofleini - Sdofleini on Tue May 16 13:50:01 CEST 2017 [blastall] WARNING: the -C 3 argument is currently experimental

Starting second BLAST pass for Sdofleini - Sdofleini on Tue May 16 13:50:02 CEST 2017 Done BLAST searches. Starting ortholog detection... Blast output file A->B is missing

[Andrzej Zielezinski]

I had the same error once. If I remember well, this had something to do with FASTA definition lines. In my case, InParanoid didn't parse FASTA sequences correctly if they contained quote characters etc. Check your query files - it would be best if you limit the FASTA definition lines to identifier only (without any descriptions).

[hlb580]

Thank you very much, I was thinking it could also be something like that, I will try it out. Thanks again

[hlb580]

No, it did not work the files are like this now, no description, simple header:

>OCTO
MDTLPSVHFFCLSLSLSLSLSDPSIYLAQSQSPYFTSYFTCSKMVYCICRTIRLDALRGY
LENCRSLQFLQAPITVHIERW
>OCTO
MNFQSNKLRDAVLVALVAGVASTATAQAQEATNLDRISVTGSRIKSTDIETSQPVLSLTR
ADIEKQGVTSVADILQRVAANGAALNRTFNNGGDGSAGVSLRNLGAERTLVLVNGRRWTT
GLDGSVDLNTIPTAMIERIDILKDGASTIYGSDAIAGVVNIITKQNFDGAEVNAYKGQYS
DGDGEREAYDFTLGTVTDRASITVGASYVNEKSVMAGDRKISAGGPPFFSGQSATGIPGS
YVRNGNQYIIVNGVETAFDPNVHGYNTAPDNYLLTPNERTSLFVLGSYNVTD

[Andrzej Zielezinski]

How about duplicated identifiers (e.g. OCTO)?

[hlb580]

Hi, Thanks again, I also changed that, so I joined the header and the description like this(separated by _ and also completely concatenated(no spaces):

>OCTO_evgtrinLoc10c0g1t1
MDTLPSVHFFCLSLSLSLSLSDPSIYLAQSQSPYFTSYFTCSKMVYCICRTIRLDALRGY
LENCRSLQFLQAPITVHIERW
>OCTO_evgtrinLoc11c0g1t1
MNFQSNKLRDAVLVALVAGVASTATAQAQEATNLDRISVTGSRIKSTDIETSQPVLSLTR
ADIEKQGVTSVADILQRVAANGAALNRTFNNGGDGSAGVSLRNLGAERTLVLVNGRRWTT
GLDGSVDLNTIPTAMIERIDILKDGASTIYGSDAIAGVVNIITKQNFDGAEVNAYKGQYS
DGDGEREAYDFTLGTVTDRASITVGASYVNEKSVMAGDRKISAGGPPFFSGQSATGIPGS
YVRNGNQYIIVNGVETAFDPNVHGYNTAPDNYLLTPNERTSLFVLGSYNVTD

Still no luck, I am digging in inparanoid and how it works in full mode.I will keep trying, thank you very much for all your suggestions

Answer 1

[huangxiaoyun1]

I met the same problem. It also said "Blast output file A->B is missing". Have you fixed this problem?