Hi all!
I am using an extra utility of HMMER: esl-sfetch, which retrieves parts of fastas based on asked coordinates (denoted by a -c FROM..TO) and sequence name, like this:
esl-sfetch -c FROM..TO input.fasta sequence name
Now, I'm finding it impossible to use FROM coordinates over 60. Bellow you can see a successful example followed by an unsuccessful one:
$ /home/src/hmmer-3.2.1/easel/miniapps/esl-sfetch -c 60..1015 allRepeats.fasta rnd-6_family-6587#Unknown
>rnd-6_family-6587#Unknown/60-1015 ATTTTCTCGTCCAGCTTGCAAGGTTTTTGAGAGAAGATCTGCACATCAGATCCAAACTCT CTCTGATTTCATCATCAGCAAATGGCTCGTNGGCTGCTTCAGATCCTGATTTACAAGTCA ACAAGAGACAAGGTTCGTCTACGACGGCTTTCGACCAAGNAGACCTTTACCTNGACGGTN CTGCAAAAGTCCTTCCCGGTGGACCGTTGCAGCTGACAAACGCTNCAGCGCANCAGATGG GTCATGCTTTCTNCAAGAANCCANTTGAGCTCAGTTCCTCTTTCTCGACNCATTTCGTGT GCGCTCTGGTGCCTAAGCCAGGCGCTGAAGGTGGCCACGGNATNGCCTTCGTNGTATCTC CTTCCACGGATTTCNCNCACGCAGAGCCAACNCGATACTTGGGGGTTTTCAACGTCTCAN CAAACGGATCTCCCTCTNCTCACGTNCTNGCTGTTGAGCTTGACACTGTNCGGAGCCCAG AGTTCGATGACATCAACGANAATCACGTNGGGATTGATGTGAACAGTCCNATGTCTGTCG NAGCNGCTCCAGCNTCTTACTATTCAGACANNGAAGGGAAGAACGAAAGCATGAACCTCT TGAGTGGAGAGCCTATNCAGGTNTGGGTGGATTACGAAGGAACTNTGCTCAACGTTTCGN TNGCTCCTCTCGAANTCCAGAAGCCAAGTCGGCCTCTCTTGTCAAGATCCATCAATCTTA CAGAGTTTTTCCGGATAGTCGAAACTGTTTGTCGGGTTCTCTGCAGCAACAGGGACAGCG GTNAGTGACCAGTACATCCTCGGGTGGAGTTTCAGCANAAGCAGAGGATCGCTGCAGAGC CTTGACATCTCAAAACTTCCCGAAGTTCCTCATCCTANAGCTACACATAAGAAGCTTCCT CTTGTTCTGCTTGNTTGTCTNGCTNTCGTGGTNTTGGCTGTTCTTGCAGGAGTTTA
$ /home/src/hmmer-3.2.1/easel/miniapps/esl-sfetch -c 61..1015 allRepeats.fasta rnd-6_family-6587#Unknown
Fatal exception (source file esl_sqio_ascii.c, line 1984):
Failed to fetch subsequence residues -- corrupt coords?
Aborted
Is this a bug? Does anyone have experience with it? I might have to replace this tool, but it's part of a pipeline of MAKER, for gene annotation.
Thank you in advance,
Ricardo
Unless you are willing to dig through the code, your best chance may be to contact the developer. I think this bug is something Sean Eddy would like to hear about.