ERROR: Error reading in FragmentPicker::read_spine_x(): does not match size of query!

[Anonymous]

I have an odd error. When I try and run make_fragments.pl for my sequences first.fa and second.fa I recieve an error about read_spine but when I run the example from make fragment’s from 1elwA it works fine.
What do I need to do different?

Below is the sample error output:
Thank you
Casey
first.fa
>133862
HHHFDNIFKKIHQIIKDMDNNIKPAEHHQHMQHLINQIHQLFDDFHQQIHEVRAKQNIHKLLDKIQHMFHNFKNHLDPLWVHNQMHNFMHDMNQFMQHFDHNFK
second.fa
>137822
NHKLHHFMHDMKHLLQHFQHHFKTETIHHQMKNLINNLKKMIHNLNNDFNSVIFDQNMHQMFKDFQQMMDDIQKQLHFLPHNHNIDQLLQHLQNMMDQLHQKFQ

casey@casey-VirtualBox:~/Downloads/rosetta3.4/rosetta_demos/top10demo$ /home/casey/Downloads/rosetta3.4/rosetta_tools/fragment_tools/make_fragments.pl first.fasta
no id specified. parsing filename instead.
INTERMEDIATE: first.fasta
ID: firs CHAIN: t
File for psipred not found! Generating from scratch instead.
picking fragments with options:
DEBUG: 1
add_pdbs_to_vall:
chain: t
cleanup: 1
exclude_homologs_by_pdb_date: 0
f: first.fasta
fastafile: first.fasta
homs: 1
id: firs
n_candidates: 1000
n_frags: 200
old_name_format: 0
pick_frags: 1
porter: 0
porter_file:
psipred: 1
psipred_file:
rundir: /home/casey/Downloads/rosetta3.4/rosetta_demos/top10demo
runid: first
sam: 0
sam_file:
torsion_bin: 0

---

FILENAME: first.fasta
Sequence: HHHFDNIFKKIHQIIKDMDNNIKPAEHHQHMQHLINQIHQLFDDFHQQIHEVRAKQNIHKLLDKIQHMFHNFKNHLDPLWVHNQMHNFMHDMNQFMQHFDHNFK
running psipred
psipred file ok.
Command: /home/casey/Downloads/rosetta3.4/rosetta_source/bin/fragment_picker.linuxgccrelease @first_picker_cmd_size3.txt -j 8

ERROR: Error reading in FragmentPicker::read_spine_x(): does not match size of query!
ERROR:: Exit from: src/protocols/frag_picker/FragmentPicker.cc line: 1168
Finished running command: /home/casey/Downloads/rosetta3.4/rosetta_source/bin/fragment_picker.linuxgccrelease @first_picker_cmd_size3.txt -j 8
Output: core.init: Mini-Rosetta version unknown from unknown
core.init: command: /home/casey/Downloads/rosetta3.4/rosetta_source/bin/fragment_picker.linuxgccrelease @first_picker_cmd_size3.txt -j 8
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1595088512 seed_offset=0 real_seed=-1595088512
core.init.random: RandomGenerator:init: Normal mode, seed=-1595088512 RG_type=mt19937
protocols.frag_picker.FragmentPicker: reading a query profile from: first.checkpoint
protocols.frag_picker.FragmentPicker: picking fragments for query profile: HHHFDNIFKKIHQIIKDMDNNIKPAEHHQHMQHLINQIHQLFDDFHQQIHEVRAKQNIHKLLDKIQHMFHNFKNHLDPLWVHNQMHNFMHDMNQFMQHFDHNFK
protocols.frag_picker.FragmentPicker: reading a query sequence from: first.fasta
protocols.frag_picker.FragmentPicker: picking fragments for query sequence: HHHFDNIFKKIHQIIKDMDNNIKPAEHHQHMQHLINQIHQLFDDFHQQIHEVRAKQNIHKLLDKIQHMFHNFKNHLDPLWVHNQMHNFMHDMNQFMQHFDHNFK

Error: expected creation of first.200.3mers after running ‘/home/casey/Downloads/rosetta3.4/rosetta_source/bin/fragment_picker.linuxgccrelease @first_picker_cmd_size3.txt -j 8’!

[caseyrrichardson]

I found it there was a ^M at the end of the sequence when I removed it it made fragments.

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