EMBL importing issue
Hi,
I have an issue which seems to be similar or the same as issue #129.
I am trying to import the latest EMBL release using the methods outlined in the wolf tutorial but I get this error below. on this file Parsing this file STD_PLN_4.dat.gz. I have tired removing the file to see if the issue only this file is the issue but I also get the fault with STD_VRL_11.dat.gz.
I have tried updating obitools using pip and currently have version 3.0.1b22 which I hope is the latest version but it doesn't seem to resolve the issue for me at least.
The sequence that cannot be imported is very long so I just attached the start and the end which I think are the only bits which may have useful information.
DEBUG /private/var/folders/hx/z6wbn36d04l48hw501jt40lm0000gn/T/pip-install-gxjlmvbt/obitools3_e27c130ed86d4de0aeeea00f0794a369/src/obiavl.c:1669:obi_create_avl, obi_errno = 20, errno = 24 : Error creating an AVL tree file DEBUG /private/var/folders/hx/z6wbn36d04l48hw501jt40lm0000gn/T/pip-install-gxjlmvbt/obitools3_e27c130ed86d4de0aeeea00f0794a369/src/obiavl.c:1013:add_new_avl_in_group, obi_errno = 20, errno = 24 : Error creating a new AVL tree in a group
Could not import sequence: {b'ID': b'LR812263', b'NUC_SEQ': b'CAAATCTAGCAAGAATAGGCCAAAACTACAAGTTTTGAGGAGTTCCCCGTAACTGGACCCCGAGGTTCCCGAAATGTTTGGATCACAGCGGGACACTAAATCAGTGACTAATAACATACAAAATTGTCTGCAGTAGTCCTAAACTGCGAGTTTTGACGAGTTCCACGTAACCGGACCCCGAGGTTCCTGAAACATCCGGATCGTAGCGGGACCCAAAATCAATGAGTAATTGCATACAAAACTGGCAAGAACAGGCCAAAACTGCGAGTTTTAACGAGTTTTCGGTAACCGGACCCCGGGGGTCCCGAAACATTCGTATCGCAGGGAAACCAAAAACAGTGACTAATGGCCTAGAAAACTAGCCAGAACAGGCCAACACTGTGAGTTTTCACGAATTCCCCGTAACCCCACCTCGGGGTTCCCGAAACGTTCGGATCGCAGCGGGACCCAAAATGAGTGAGTAATAGCATATAAAACTAGCCAGAATAGGCCAAAACTGCGAGTTTGAAGAGTTCCCCGTAACCACACCCCGGGGTTCCCGAAATGTTCGGATCGTAGTAGGACCCCAAATCAGTCAGTAATAGCATACAAATCTAGCAAGAATAGGCCAAAACTACAAGTTTTGAGGAGTTCCCCGTAACTGGACCCCGAG
.........
GACACGCTCGTCGGACACCGGCAGGGCAGCTAGCTAGTCTGTGCGCGTCGCGACTCCCTTCACCAGCCGTCTTCTTCGTCAACGCTCGCAAGTTGTTCGACGGTTTGCCAAGGTACAAAATGGACTCCGTCGACGAGTTCTTTTTTCACAATTTCCTTTGCGACTCCGACGATTCGTCATCCGATGACGAGGAGGAGGTATTGGCTGCCGTGTTGGTCCATCACCTGCTCAATAGCTAGCGGCCGTTGTTCCGTGGCTCCATTCCGAGCCACCTTCCGGTGTTGA', b'DEFINITION': b'Hordeum vulgare subsp. vulgare genome assembly, chromosome: 3H', b'TAXID': 112509, b'organism': b'Hordeum vulgare subsp. vulgare'} Error raised: Problem setting a value in a column /!\ Check if '--input-na-string' option needs to be set zsh: segmentation fault obi import --embl-input EMBL Guate/embl_refs
I hope I have included the relevant info, and any help would be greatly appreciated!
Best,
Tom