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shandley / hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
MIT License
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"Invalid database read" Error: creattsv died #118

Open RyCrobe opened 4 weeks ago

RyCrobe commented 4 weeks ago

Everything seemed to be going smoothly for a few hours until the very end and it couldn't make the output tables.

Invalid database read for database data file=hecatomb.out/processing/mmseqs_aa_primary/mmseqs_aa_tmp/18413792167212729467/query_h, database index=hecatomb.out/processing/mmseqs_a$Invalid database read for database data file=hecatomb.out/processing/mmseqs_aa_primary/mmseqs_aa_tmp/18413792167212729467/query_h, database index=hecatomb.out/processing/mmseqs_a$Invalid database read for database data file=hecatomb.out/processing/mmseqs_aa_primary/mmseqs_aa_tmp/18413792167212729467/query_h, database index=hecatomb.out/processing/mmseqs_a$Invalid database read for database data file=hecatomb.out/processing/mmseqs_aa_primary/mmseqs_aa_tmp/18413792167212729467/query_h, database index=hecatomb.out/processing/mmseqs_a$Invalid database read for database data file=hecatomb.out/processing/mmseqs_aa_primary/mmseqs_aa_tmp/18413792167212729467/query_h, database index=hecatomb.out/processing/mmseqs_a$getData: local id (4294967295) >= db size (3170867) Invalid database read for database data file=hecatomb.out/processing/mmseqs_aa_primary/mmseqs_aa_tmp/18413792167212729467/query_h, database index=hecatomb.out/processing/mmseqs_a$getData: local id (4294967295) >= db size (3170867) Invalid database read for database data file=hecatomb.out/processing/mmseqs_aa_primary/mmseqs_aa_tmp/18413792167212729467/query_h, database index=hecatomb.out/processing/mmseqs_a$getData: local id (4294967295) >= db size (3170867) Invalid database read for database data file=hecatomb.out/processing/mmseqs_aa_primary/mmseqs_aa_tmp/18413792167212729467/query_h, database index=hecatomb.out/processing/mmseqs_a$Invalid database read for database data file=hecatomb.out/processing/mmseqs_aa_primary/mmseqs_aa_tmp/18413792167212729467/query_h, database index=hecatomb.out/processing/mmseqs_a$Invalid database read for database data file=hecatomb.out/processing/mmseqs_aa_primary/mmseqs_aa_tmp/18413792167212729467/query_h, database index=hecatomb.out/processing/mmseqs_a$free(): corrupted unsorted chunks Invalid database read for database data file=hecatomb.out/processing/mmseqs_aa_primary/mmseqs_aa_tmp/18413792167212729467/query_h, database index=hecatomb.out/processing/mmseqs_a$getData: local id (4294967295) >= db size (3170867) hecatomb.out/processing/mmseqs_aa_primary/mmseqs_aa_tmp/18413792167212729467/easy-taxonomy.sh: line 33: 1167404 Segmentation fault (core dumped) "$MMSEQS" createtsv "${TMP_P$Error: createtsv died has context menu Compose

beardymcjohnface commented 3 weeks ago

Hi Ryan, I think it's complaining about either the primary AA database or the DB made from the seqtable (for the first pass primary aa search). I would try deleting the hecatomb.out/processing/mmseqs_aa_primary directory and rerunning the pipeline and see if it happens again. Failing that, you could try deleting the seqtable and rerunning (i think it's in hecatomb.out/results/seqtable.fasta). Otherwise try deleting and reinstalling the aa database (the path should be in the config).