2019-03-14

Hey, Please download raw data (https://github.com/linnabrown/error_data) to test the code.
The error of running macsypy:

Sequence number 17..Traceback (most recent call last):
  File "/home/ciillab/huangle/CRISPRCasFinder/bin/macsyfinder", line 329, in <module>
    idx.build(force = config.build_indexes)
  File "/home/ciillab/huangle/CRISPRCasFinder/macsyfinder-1.0.5/macsypy/database.py", line 118, in build
    raise RuntimeError(msg)
RuntimeError: an error occurred during databases indexation see formatdb.log

What's more, I saw the code snapets
is related to it:

#################################
# synchronization point between #
# hmmer_indexes and my_indexes  #
#################################
        if force or not hmmer_indexes:
            hmmer_indexes_proc.wait()
            if hmmer_indexes_proc.returncode == 127:
                msg = "neither makeblastdb nor formatdb can be found, check your config or install makeblastb"
                _log.critical(msg, exc_info=True)
                raise RuntimeError(msg)
            if hmmer_indexes_proc.returncode != 0:
                msg = "an error occurred during databases indexation see formatdb.log"
                _log.critical(msg, exc_info=True)
                raise RuntimeError(msg)
        self._hmmer_indexes = self.find_hmmer_indexes()
        self._my_indexes = self.find_my_indexes()
        assert self._hmmer_indexes, "failed to create hmmer indexes"
        assert self._my_indexes, "failed create macsyfinder indexes"

This is the wrong code of this sequence. The length of genome sequence may be too small compared with other genome sequences in the file of GCF_001983215.1_ASM198321v1_genomic.fna

 36723 >NZ_MOWP01000024.1 Frankia sp. CcI49 contig_23, whole genome shotgun sequence
 36724 GACCCGGTCGACCCACCCTGGGACCCGCCCTTACCGAACGACCCGGTCGACCCACCCTGAGCGCCACCCTTACCGAACGA
 36725 CCCGGTCGTCTCCTTGCCGCCAAGGTTCCGCGGTGTGGAGATATCGATGGTCACGCCTTCCTCAACCGGTCTGGTTGTTT
 36726 GGGATGACCCGCCCTGGGTTCCGTCGCCATCGAACGAGCCAGTCGACCCACCCTGAGCGCTGGACGCCGCACCGAAGGTA
 36727 CTCGTCGGGCCACCGACAATGGTCTCCGCAGTAACCGGCGCGCCAATACCGATCGTGATGCTTCCGGTCGACAGAATGGA
 36728 GAGGTTCAATCCGCTCGGAATAGCCAGGCCCTGCCCGGCATCCAAAACCCTGGGCTCCACTTCTCCGACACTCTCCTGGC
 36729 CATCTCCTACAGCGACCACGGGCGCCACCAGGTTGGCTGGAGCCGGATCAACGGCTATCGATATGTCAGCCCTGGCAGGA
 36730 GACGCCGGCAAGATAGCAGCAGCAGATATTCCACCGGCCAGAGCCAGAACGGACCAAGTCTTCTTAACAATCATGATTTC
 36731 CCCGCTCGACATCAGGATCCACCTCGTCGCAGCGGGATGGTAGCTATCAAGCCGTCGGATCAACCGCTTCCACCAGACCG
 36732 GCGTGTTGCGGAAAAATTTCGAGTGACATATTTCGCGACAGCAAAGCGTCGAACTCATCCGGACCGGATCACATGGCAAA
 36733 AGTAGATCAGATCACCAACCCGGCCCACCTGGTGTGATTGGTGCGAGTACACACCCCTATCAGGGAGATCCTCGCAACAT
 36734 CATTCCACCCAGCTCTTCATGCATGCGACAGCCCTCCGCCTCTCCCACCTGGCAGATTTCTCCAGATGGGAGAAGGGAGG
 36735 GCTGCCCGTCACACCCAAACAAAAATTAGGCGGAC

Please download all the data (faa, fna, gff) from my github to test it.