bathsearch failed for a sample, and generated strange output for another two samples

[augustkx]

Hi,

I used bathbuild to build BATH formatted profile from an unaligned sequences file successfully. But when running bathsearch on a samples, it gives the error:

Fatal exception (source file p7_alidisplay.c, line 1822):
zero malloc disallowed
Aborted (core dumped)

I would appreciate it very much if you could help me figure the issue out.

[augustkx]

I tried on another sample, this time bathsearch runs, but there seems to be a bug on the output file. The file size grew to 196G and I stopped the process. I opened the file, there were repeated lines under the "Alignment".

Query: 0|EAC4468893.1|1|1|emrC_Lis|emrC_Lis||1|QUATERNARY_AMMONIUM|QUATERNARY_AMMONIUM|multidrug_efflux_transporter_outer_membrane_subunit_EmrC [M=128]
Scores for complete hits:
E-value score bias Sequence start end shifts stops Description
------- ------ ----- -------- ----- ----- ------ ----- -----------
1.9e-19 74.4 9.4 contig_343 53530 53823 0 0
7.3e-10 46.6 0.0 contig_316 277856 278155 0 0
1.4e-08 39.4 4.3 contig_190 286658 286867 0 0
3.5e-06 34.7 0.0 contig_668 11271 11500 3 0
4.9e-06 31.2 6.5 contig_58 116389 116159 0 0
8.3e-06 30.4 0.9 contig_1174 3808 3963 0 0
8.4e-06 33.5 0.0 contig_316 277536 277834 1 0
0.006 24.3 0.0 contig_584 50534 50822 2 0

Annotation for each hit (and alignments):

contig_343
score bias Evalue hmm-from hmm-to ali-from ali-to env-from env-to shifts stops sq-len acc

---

! 74.4 9.4 1.9e-19 1 98 [. 53530 53823 .. 53530 53823 .. 0 0 172833 0.96

Alignment:
score: 74.4 bits
0|EAC4468893.1|1|1|emrC_Lis|emrC_Lis||1|QUATERNARY_AMMONIUM|QUATERNARY_AMMONIUM|multidrug_efflux_transporter_outer_membrane_subunit_EmrC 1 0

                                                                                                                            contig_343     -      -
                                                                                                                                              PP

0|EAC4468893.1|1|1|emrC_Lis|emrC_Lis||1|QUATERNARY_AMMONIUM|QUATERNARY_AMMONIUM|multidrug_efflux_transporter_outer_membrane_subunit_EmrC 1 0

                                                                                                                            contig_343     -      -
                                                                                                                                              PP

0|EAC4468893.1|1|1|emrC_Lis|emrC_Lis||1|QUATERNARY_AMMONIUM|QUATERNARY_AMMONIUM|multidrug_efflux_transporter_outer_membrane_subunit_EmrC 1 0

                                                                                                                            contig_343     -      -
                                                                                                                                              PP

0|EAC4468893.1|1|1|emrC_Lis|emrC_Lis||1|QUATERNARY_AMMONIUM|QUATERNARY_AMMONIUM|multidrug_efflux_transporter_outer_membrane_subunit_EmrC 1 0

                                                                                                                            contig_343     -      -
                                                                                                                                              PP

0|EAC4468893.1|1|1|emrC_Lis|emrC_Lis||1|QUATERNARY_AMMONIUM|QUATERNARY_AMMONIUM|multidrug_efflux_transporter_outer_membrane_subunit_EmrC 1 0

                                                                                                                            contig_343     -      -
                                                                                                                                              PP

0|EAC4468893.1|1|1|emrC_Lis|emrC_Lis||1|QUATERNARY_AMMONIUM|QUATERNARY_AMMONIUM|multidrug_efflux_transporter_outer_membrane_subunit_EmrC 1 0

This line goes endlessly in the 196G file.

[GenevieveKrause]

Thank you for bringing this to our attention. Can you please attach the input data (hmm file and sequence file) and show me the exact bathsearch command you used so I can try to reproduce the error?

[augustkx]

Hi, thanks for the quick response!

I created the hmm file usingbathbuild --unali AMRProt.bhmm AMRProt.fa , with the protein data downloaded from:

https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/latest/AMRProt.fa

Then, I used the following command to search:
bathsearch -o SRR16329111_1.out AMRProt.bhmm flye.SRR16329111_1.fastq.gz.fasta
bathsearch -o ERR7927093.out AMRProt.bhmm flye.ERR7927093.fastq.gz.fasta

The first sample resulted in the error

Fatal exception (source file p7_alidisplay.c, line 1822):
zero malloc disallowed
Aborted (core dumped)

The second sample resulted in a large but not correct output file.

The sequence file is too large to upload here, could you please let me know your email? thanks!
I tried to run BATH on part of the contigs in the sample, and it worked. So I need to send you the whole sample.

[augustkx]

Hi,
could you please check the email address, as

The Domain Name System (DNS) reported that the recipient's domain does not exist.

Thanks

[GenevieveKrause]

Sorry. Try gkrause@pharmacy.arizona.edu.

[GenevieveKrause]

I think I have fixed the bug. For some reason my email won't let me download the second sequence file you sent, so I was only able to test on flye.SRR16329111_1.fastq.gz.fasta, but I believe it was the same issue. You will need to run 'git pull' and then 'make' from inside the BATH directory. If you have any further problems please let me know.

[augustkx]

Yes, they work now. Thank you very much for your help!