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sanger-pathogens / snp-sites

Finds SNP sites from a multi-FASTA alignment file
http://sanger-pathogens.github.io/snp-sites/
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SegFault for unknown reason #72

Closed flashton2003 closed 6 years ago

flashton2003 commented 6 years ago

I'm getting a somewhat mysterious segfault when running snp-sites (latest version in conda, installed as in instructions).

The reason it's mysterious is that the file which is causing the segfault is just a cat of two files which individually run through snp-sites without error. The genomes in the two files input to cat are the same length (both in 60 bp per line fasta format), and the output of cat looks fine by both seqkit stats and by visually inspecting where the two files have been joined.

Any thoughts?

Details below...

ubuntu@pennaeth:~/tm_data/phylo/results$ seqkit stats 2018.10.12/2018.10.12.all_tm.fasta
file                                format  type  num_seqs        sum_len     min_len     avg_len     max_len
2018.10.12/2018.10.12.all_tm.fasta  FASTA   DNA        191  5,470,978,215  28,643,865  28,643,865  28,643,865

ubuntu@pennaeth:~/tm_data/phylo/results$ seqkit stats 2018.10.15/2017.12.11.prelim_tm_data.reform.fa
file                                          format  type  num_seqs        sum_len     min_len     avg_len     max_len
2018.10.15/2017.12.11.prelim_tm_data.reform.fa  FASTA   DNA         35  1,002,535,275  28,643,865  28,643,865  28,643,865

ubuntu@pennaeth:~/tm_data/phylo/results$ cat 2018.10.12/2018.10.12.all_tm.fasta 2018.10.15/2017.12.11.prelim_tm_data.reform.fa > 2018.10.15/tmp.fa

ubuntu@pennaeth:~/tm_data/phylo/results$ seqkit stats 2018.10.15/tmp.fa
file               format  type  num_seqs        sum_len     min_len     avg_len     max_len
2018.10.15/tmp.fa  FASTA   DNA        226  6,473,513,490  28,643,865  28,643,865  28,643,865

ubuntu@pennaeth:~/tm_data/phylo/results$ snp-sites 2018.10.12/2018.10.12.all_tm.fasta
ubuntu@pennaeth:~/tm_data/phylo/results$ snp-sites 2018.10.15/2017.12.11.prelim_tm_data.reform.fa
ubuntu@pennaeth:~/tm_data/phylo/results$ snp-sites 2018.10.15/tmp.fa 
Segmentation fault (core dumped)
ubuntu@pennaeth:~/tm_data/phylo/results$ 

ubuntu@pennaeth:~/tm_data/phylo/results$ ls -lh *
-rw-rw-r-- 1 ubuntu ubuntu 2.7M Oct 15 07:39 2017.12.11.prelim_tm_data.reform.fa.snp_sites.aln
-rw-rw-r-- 1 ubuntu ubuntu  45M Oct 15 07:38 2018.10.12.all_tm.fasta.snp_sites.aln

2018.10.12:
total 5.3G
-rw-rw-r-- 1 ubuntu ubuntu 5.2G Oct 12 05:33 2018.10.12.all_tm.fasta

2018.10.15:
total 21G
-rw-rw-r-- 1 ubuntu ubuntu 957M Oct 15 06:37 2017.12.11.prelim_tm_data.fa
-rw-rw-r-- 1 ubuntu ubuntu 973M Oct 15 06:58 2017.12.11.prelim_tm_data.reform.fa
-rw-rw-r-- 1 ubuntu ubuntu 6.2G Oct 15 07:36 tmp.fa
flashton2003 commented 6 years ago

Actually, please ignore this. Error on my end.