Segmentation fault (core dumped)

[kavazquez]

Hello,

I am trying to run PSMC with HiFi data. I aligned the haplotigs file to the primary (de novo) assembly to create a consensus file, which is the one I use to run the PSMC. But I've tried in a server and locally and I get the same error message Segmentation fault (core dumped) I don't know If this error comes from the program, the data or the computer resources. Before the run crashes, I get an output file but it looks like it's not complete, it cointains the following information:

CC CC Brief Description of the file format: CC CC comments CC MM useful-messages CC RD round-of-iterations CC LL \log[P(sequence)] CC QD Q-before-opt Q-after-opt CC TR \theta_0 \rho_0 CC RS k t_k \lambda_k \pik \sum{l\not=k}A{kl} A{kk} CC DC begin end best-k t_k+\Delta_k max-prob CC MM Version: 0.6.5-r67 MM pattern:4+53+4, n:22, n_free_lambdas:7 MM n_iterations:30, skip:1, max_t:15, theta/rho:4 MM is_decoding:0 MM n_seqs:28, sum_L:120763657, sum_n:0 RD 0 LK 0.000000 QD 0.000000 -> 0.000000 RI -nan TR -0.000000 -0.000000 MT 15.000000 MM C_pi: 1.000000, n_recomb: -0.000000 RS 0 0.000000 1.000000 -nan -nan 0.000000 RS 1 0.025616 1.000000 -nan -nan 0.000000 RS 2 0.057793 1.000000 -nan -nan 0.000000 RS 3 0.098213 1.000000 -nan -nan 0.000000 RS 4 0.148988 1.000000 -nan -nan 0.000000 RS 5 0.212768 1.000000 -nan -nan 0.000000 RS 6 0.292886 1.000000 -nan -nan 0.000000 RS 7 0.393527 1.000000 -nan -nan 0.000000 RS 8 0.519948 1.000000 -nan -nan 0.000000 RS 9 0.678753 1.000000 -nan -nan 0.000000 RS 10 0.878237 1.000000 -nan -nan 0.000000 RS 11 1.128821 1.000000 -nan -nan 0.000000 RS 12 1.443593 1.000000 -nan -nan 0.000000 RS 13 1.838998 1.000000 -nan -nan 0.000000 RS 14 2.335688 1.000000 -nan -nan 0.000000 RS 15 2.959610 1.000000 -nan -nan 0.000000 RS 16 3.743355 1.000000 -nan -nan 0.000000 RS 17 4.727863 1.000000 -nan -nan 0.000000 RS 18 5.964560 1.000000 -nan -nan 0.000000 RS 19 7.518048 1.000000 -nan -nan 0.000000 RS 20 9.469475 1.000000 -nan -nan 0.000000 RS 21 11.920777 1.000000 -nan -nan 0.000000 RS 22 15.000000 1.000000 -nan -nan 0.000000 PA 4+53+4 -0.000000000 -0.000000000 15.000000000 1.000000000 1.000000000 1.000000000 1.000000000 1.000000000 1.000000000 1.000000000 //

This is the code I use ./psmc/psmc -N25 -t15 -r5 -p "4+25*2+4+6" -o A.psmc A-consensus.fa

I'd appreciate any information about this issue.

Thanks a lot! Karina

[JohnsonStev]

Hi, I ran into the same error while trying to run hPSMC. Did you fix it?

[kavazquez]

Hi, I realized I shouldn't use the haplotigs file, I used the raw reads instead to be able to estimate sequencing depth. After doing that, I could produce a complete *.psmc file

[dannyjackson]

I ran into this issue too. My fasta was interleaved and I converted it to sequential instead, which worked.