Iq-tree crashes with segmentation fault

[DeadlineWasYesterday]

Hey there, Dr. Quang Minh, I've been following your work for a few weeks now. Really appreciate your contributions and effort. Now, about the issue—

I've tried both iq-tree 1.6.12 and 2.1.1. It's the same.

Seconds before this error message shows up, my ram is at 98% usage. Using the -mem flag does not restrict my ram usage by iq-tree for some reason. I've tried -mem 16G and -mem 24G , it always exceeds the limit and goes up to 28G on my 29G machine. I've also tried -nt 1 and -nt 4 to no avail.

I am working with a large 6GB phylip file with 175 sequences.

Here are the log file contents. I can try and upload the whole sequence file as well.

IQ-TREE multicore version 1.6.12 for Windows 64-bit built Aug 15 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host: DESKTOP-1S9PIG2 (AVX2, FMA3, 29 GB RAM) Command: C:\Users\Michael\Downloads\iqt\bin\iqtree.exe -nt 3 -mem 16G -s 175.phy Seed: 784342 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Fri Aug 21 07:12:50 2020 Kernel: AVX+FMA - 3 threads (4 CPU cores detected)

Reading alignment file 175.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 175 sequences with 32064217 columns, 20425493 distinct patterns 7980114 parsimony-informative, 2372259 singleton sites, 21711844 constant sites Gap/Ambiguity Composition p-value 1 Ref 0.00% failed 0.00% 2 22 23.06% failed 0.00% 3 23 20.17% failed 0.00% 4 26 18.30% failed 0.00% 5 28 20.73% failed 0.00% 6 29 20.88% failed 0.00% 7 32 21.47% failed 0.00% 8 33 19.61% failed 0.00% 9 35 19.78% failed 0.00% 10 37 20.65% failed 0.00% 11 70 21.72% failed 0.00% 12 71 17.47% failed 0.00% 13 73 26.63% failed 0.00% 14 109 24.17% failed 0.00% 15 110 16.99% failed 0.00% 16 119 20.24% failed 0.00% 17 128 20.77% failed 0.00% 18 151 20.26% passed 96.78% 19 155 16.04% failed 0.00% 20 156 15.86% failed 0.00% 21 168 24.17% failed 0.00% 22 181 18.67% failed 0.65% 23 189 19.68% failed 0.00% 24 196 20.93% failed 0.00% 25 207 21.95% failed 0.00% 26 215 19.16% failed 0.00% 27 218 20.91% failed 0.00% 28 225 20.29% failed 0.00% 29 228 20.80% failed 0.00% 30 229 22.99% failed 0.00% 31 241 17.54% passed 71.36% 32 242 20.01% failed 0.00% 33 265 14.21% passed 42.64% 34 266 17.22% passed 86.46% 35 268 19.28% failed 0.00% 36 277 20.25% failed 0.00% 37 278 17.24% passed 10.18% 38 279 19.55% failed 0.00% 39 289 21.86% failed 0.00% 40 296 17.58% failed 0.19% 41 297 19.36% failed 0.00% 42 307 20.75% failed 0.00% 43 313 20.57% failed 0.00% 44 340 18.08% failed 0.00% 45 347 19.13% failed 0.00% 46 467 17.76% failed 0.00% 47 502 20.91% failed 0.00% 48 509 18.93% failed 0.00% 49 522 20.04% failed 0.00% 50 535 19.03% passed 16.85% 51 551 19.68% passed 92.71% 52 940 19.91% failed 0.00% 53 941 21.83% failed 0.00% 54 942 18.14% failed 0.00% 55 943 18.19% passed 23.49% 56 945 23.68% failed 0.00% 57 946 19.35% passed 43.29% 58 1002 19.69% failed 0.00% 59 1003 19.80% failed 0.00% 60 1133 15.64% failed 0.00% 61 1338 17.28% failed 0.00% 62 1358 19.34% failed 0.00% 63 1388 19.54% failed 0.00% 64 1436 18.54% failed 0.00% 65 1458 13.10% failed 0.00% 66 1480 18.19% failed 0.00% 67 1646 18.68% failed 0.00% 68 1648 29.44% failed 0.00% 69 1691 21.55% failed 0.00% 70 1693 22.89% failed 0.00% 71 1694 25.55% failed 0.00% 72 1696 24.99% failed 0.00% 73 1697 21.31% failed 0.00% 74 1699 25.11% failed 0.00% 75 1700 19.47% failed 0.00% 76 1701 16.93% passed 87.58% 77 1702 22.42% failed 0.00% 78 1703 17.78% passed 29.55% 79 1704 25.58% failed 0.00% 80 2013 19.43% failed 0.00% 81 2014 25.85% failed 0.00% 82 2015 19.12% failed 0.00% 83 2021 22.77% failed 0.00% 84 2022 22.64% failed 0.00% 85 2024 21.67% passed 38.62% 86 2025 20.85% passed 75.79% 87 2026 16.82% passed 72.00% 88 2027 19.43% failed 0.00% 89 2028 19.50% passed 63.88% 90 2029 19.99% failed 0.00% 91 2030 21.16% failed 0.00% 92 2031 20.25% failed 0.00% 93 2032 21.06% failed 0.00% 94 2033 21.58% failed 0.00% 95 2035 21.28% failed 0.00% 96 2037 21.60% failed 0.13% 97 2038 17.44% passed 72.50% 98 2039 19.66% failed 0.00% 99 2057 20.28% failed 1.89% 100 2058 21.00% failed 0.00% 101 2059 19.11% failed 0.00% 102 2061 18.71% failed 0.00% 103 2062 19.91% failed 0.00% 104 2063 20.00% failed 0.00% 105 2064 21.04% failed 0.00% 106 2095 18.30% failed 0.00% 107 2096 17.85% failed 0.00% 108 2097 19.29% failed 0.00% 109 2098 17.97% failed 0.00% 110 2100 17.17% failed 0.00% 111 2101 17.39% failed 0.00% 112 2102 18.96% failed 0.00% 113 2105 18.29% failed 0.00% 114 2106 18.09% failed 0.00% 115 2107 17.27% failed 0.00% 116 2108 18.29% failed 0.00% 117 2109 21.20% failed 0.00% 118 2110 21.38% failed 0.00% 119 2111 14.93% failed 0.00% 120 2112 20.19% failed 0.00% 121 2113 17.39% passed 34.58% 122 2114 22.88% failed 0.00% 123 2116 12.85% failed 0.00% 124 2117 20.87% failed 0.00% 125 2118 16.89% failed 0.00% 126 2119 16.63% failed 0.00% 127 2120 18.24% failed 0.00% 128 2156 25.58% failed 0.00% 129 2157 17.70% failed 0.00% 130 2158 17.18% failed 0.00% 131 2159 22.31% failed 0.00% 132 2160 22.78% failed 0.13% 133 2161 24.25% failed 0.00% 134 2169 23.90% failed 0.00% 135 2170 23.91% failed 0.00% 136 2203 25.26% failed 0.00% 137 2213 22.37% failed 0.00% 138 2242 23.26% failed 0.00% 139 2243 19.74% failed 0.00% 140 2244 18.05% passed 18.70% 141 2245 19.30% failed 0.18% 142 2246 22.13% failed 0.00% 143 2247 21.68% failed 0.00% 144 2249 21.15% failed 0.00% 145 2250 21.06% failed 0.00% 146 2252 22.41% failed 0.00% 147 2253 22.79% failed 0.00% 148 2254 20.67% failed 0.00% 149 2255 21.95% failed 0.00% 150 2256 18.38% passed 48.75% 151 2257 15.24% failed 0.00% 152 2258 22.24% passed 59.51% 153 2259 20.12% failed 0.00% 154 2260 19.40% failed 0.00% 155 2262 20.08% failed 0.00% 156 2263 18.34% failed 0.00% 157 2264 18.32% passed 43.17% 158 2265 19.05% failed 1.16% 159 2266 19.51% failed 0.00% 160 2267 21.61% failed 0.00% 161 2268 19.56% failed 0.00% 162 2269 18.07% failed 0.60% 163 2270 19.77% failed 0.00% 164 2271 20.07% failed 0.00% 165 2282 17.49% passed 61.38% 166 2361 18.47% failed 0.00% 167 2362 20.50% failed 0.00% 168 2363 19.68% failed 0.00% 169 2364 19.16% failed 0.00% 170 2367 21.87% failed 0.00% 171 2439 20.16% failed 0.00% 172 2440 20.07% failed 0.00% 173 2441 16.48% failed 0.00% 174 2442 20.30% failed 0.00% 175 2444 21.53% failed 0.00% ** TOTAL 19.92% 153 sequences failed composition chi2 test (p-value<5%; df=3) NOTE: minimal branch length is reduced to 0.000000003119 for long alignment ERROR: ERROR: ** IQ-TREE CRASHES WITH SIGNAL SEGMENTATION FAULT ERROR: For bug report please send to developers: ERROR: Log file: 175.phy.log ERROR: Alignment files (if possible)

[bqminh]

Does it work if you run with -t PARS option?

[DeadlineWasYesterday]

Just did. This time it crashed earlier. I am exceedingly led to believe that this is a memory issue. I believe the -mem flag is not restricting RAM usage.

Here is the new log file.

IQ-TREE multicore version 2.1.1 COVID-edition for Windows 64-bit built Aug 20 2020 Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Host: DESKTOP-1S9PIG2 (AVX2, FMA3, 29 GB RAM) Command: bin\iqtree2.exe -s 175p.phy -nt 3 -mem 24G -t PARS Seed: 113113 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Sat Aug 22 20:18:33 2020 Kernel: AVX+FMA - 3 threads (4 CPU cores detected)

Reading alignment file 175p.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences ERROR: ERROR: IQ-TREE CRASHES WITH SIGNAL ABORTED ERROR: For bug report please send to developers: ERROR: Log file: 175p.phy.log ERROR: Alignment files (if possible)

[jcgrenier]

Hello all, I'm having the same issue. Is there any solution for this yet? Thanks a lot!