glennhickey
commented
1 year ago I'm not sure. All I can think of is installation or temporary directory problems. There's a similar issue here.
Something to try in order to debug would be to run cactus with --disableCaching --cleanWorkDir never. Then when it fails copying and pasting the command and running it yourself ex blossom5 -e /tmp/stTmpLBIJUm -w /tmp/stTmpPg60GW (hopefully those above flags will make sure the inputs are still there).
Elapsed Time: 0.000000 Connected Components: 34 Ran the cactus core script. Finished filling in the alignments for the flower Created the poa alignments: 142 poa alignment blocks for flower
Computing 3edge connected components using Dr. Tsin's algorithm(The one with reduction)...
Complexity of the given graph: |V| + |E| = 144 + 146 = 290 Found components
Elapsed Time: 0.000000 Connected Components: 144 Ran the cactus core script. Finished filling in the alignments for the flower Created the poa alignments: 149 poa alignment blocks for flower
Computing 3edge connected components using Dr. Tsin's algorithm(The one with reduction)...
Complexity of the given graph: |V| + |E| = 151 + 153 = 304 Found components
Elapsed Time: 0.000000 Connected Components: 151 Ran the cactus core script. Finished filling in the alignments for the flower Created the poa alignments: 274 poa alignment blocks for flower
Computing 3edge connected components using Dr. Tsin's algorithm(The one with reduction)...
Complexity of the given graph: |V| + |E| = 276 + 278 = 554 Found components
Elapsed Time: 0.000000 Connected Components: 276 Ran the cactus core script. Finished filling in the alignments for the flower Ran cactus bar (use poa:1), 78 seconds have elapsed There are 3 layers in the flowers hierarchy In the 0 layer there are 1 flowers in the flowers hierarchy Processing flower 0 Chose reference event 2: N0 For flower: 0 we have 64 nodes for: 293872 ends, 189 chains, 40 stubs and 146670 blocks Building a matching for 40 stub nodes in the top level problem from 532 total stubs of which 354 attached , 293872 total ends, 189 chains, 146670 blocks 146831 groups and 266 sequences Running command blossom5 -e /tmp/stTmpLBIJUm -w /tmp/stTmpPg60GW > /dev/null 2>&1 cactus_consolidated(+0x5be72)[0x557d71456e72] cactus_consolidated(+0x32a71)[0x557d7142da71] cactus_consolidated(+0x36c24)[0x557d71431c24] cactus_consolidated(+0x32cba)[0x557d7142dcba] cactus_consolidated(+0xdede)[0x557d71408ede] cactus_consolidated(+0xe6a4)[0x557d714096a4] /lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x46)[0x7f9850297a16] cactus_consolidated(+0xe959)[0x557d71409959] cactus_consolidated(+0x4adf)[0x557d713ffadf] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f9850084d90] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f9850084e40] cactus_consolidated(+0x50f5)[0x557d714000f5] ERROR: Something went wrong with the command: blossom5 -e /tmp/stTmpLBIJUm -w /tmp/stTmpPg60GW > /dev/null 2>&1
This is part of the mistakes. I want to know what this ERROR means? Why did this error occur？