soedinglab
Alignment step died
Current Behavior
We are consistently receiving the following error: munmap_chunk(): invalid pointer leading to .../linclust/sh: line 76: 2444 Aborted (core dumped) $RUNNER "$MMSEQS" "${ALIGN_MODULE}" "$INPUT" "$INPUT" "$RESULTDB" "${TMP_PATH}/aln" ${ALIGNMENT_PAR} leading to: "Error: Alignment step died" "Error: Search died"
Steps to Reproduce (for bugs)
file used: seqs.fasta (download seqs.txt from this issue, then change the file name extension to .fasta) command used: mmseqs easy-linclust seqs.fasta /tmp/mmseqs /tmp --min-seq-id 0.9 -c 1.0 --cov-mode 0
MMseqs Output (for bugs)
see screenshot
Your Environment
Include as many relevant details about the environment you experienced the bug in.
- Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters): 13.4511 (see screenshot)
- Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.): Bioconda
- For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation: /
- Server specifications (especially CPU support for AVX2/SSE and amount of system memory): support for both AVX2 and SSE
- Operating system and version: centos 8, 48 CPU, 192 GB RAM, 512 GB disk memory (m5.12xlarge instance AWS)
Please let us know if there is anything else you need. Thanks in advance!
This is a small bug in the release, which only occurs with sequences smaller than alphabet size, it is already fixed in the current github version. The relevant commit is c7f6a37
