Closed acpguedes closed 5 years ago
Could you please update your version and recreate the index there was a bug in this version. If the bug still persists please could you please send us the debug backtrace? To debug first compile MMseqs2 in debug mode
cmake -DCMAKE_BUILD_TYPE=Debug ..
make
And then run the alignment with gdb
gdb --args mmseqs align tcdb_query.nr.db /databases/fadb/freeze/all.mmseqs tmp/18071041534032520912/pref_0 tmp/18071041534032520912/aln_0 --sub-mat blosum62.out -a 1 --alignment-mode 2 -e 0.1 --min-seq-id 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 0 --max-seq-len 65535 --max-seqs 17702628 --comp-bias-corr 1 --realign 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 1 --db-load-mode 0 --pca 1 --pcb 1.5 --score-bias 0 --gap-open 11 --gap-extend 1 --threads 15 -v 3
After the crash just type
bt
Is this problem resolved now?
Unfortunately no. Also, sorry for don't ask before.
So I did this way:
1- Download the MMseqs2 Version: aa14ce37feb5eda7231af20259d8f2b659162236
2- Compile as described here but changing cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..
by cmake -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX=. ..
3- Run all steps below:
mmseqs createdb tcdb_query.nr.fa tcdb_query.nr.db 2>&1 >> log
mmseqs createdb all.fa all.db 2>&1 >> log;
mmseqs search tcdb_query.nr.db all.db tcdb_result.db tmp --threads 40 -s 7.5 --num-iterations 3 -a --max-seqs 17702628 -c 0.8 --add-self-matches 2>&1 >> log
4- After crash:
gdb --args mmseqs align tcdb_query.nr.db all.db tmp/1072319213335698383/pref_0 tmp/1072319213335698383/aln_0 --sub-mat blosum62.out -a 1 --alignment-mode 2 -e 0.1 --min-seq-id 0 --seq-id-mode 0 --alt-ali 0 -c 0.8 --cov-mode 0 --max-seq-len 65535 --max-seqs 17702628 --comp-bias-corr 1 --realign 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 1 --db-load-mode 0 --pca 1 --pcb 1.5 --score-bias 0 --gap-open 11 --gap-extend 1 --threads 40 -v 3
return:
GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-114.el7
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /home/acpguedes/source/MMseqs2/build/bin/mmseqs...done.
(gdb) bt
No stack.
Important note:
I send the STDOUT and STDERR to log file but there are one message that was printed on the screen and not on log file:
scoreIdentical has different length L: scoreIdentical has different length L: 604154 query_length: 126 query_length: 626
I can send you the entire directory but it is too large to upload on github.
The --add-self-matches
flag just works with databases that have the same size and entry identifiers. I assume this makes the example crash.
Expected Behavior
Search 13311 queries against database of 17M sequences
Current Behavior
Fails in alignment step:
Steps to Reproduce (for bugs)
mmseqs search tcdb_query.nr.db /databases/fadb/freeze/all.mmseqs tcdb_result.db tmp --threads 15 -s 7.5 --num-iterations 3 -a --max-seqs 17702628 -c 0.8 --add-self-matches
MMseqs Output (for bugs)
Context
I have two databases, they don't have equal entries but some sequences have 100% identity. I try to search using --add-self-matches to cluster the result. The search fails in alignment step when I use this options, without this options the search run well.
Your Environment
lscpu:
Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 36 On-line CPU(s) list: 0-35 Thread(s) per core: 2 Core(s) per socket: 18 Socket(s): 1 NUMA node(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 85 Model name: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz Stepping: 4 CPU MHz: 2680.333 BogoMIPS: 4600.00 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 1024K L3 cache: 25344K NUMA node0 CPU(s): 0-35 Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin mba ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts pku ospke