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mcveanlab / mccortex

De novo genome assembly and multisample variant calling
https://github.com/mcveanlab/mccortex/wiki
MIT License
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Assert Failed assem2str(): strlen(assem_stop_str[assem]) < size #37

Closed tseemann closed 8 years ago

tseemann commented 8 years ago

Any value for -C <float> in contigs causes assert error:

% mccortex63 contigs -C 0.5 -f -o foo1.fa -p infer.ctp.gz infer.ctx

[25 Apr 2016 10:59:35-XuR][cmd] mccortex63 contigs -C 0.5 -f -o foo1.fa -p infer.ctp.gz infer.ctx
[25 Apr 2016 10:59:35-XuR][cwd] /mnt/seq/JOBS/MDU/J2016-06490/nullarbor.ST80/2014-23625
[25 Apr 2016 10:59:35-XuR][version] mccortex=86b4ffe zlib=1.2.7 htslib=1.3-37-gfc93dfc ASSERTS=ON hash=Lookup3 CHECKS=ON k=33..63
[25 Apr 2016 10:59:35-XuR] Taking number of kmers as genome size: 2,918,130
[25 Apr 2016 10:59:35-XuR][memory] 202 bits per kmer
[25 Apr 2016 10:59:35-XuR][memory] graph: 94.9MB
[25 Apr 2016 10:59:35-XuR][memory] paths: 30.1MB
[25 Apr 2016 10:59:35-XuR][memory] total: 95.1MB of 377.6GB RAM
[25 Apr 2016 10:59:35-XuR][hasht] Allocating table with 3,932,160 entries, using 60.2MB
[25 Apr 2016 10:59:35-XuR][hasht]  number of buckets: 131,072, bucket size: 30
[25 Apr 2016 10:59:35-XuR][graph] kmer-size: 63; colours: 1; capacity: 3,932,160
[25 Apr 2016 10:59:35-XuR][GPathReader] need 7216 paths 16810 bytes
[25 Apr 2016 10:59:35-XuR][GPathSet] Allocating for 7,216 paths, 7KB colset, 9.4KB seq => 143.3KB total
[25 Apr 2016 10:59:35-XuR][FileFilter] Loading file infer.ctx [1 colour]
[25 Apr 2016 10:59:35-XuR][GReader] 2,918,130 kmers, 58.4MB filesize
[25 Apr 2016 10:59:35-XuR][GReader] Loaded 2,918,130 / 2,918,130 (100.00%) of kmers parsed
[25 Apr 2016 10:59:35-XuR][hasht] buckets: 131,072 [2^17]; bucket size: 30; memory: 60.2MB; occupancy: 2,918,130 / 3,932,160 (74.21%)
[25 Apr 2016 10:59:35-XuR][hasht]  collisions  0: 2901076
[25 Apr 2016 10:59:35-XuR][hasht]  collisions  1: 16416
[25 Apr 2016 10:59:35-XuR][hasht]  collisions  2: 609
[25 Apr 2016 10:59:35-XuR][hasht]  collisions  3: 25
[25 Apr 2016 10:59:35-XuR][hasht]  collisions  4: 3
[25 Apr 2016 10:59:35-XuR][hasht]  collisions  5: 1
[25 Apr 2016 10:59:35-XuR][FileFilter] Loading file infer.ctp.gz [1 colour]
[25 Apr 2016 10:59:35-XuR][GPathSet] Allocating for 32,768 paths, 32KB colset, 384KB seq => 1MB total
[25 Apr 2016 10:59:35-XuR] Loaded 7,216 paths from 1,688 kmers
[25 Apr 2016 10:59:35-XuR][Assemble] Assembling contigs with 2 threads, walking colour 0
[25 Apr 2016 10:59:35-XuR][Assemble] Using missing info check: yes
[25 Apr 2016 10:59:35-XuR][Assemble] Stop traversal if step cummulative confidence < 0.500000
[25 Apr 2016 10:59:35-XuR][Assemble]   Writing contigs to foo1.fa
[25 Apr 2016 10:59:35-XuR][Assemble] Seeding with random kmers...
[src/tools/assemble_stats.c:43] Assert Failed assem2str(): strlen(assem_stop_str[assem]) < size
[25 Apr 2016 10:59:35-XuR] Assert Error
Aborted (core dumped)
noporpoise commented 8 years ago

Fixed - thanks for all the testing. Much appreciated.