Closed tseemann closed 8 years ago
Any value for -C <float> in contigs causes assert error:
-C <float>
contigs
% 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)
Fixed - thanks for all the testing. Much appreciated.
Any value for
-C <float>
incontigs
causes assert error: