Recent changes to bugs

off-by-one kmer coverage print

Rayan Chikhi — Sat, 08 Nov 2014 16:11:28 -0000

Hi Zam,

When using Cortex during the hackathon, I ran into a bug when printing coverage information per unitig.

Line 10535 of CORTEX_release_v1.0.5.21/src/cortex_var/core/dB_graph_population.c:

for (i=0; i<len; i++)

should be

for (i=0; i<=len; i++)

as I believe that otherwise, it misses the coverage of the last kmer for each unitig.

Sample output (supernodes.fa) of the problem:

node_0 length:18 INFO:KMER=11
ATGGTTACCAAATTTTCC
Covg in Colour 0:
2 2 2 2 2 2 2

That sequence has length 18 so it contains exactly 18-11+1=8 11-mers, however only 7 coverages were printed.

#6 Parsing errors when using run_calls.pl

Zamin Iqbal — Fri, 21 Jun 2013 08:56:37 -0000

Hi! So Sorry for not replying, sourceforge is meant to email me when bugs get raised, but it didn't, and so I didn't know about this. Thanks for the patch, I'll take a look. Some of the things you mention are definitely bugs which I think I have fixed since then. THANKs for this!

Parsing errors when using run_calls.pl

Wed, 27 Mar 2013 07:56:07 -0000

Hey, thanks for writing this. It seems to work pretty well.

run_calls.pl seemed to run clean as in your manual/docs once for me. After that it seems to crash out with some minor bugs. There is an illegal line that gets output by VCFFile.pm if there are undefined lines (not sure how they got in there) that causes errors in downstream processing. The script also crashes out if one of the kmers gives no snps, in one place due to a file not getting made (it's ok for later scripts if it's empty) and in another due to a logical error that assumes there is >= 1 variant. I tracked them down and am attaching a patch that fixes things for me and now it runs through without problems so far.

I hope the patch does the right thing and doesn't contaminate results that come out, but they seem like minor bugs that won't affect anything seriously.

Thanks again.

install.sh error

Anonymous — Mon, 26 Nov 2012 19:16:58 -0000

Installing on Mac OSX 10.6.8

bash install.sh
...
>3000 lines
...
ar -csru libseqfile.a seq_file.o seq_common.o seq_fasta.o seq_fastq.o seq_plain.o seq_sam.o
cc -o seq_convert -O3 -Wall -Wextra -I../samtools-0.1.18 -I../string_buffer -L. -L../samtools-0.1.18 -L../string_buffer seq_convert.c -lseqfile -lbam -lstrbuf -lz -lm
if test -e needleman_wunsch; then rm needleman_wunsch; fi
for file in ; do rm -r $file; done
for file in ; do rm $file; done
gcc -o needleman_wunsch -O3 -fnested-functions -DCOMPILE_TIME='"Mon Nov 26 14:03:15 EST 2012"' -DSCORE_TYPE='int' -Wall \ -I . -I ./libs/utility_lib -I ./libs/string_buffer \ -I ./libs/bioinf -I ./libs/alignment_scoring \ nw_cmdline.c needleman_wunsch.c \ ./libs/alignment_scoring/*.c ./libs/utility_lib/utility_lib.c \ ./libs/bioinf/bioinf.c ./libs/string_buffer/string_buffer.c -lz
Undefined symbols:
"_gzbuffer", referenced from:
__set_seq_filetype in libseqfile.a(seq_file.o)
ld: symbol(s) not found
collect2: ld returned 1 exit status
make: *** [all] Error 1

zam-specific stuff in GSL dir

Zamin Iqbal — Fri, 13 Jan 2012 23:19:47 -0000

cd gsl-1.15/
zam@sequoia:/Net/birch/data/zam/test/bgi/cortex_var_1.0.5.3/gsl-1.15$ grep -r zam *
blas/blas.c:gsl_blas_izamax (const gsl_vector_complex * X)
blas/blas.c: return cblas_izamax (INT (X->size), X->data, INT (X->stride));
blas/gsl_blas.h:CBLAS_INDEX_t gsl_blas_izamax (const gsl_vector_complex * X);
blas/Makefile:ACLOCAL = ${SHELL} /home/zam/dev/hg/CORTEX_release/gsl-1.15/missing --run aclocal-1.11
blas/Makefile:AMTAR = ${SHELL} /home/zam/dev/hg/CORTEX_release/gsl-1.15/missing --run tar
blas/Makefile:AUTOCONF = ${SHELL} /home/zam/dev/hg/CORTEX_release/gsl-1.15/missing --run autoconf
blas/Makefile:AUTOHEADER = ${SHELL} /home/zam/dev/hg/CORTEX_release/gsl-1.15/missing --run autoheader
blas/Makefile:AUTOMAKE = ${SHELL} /home/zam/dev/hg/CORTEX_release/gsl-1.15/missing --run automake-1.11
blas/Makefile:MAKEINFO = ${SHELL} /home/zam/dev/hg/CORTEX_release/gsl-1.15/missing --run makeinfo
blas/Makefile:abs_builddir = /home/zam/dev/hg/CORTEX_release/gsl-1.15/blas

Bug pointed out to me by Tristan Carland at Scripps.

This is not fixed by
make clean

It appears to be improved, but not fixed completely by using
./configure --prefix=/something/else

A totally new GSL dir would fix it.

bug report:Floating point exception

Andrew — Fri, 13 Jan 2012 13:27:03 -0000

[xwb@node8 xa1326]$ gdb ../bin/cortex_var_63_c203
GNU gdb Fedora (6.8-37.el5)
Copyright (C) 2008 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"...
(gdb) run --kmer_size 41 --mem_height 17 --mem_width 100 --remove_seq_errors --colour_list colour_list --dump_binary BGI-203-all-clean.ctx
Starting program: /public3/xwb/solexa_seq/BGI_NCGR/cortex_var_1.0.5.3/bin/cortex_var_63_c203 --kmer_size 41 --mem_height 17 --mem_width 100 --remove_seq_errors --colour_list colour_list --dump_binary BGI-203-all-clean.ctx

-----
Sat Jan 14 05:05:08 2012
Starting Cortex
Command: /public3/xwb/solexa_seq/BGI_NCGR/cortex_var_1.0.5.3/bin/cortex_var_63_c203 --kmer_size 41 --mem_height 17 --mem_width 100 --remove_seq_errors --colour_list colour_list --dump_binary BGI-203-all-clean.ctx
colour list is set to colour_list
Maximum k-mer size (compile-time setting): 63
Actual K-mer size: 41
Hash table created, number of buckets: 131072

-----
Sat Jan 14 05:05:08 2012

-----
Sat Jan 14 05:05:08 2012
List of colours: colour_list (contains one filelist per colour). Load data into consecutive colours starting at 0
Loaded next binary; total kmers in graph is now 22767
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-----
Sat Jan 14 05:05:55 2012
Finished loading single_colour binaries
Total kmers in table: 446503
****************************************
SUMMARY:
Colour: MeanReadLen TotalSeq
0 89 78019
1 90 57510
2 89 37844
3 90 46710
4 90 76590
5 90 46800
6 89 50215
7 90 43830
8 89 67769
9 89 42630
10 90 39780
11 90 78120
12 90 35820
13 90 75600
14 90 44370
15 90 38700
16 89 41989
17 90 32850
18 90 46980
19 90 46710
20 89 43367
21 89 36945
22 90 34740
23 90 73170
24 90 37350
25 89 34649
26 89 49409
27 90 45180
28 90 43200
29 90 75420
30 89 74069
31 90 38070
32 89 39484
33 90 34200
34 90 81450
35 89 44899
36 90 45990
37 90 72810
38 90 82980
39 90 74340
40 90 42750
41 90 70560
42 90 61380
43 89 37584
44 90 81360
45 90 39150
46 90 40950
47 90 72450
48 90 47700
49 90 70110
50 90 67770
51 89 46528
52 89 43289
53 89 45179
54 90 38160
55 89 38969
56 89 67127
57 90 47340
58 90 43110
59 90 44280
60 90 42930
61 90 76230
62 90 36630
63 89 69929
64 90 46440
65 90 39690
66 89 43729
67 90 45180
68 90 37080
69 90 54810
70 90 43020
71 90 68130
72 90 42300
73 90 42750
74 90 41130
75 90 44640
76 90 39150
77 90 76140
78 89 38758
79 89 44502
80 90 50040
81 90 49320
82 89 45505
83 90 46710
84 90 40320
85 89 72406
86 89 67112
87 90 38160
88 90 72990
89 90 50850
90 89 77273
91 90 41940
92 89 84025
93 89 42438
94 90 37890
95 89 43556
96 90 66780
97 90 64710
98 90 37440
99 89 49588
100 89 81865
101 89 47471
102 89 74827
103 90 42930
104 89 43369
105 89 37490
106 89 78566
107 89 43559
108 89 55328
109 89 67675
110 89 40308
111 89 46438
112 89 37348
113 89 86787
114 89 43065
115 90 42750
116 89 39973
117 89 66775
118 90 37170
119 89 65887
120 90 48600
121 90 34110
122 89 43092
123 89 74695
124 90 41670
125 90 44280
126 90 42840
127 89 42659
128 90 63360
129 90 42210
130 90 37800
131 89 40072
132 90 66780
133 90 44550
134 90 42390
135 90 44820
136 90 82620
137 90 50040
138 90 81000
139 90 43920
140 90 66060
141 89 45334
142 90 46440
143 90 38520
144 90 70020
145 89 39775
146 90 48240
147 89 75878
148 90 39510
149 89 42479
150 90 36090
151 90 44910
152 89 57868
153 89 41759
154 89 34829
155 89 37168
156 89 47879
157 90 34920
158 90 40950
159 90 42390
160 89 43019
161 89 72088
162 89 51029
163 89 32939
164 90 34200
165 89 44367
166 89 58409
167 89 48059
168 90 40500
169 90 45090
170 90 36450
171 90 47160
172 90 38160
173 90 47250
174 89 41218
175 90 61110
176 89 76565
177 90 77220
178 90 35190
179 90 44010
180 90 45000
181 90 72990
182 90 81090
183 90 65970
184 90 37080
185 90 35280
186 90 41400
187 90 41040
188 89 74937
189 90 43380
190 90 74610
191 90 32670
192 90 41850
193 90 44010
194 90 43560
195 90 36630
196 90 54270
197 90 86400
198 90 48690
199 90 45990
200 89 70998
201 90 51480
202 90 47250
****************************************

-----
Sat Jan 14 05:05:55 2012
Remove nodes that look like sequencing errors. Clip tips first
Thesh is 1

Program received signal SIGFPE, Arithmetic exception.
0x000000000043331c in get_total_depth_of_coverage_across_colours (ginfo=0x7fffffff0b20, genome_length=0) at src/cortex_var/core/graph_info.c:110
110 if (total_seq/genome_length<1)
(gdb) bt
#0 0x000000000043331c in get_total_depth_of_coverage_across_colours (ginfo=0x7fffffff0b20, genome_length=0) at src/cortex_var/core/graph_info.c:110
#1 0x000000000041e7f6 in prune_supernode_if_it_looks_like_is_induced_by_singlebase_errors (node=0x2aaaab117010) at src/cortex_var/core/dB_graph_population.c:3888
#2 0x000000000040e451 in hash_table_traverse_returning_sum (f=0x7ffffffef374, hash_table=0x64d090) at src/hash_table/open_hash/hash_table.c:221
#3 0x000000000041e76e in db_graph_remove_supernodes_more_likely_errors_than_sampling (db_graph=0x64d090, ginfo=0x7fffffff0b20, model_info=0x7fffffff0af0,
max_length_allowed_to_prune=10000, sum_of_covgs_in_desired_colours=0x409814 <element_get_covg_union_of_all_covgs>,
get_edge_of_interest=0x409727 <element_get_colour_union_of_all_colours>, apply_reset_to_specified_edges=0x41cc63 <apply_reset_to_specific_edge_in_union_of_all_colours>,
apply_reset_to_specified_edges_2=0x41cca7 <apply_reset_to_all_edges_in_union_of_all_colours>, max_expected_sup=10000, manual_threshold=1)
at src/cortex_var/core/dB_graph_population.c:3910
#4 0x0000000000407506 in main (argc=12, argv=0x7fffffffe0f8) at src/cortex_var/many_colours/cortex_var.c:805
(gdb) quit

help menu typos

Matthias Haimel — Tue, 12 Apr 2011 13:25:58 -0000

The help menu for the command line option has typos and my lazy copy-past approach fails ;)

--ouput_contigs
--ouput_supernodes

report an bug about cortex

ba hengxing — Tue, 05 Apr 2011 05:58:52 -0000

[bah@impala ~]$ ./cortex_con_31 --input cattle --kmer_size 27 --mem_width 100 --mem_height 18 --tip_clip 100 --remove_seq_errors --remove_bubbles --input_format fasta --output_contigs cattle15.fa

Cortex Con

Command: ./cortex_con_31 --input cattle --kmer_size 27 --mem_width 100 --mem_height 18 --tip_clip 100 --remove_seq_errors --remove_bubbles --input_format fasta --output_contigs cattle15.fa
Unit size: 16
Max k: 31

-----
Tue Apr 5 17:55:54 2011

Input file of filenames: cattle
Kmer size: 27 Hash table size (18 bits): 262,144 Hash table bucket size: 100 Total size: 26,214,400

-----
Tue Apr 5 17:55:54 2011

Table created: 262,144
dBGraph:
unique kmers: 0
Capacity: 26,214,400
Occupied: 0.000000%

Reading fasta file 1: cattle_1_A_Solexa_50_1000.fa
Read 1,000,000 kmers
Read 2,000,000 kmers
Read 3,000,000 kmers
Read 4,000,000 kmers

-----
Tue Apr 5 17:56:22 2011

Read of file 1 complete. Total kmers: 4,970,831 Bad reads: 4,301 Seq length: 17,808,600 Total seq length: 17,808,600

Hash:
unique kmers: 4,970,831
Capacity: 26,214,400
Occupied: 18.96%
Collisions:
tries 0: 8,441,282

Reading fasta file 2: cattle_1_B_Solexa_50_1000.fa
Read 5,000,000 kmers
Read 6,000,000 kmers
Read 6,000,000 kmers
Read 6,000,000 kmers
Read 6,000,000 kmers
Read 6,000,000 kmers
Read 6,000,000 kmers
Read 6,000,000 kmers
Read 6,000,000 kmers
Read 6,000,000 kmers
Read 6,000,000 kmers
Read 7,000,000 kmers
Read 8,000,000 kmers

-----
Tue Apr 5 17:56:49 2011

Read of file 2 complete. Total kmers: 8,091,220 Bad reads: 8,525 Seq length: 35,617,200 Total seq length: 53,425,800

Hash:
unique kmers: 8,091,220
Capacity: 26,214,400
Occupied: 30.87%
Collisions:
tries 0: 16,883,943

-----
Tue Apr 5 17:56:49 2011

Clip tips
Cleaning flags...

100% [====================================================================================================]

100% [====================================================================================================]
clip_tip removed nodes 4,355,299
371,318 tips clipped

-----
Tue Apr 5 17:57:10 2011

Removing paths with low coverage...
Cleaning flags...

100% [====================================================================================================]

100% [====================================================================================================]
1,592,579 nodes removed

-----
Tue Apr 5 17:57:35 2011

Removing bubbles
Cleaning flags...

100% [====================================================================================================]

cortex_con_31: src/cortex_con/path.c:1084: path_get_step_at_index: Assertion `index < path->length' failed. ]
Aborted