cortex

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code in git colne ~~ cd cortex bash install.sh libs/seq_file/seq_file.h:17:10: fatal error: zlib.h: No such file or directory #include ^~~~~~~~ compilation terminated. make: *** [Makefile:29: src/alignment_cmdline.o] Error 1 make: Leaving...

kdyoung100

Currently we bundle a 2012-version of [seq_file](https://github.com/noporpoise/seq_file) and also an old version of `htslib` (im not sure which version however). If we bump up `seq_file` to latest version (I see...

bricoletc

System-wide htslib can fail linkage

1

When running `make NUM_COLS=1 cortex_var` I got the following: ``` mkdir -p bin; gcc -Iinclude/cortex_var/core -Iinclude/basic -Iinclude/hash_table -Iinclude/cortex_var/many_colours -Iinclude/basic/event_encoding/base_encoding -L/usr/local/lib -Ilibs/htslib/htslib -Ilibs/seq_file -Ilibs/string_buffer -Llibs/htslib/htslib -Llibs/seq_file -Llibs/string_buffer -O3 -m64 -Wall -DVERSION_STR='""'...

bricoletc

This is because of this line https://github.com/iqbal-lab/cortex/blob/6d8e2f9f1984651c253bdd9d748acf6efa54c165/scripts/calling/run_calls.pl#L1511 one solution might be to simply print VCF header here

iqbal-lab

Just got this error message running run_calls in the clockwork singularity container. ``` Possible precedence issue with control flow operator at /bioinf-tools/cortex/scripts/analyse_variants/bioinf-perl/lib/RefGenome.pm line 287. Possible precedence issue with control flow...

iqbal-lab

make MAXK=31 NUM_COLS=1 cortex_var

5

As instructed in #0 of the README in example, I used the commands make clean and make MAXK=31 NUM_COLS=1 cortex_var. I received the error: collect2: ld returned 1 exit status...

EmilyWesel

In function `print_usage': nw_cmdline.c undefined reference to `string_buff_strlen'

5

This is `bash install.sh` result now: ``` for file in ; do rm -r $file; done for file in ; do rm $file; done gcc -o needleman_wunsch -O3 -DCOMPILE_TIME='"Thu Mar...

tseemann

Running the run_calls wrapper with different numbers of samples produces different SNPs

1

Hi Zam, I have three bacterial samples that I want to use to look for SNPs against an assembled reference. To do this, I have tried two methods using the...

bioinfo11

When running the indep pipeline to create a massive vcf of variants in a groups of samples, get errors from bcf merge step. Here are some examples of pairs of...

rmcolq

run_indep_wkflow_with_gnu_par hangs after parallel build step before combine

7

So I think the problem is that the list_all_raw_vcfs file ends up empty. Because it exists, no error is thrown by combine_vcfs.pl and instead it hangs. I believe that the...

rmcolq