ERROR: Could not find .aligned.fa/.vcf in samplename make: *** [Makefile:108: core.aln] Error 2

[sharbie88]

I've been running Nullarbor for a while and working fine. Left it for a couple of weeks and now not working - maybe something needs updating?, although I've run conda update -n nullarbor_env --all

make preview appeared to work ok from the index.html: file:///home/sharb/Documents/Nullarbor/8_ST22_testmakefile/report/index.html

when I ran the full program, however, no report file was created, all the .gff files remained and I got the .aligned.fa/.vcf and core.aln error 2 - see attached log file and makefile

nullarbor.log Makefile.txt

Can you help please?

[andersgs]

Hi @sharbie88. From the logs it looks like you need to downgrade samtools from version 1.10 to 1.9. That is a known bug that is being fixed.

You can try conda install -c bioconda samtools=1.9

Then, remove all the .gff files:

rm *.gff

Then run make.

Good luck.

[andersgs]

It seems there is also some confusion around kraken. It is running kraken 1 but it is calling a classify executable from Kraken 2! @tseemann this is truly bizarre!

/home/sharb/miniconda3/envs/nullarbor_env/libexec/classify: invalid option -- 'd'
Usage: classify [options] <fasta/fastq file(s)>

Options: (*mandatory)
* -H filename      Kraken 2 index filename
* -t filename      Kraken 2 taxonomy filename
* -o filename      Kraken 2 options filename ```

@sharbie88 can you paste the output of `conda list` while in the active env? Thank you. 

[sharbie88]

@andersgs here's the 'conda list' from inside nullarbor_env after downgrading samtools.

condalist.txt

The small batch I was trying to run has now worked to product a report folder and .log has no errors. Thanks.

However, I am getting this message when I open a new terminal window and I've discovered my conda is in miniconda3, not anaconda3 as other users' seems to be - don't know if this impacts your discovery above re kraken. (And if I follow the instructions here, https://github.com/conda/conda/issues/9505#, I get conda: command not found.)

Traceback (most recent call last):
  File "<stdin>", line 3, in <module>
ImportError: No module named conda

[tseemann]

ead1="PC0051a-S0051/R1.fq.gz" read2="PC0051a-S0051/R2.fq.gz" outfile="PC0051a-S0051/kraken.tab" cpus=4 opts="" /home/sharb/miniconda3/envs/nullarbor_env/bin/../plugins/taxoner/kraken.sh
/home/sharb/miniconda3/envs/nullarbor_env/libexec/classify: invalid option -- 'd'
Usage: classify [options] <fasta/fastq file(s)>

This is an old problem with conda recipes for kraken1 and kraken2 clashing and breaking each other.

The only way people have resolved it is to install the latest miniconda3 from scratch... It's not a nullarbor issue specifically.

[sharbie88]

@tseemann 'from scratch' - do you mean rm miniconda3 and then reinstall the latest miniconda3 from the website? and all of the dependencies, e.g. Nullarbor, will still be ok?

[tseemann]

Yes. Assuming it's in the standard place:

rm -fr ~/miniconda3
rm -fr ~/.conda
rm -f ~/.condarc

Then follow all these exactly: https://bioconda.github.io/user/install.html

Then

conda create -n nullarbor_env nullarbor
conda activate nullarbor_env
nullarbor.pl --check