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

[sharbie88]

Hi, I keep getting the above error:
ERROR: Could not find .aligned.fa/.vcf in PC0086b-S0390 make: *** [Makefile:108: core.aln] Error 2 make: *** Waiting for unfinished jobs.... make: Leaving directory '/home/.....

My make preview file was ok. I'm using the same ref.fasta file I've been using for ages. The file named above 'PC00....' changes when I retry to make again.

I've also tried the following:
rm -fv */resistome.tab rm -fv */virulome.tab rm -f *.gff rm -fr roary find . -type f -size 0 -delete -print make

I've attached the makefile and log file.
Thank you.
nullarborlog.txt
Makefile.txt

Tried to use another input file, all else the same, and got the following makefile and log file for make preview.
nullarborlog2.txt

Makefile2.txt

[tseemann]

grep -i 'error|warn' nullarborlog.txt | less`

These are unusual:

WARNING: --max_kmer_count 10 to 14 because of high coverage for genome size 3532748
WARNING: --min_count changed from 2 to 3 because of high coverage for genome size 13039046
WARNING: --max_kmer_count 10 to 17 because of high coverage for genome size 13039046
WARNING: --min_count changed from 2 to 4 because of high coverage for genome size 2492743
WARNING: --max_kmer_count 10 to 22 because of high coverage for genome size 2492743
WARNING: --min_count changed from 2 to 3 because of high coverage for genome size 3747682

1. They seem to suggest your data has impure isolates, and also too much data maybe?

What variation in depth are you seeing? Hopefully < 200

grep Depth */yield.tab | sed 's/x$//' | sort -k2nr

2. What does the tree produced by make preview look like?

[sharbie88]

This batch is just a subset of 401 isolates I’ve put through earlier. So they should be ok.

I've attached the preview.nwk file (in .txt form) - looks ok to me. The coverage in my QC file is >200 for about 20 isolates.
Can you please broaden your grep line instructions?
previewnwk.txt

I just noticed some similarities to #261. I just tried to use snippy separately and got the same message that I have v 1.10 and should upgrade to 1.7. My snippy is v 4.4.3-0 also. However, I reinstalled my nullarbor_env mid december 2019. Are the 2 problems related?

On this point, when I forced an upgrade to samtools v1.7, I got:

environment location: /home/sharb/miniconda3

added / updated specs:
- samtools=1.7

The following packages will be downloaded:

package                    |            build
---------------------------|-----------------
samtools-1.7               |                1         1.0 MB  bioconda
------------------------------------------------------------
                                       Total:         1.0 MB

The following NEW packages will be INSTALLED:

libgcc conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2

The following packages will be REMOVED:

nullarbor-2.0.20191013-1
shovill-1.0.9-0
snippy-4.4.3-0

The following packages will be DOWNGRADED:

samtools 1.10-h9402c20_2 --> 1.7-1

Was this going to remove my nullarbor, shovill and snippy? or just the snippy1.10 in them and replace with snippy1.7