tseemann/nullarbor

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

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#264 opened on Apr 6, 2020

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Description

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

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Research direction
Trace the alignment step in the Makefile to understand which rule generates .aligned.fa/.vcf, and examine the logs to see if the alignment command was executed and if it succeeded.
Tech stack
perl
Domain
data
Issue type
Bug
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
GitUnix command lineMake
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
75