Encountering Error while Running 'make vcf' in Biostar Handbook

Question

[Tully]

Hello everyone, I'm a beginner currently studying the Biostar Handbook.

After completing the system installation and bioinformatics environment setup, I attempted to [Run a realistic analysis][1].

However, I encountered the following error after running the make vcf command and am unsure how to resolve it. I hope to receive assistance from the community.

[Tully]

System Information: Ubuntu 22.04 (WSL2)

Shell: zsh

Installation Verification: Yes, doctor.py OK

[Tully]

# Obtain the makefile
curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile

# Run the makefile
make vcf

Error message:

.........
00:00:00 Caracterizing exons by splicing (stage 1) :

00:00:00 Caracterizing exons by splicing (stage 2) :
        00:00:00 done.
00:00:00 [Optional] Rare amino acid annotations
WARNING_FILE_NOT_FOUND: Rare Amino Acid analysis: Cannot read protein sequence file '/home/tully/work/redo/1_PMID25214632_EbolaVirus/./data/AF086833/protein.fa', nothing done.
00:00:00 CDS check: GenBank file format, skipping

00:00:00 Protein check file: '/home/tully/work/redo/1_PMID25214632_EbolaVirus/./data/AF086833/genes.gbk'

00:00:00 Checking database using protein sequences
00:00:00 Comparing Proteins...
        Labels:
                '+' : OK
                '.' : Missing
                '*' : Error
        ++++++++*00:00:00

        Protein check:  AF086833        OK: 8   Not found: 0    Errors: 1       Error percentage: 11.11111111111111%
00:00:00        Protein sequences comparison failed!
ERROR: Database check failed.
00:00:00 Logging
00:00:01 Checking for updates...
00:00:02 Done.
make: *** [Makefile:154: data/AF086833/snpEffectPredictor.bin] Error 255

[Tully]

Istvan Albert ,I am deeply immersed in the fog and request the help ,please

Answer 1

[Istvan Albert]

this appears to be a problem that comes from snpEff, all the other steps completed correctly

I'll have to check what is up with snpEff, but sometimes that happens, GenBank formats are notoriously fickle

study the subsequent chapters and see the chapters in the Biostar Workflows for more details

[Istvan Albert]

I would also say that the example I gave is just for fun to show what someone new to the field could get done right away after installing the software.

For additional complete data analysis examples, see the makefiles in the Biostar Workflows books.

[Tully]

Thank you for your guidance, very useful! Thank you!