Error running test data

Shankar Chereddy

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Dec 11, 2021, 7:01:23 AM12/11/21

to EvidentialGene

Dear Dr. Don Gilbert,

I have been trying to use Evigene for my data however I was hoping to first try the test data set to get an idea on how to use the program. I was having an error while running the pipeline on the test data and was hoping to know if you could help me with the issue.

I ran the initial "run_evgsra2genes4v.sh" script with the suggested parameters.

env name=arath16test species=Arabidopsis_thaliana runsteps=start7 ncpu=8 maxmem=16000 datad=`pwd` bash /home/shankar2318/software/evigene_all/sra2genes4v_testdrive/sra2genes_start7test/run_evgsra2genes4v.sh

The "run_s07_tr2aacds.arath16test.sh" file was generated. But I encountered an error after running the script.

BLAST Database error: No alias or index file found for nucleotide database [arath16testnrcd1x_db] in search path [/lustre7/home/shankar2318/software/evigene_all/sra2genes4v_testdrive/sra2genes_start7test::]

#t2ac: FATAL ERR=blastn_cds_ncpu nfail=8, nok=0, fatal cmd= /home/shankar2318/software/ncbi-blast-2.11.0+/bin/blastn -task megablast -ungapped -xdrop_ungap 4 -dust no -perc_identity 98 -evalue 1e-19 -outfmt 7 -db arath16testnrcd1x_db

I am not sure about the error so I was hoping to get some help in resolving it.

Thank you for your time,

Best regards,

Shankar Chereddy

Don Gilbert

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Dec 11, 2021, 3:42:20 PM12/11/21

to Shankar Chereddy, EvidentialGene

It could be a few things, Shakar. Most likely edit "run_evgsra2genes4v.sh" to change path to the applications including blast.

Or it may be the compiled bio-apps I packaged for use are not working properly on your computer.

From sra2genes_testdrive_help.txt:

cd sra2genes4v_testdrive
tar -xf evigene20may20.tar   # expands to evigene/..
tar -zxf evigene_apps_linux_x86_64_19may14.tar.gz     # expands to bio/apps/..
# NOTE: some of these compiled apps_linux_x86_64_19may14 may not work on your linux system, need update
mv evigene bio/apps/         # move to common software folder
cd sra2genes_start7test

** if not done, do this step, using some text editor (vi, emacs, other)

edit run_evgsra2genes4v.sh

edit bioapps path to this bioapps=../bio/apps

The log files will have some further information on what the error is. I should change this file later on so the path edit isn't required.

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Shankar Chereddy

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Dec 13, 2021, 8:22:09 AM12/13/21

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Dear Dr. Don Gilbert

I actually changed the path for all the programs required in the "run_evgsra2genes4v.sh" when I did the run. I think the issue might have been Blast which is version "2.11.0".

I tried using the "bio/apps" provided with the testdrive and it worked alright and I was able to complete the entire procedure i.e. steps 7-12.

Later, I tried it with past versions of Blast and none of them seemed to work. The only Blast version that worked was the latest version "2.12.0".