NOVOPlasty ran successfully but did not generate a contig

[laribritto]

Hello, how are you? I'm currently running NOVOPlasty for two fish species, and while there haven't been any errors reported, I've encountered an issue. The Circularized_assembly_1_zfish.fasta file appears to be empty, lacking any contigs. Similarly, the contigs.txt file is empty as well. Strangely, the log file doesn't indicate any errors. Any insights on what might be causing this?

Extended log file:

Project:

Project name = zfish
Type = mito
Genome range =
K-mer = 33
Max memory =
Extended log = 1
Save assembled reads =
Seed Input = /data/home/larissa.brito/ciclideos/GU737126.1.fasta
Extend seed directly =
Reference sequence =
Variance detection =
Chloroplast sequence =

Dataset 1:

Read Length = 151
Insert size = 300
Platform = illumina
Single/Paired = PE
Combined reads =
Forward reads = /data/home/larissa.brito/ciclideos/ERR10768239_1.fastq
Reverse reads = /data/home/larissa.brito/ciclideos/ERR10768239_2.fastq
Store Hash =

Heteroplasmy:

MAF =
HP exclude list =
PCR-free =

Optional:

Insert size auto = yes
Use Quality Scores =
Output path =

GGCGTCACGAGGGCTTAACTGTCTCCTTTTTCCCGTCAATGAAATTGATCCCCCCGTGCAGAAGCGGGGATAACCCCATAAGACGAGAAGACCCTATGGAGCTTCAGGCTCCTGAGCAGACTATGTTAAACAACCTAAAATAAAAGACCAG
GGCGTCACGAGGGCTTAACTGTCTCCTTTTTCCAGTCAATGAAATTGATCCCCCCGTGCAGAAGCGGGGATAACCCCATAAGACGAGAAGACCCTATGGAGCTTCAGGCTCCTGAGCAGACTATGTTAAACAACCTAAAATAAAAGACCAT CORRECTED READ

Initial read retrieved successfully1: GGCGTCACGAGGGCTTAACTGTCTCCTTTTTCCAGTCAATGAAATTGATCCCCCCGTGCAGAAGCGGGGATAACCCCATAAGACGAGAAGACCCTATGGAGCTTCAGGCTCCTGAGCAGACTATGTTA>

1

501876532 SEED_exists

151 READ_LENGTH
300 INSERT_SIZE

151 POSITION
0 POSITION_BACK
LAST_CHANCE
GACTATGTTAAACAACCTAAAATAAAAGACCAT READ_END
GGCGTCACGAGGGCTTAACTGTCTCCTTTTTCC READ_START
1588 MATCH_ARRAY_READ
0 MATCH_ARRAY_BACK_READ
3 TIME1

1435 READ_COUNT
0 READ_EX
1425 EXTENSIONS
1425 AVERAGE_COVERAGE
AACCCATTAGACCCTGCCCTACATGCCTTTGGTTGGGGCGACCACGGGGAAAA BEST_EXTENSION

stop NOBACK
yes LASTCHANCE
1 COUNTSEED

-----------------Assembly 1 finished successfully: The genome has been circularized-----------------

501876532

[ndierckx]

Hi,
You should fill in the genome range...

[laribritto]

The config.txt file contains this information ,but the log file does not

[laribritto]

I tried with another seed, and still the fasta file came up empty

[laribritto]

I've changed the parameters several times, as well as the seed, and still no results are coming out.

[ndierckx]

Can you try to redownload the config file? How does your log file looks like, are all parameters correctly? If not redownload the config file, sometimes it gets corrupted with some users, not sure how though