Penguin: no assembled contigs

[cv-1993]

Hi There,

I tried using PenguiN the other day to do assembly. However, after the assembly finish, there are no any contigs in the output fasta.

Here is the script that I used:
penguin guided_nuclassemble ./trimReads/Read_val_1.fq.gz ./trimReads/Read_val_2.fq.gz --threads 8 --num-iterations aa:5,nucl:10 --use-all-table-starts 1 --min-length 30 --contig-output-mode 0 ./deNovo_penguin/assembly_penguin.fas ./deNovo_penguin/tmp

Here is the final section of the process:

Clustering mode: Greedy
Total time: 0h 0m 0s 2ms

Size of the sequence database: 0
Size of the alignment database: 0
Number of clusters: 0

Writing results 0h 0m 0s 0ms
Time for merging to clust: 0h 0m 0s 7ms
Time for processing: 0h 0m 0s 25ms
mergeclusters /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/nuclassembly /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/clu /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/clu_tmp/14600481272316038322/pre_clust /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/clu_tmp/14600481272316038322/clust --threads 8 --compressed 0 -v 3

Clustering step 1
Clustering step 2
Write merged clustering
Time for merging to clu: 0h 0m 0s 23ms
Time for processing: 0h 0m 0s 73ms
result2repseq /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/nuclassembly /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/clu /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/nuclassembly_rep --threads 8 -v 3

Time for merging to nuclassembly_rep: 0h 0m 0s 27ms
Time for processing: 0h 0m 0s 70ms
createhdb /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/nuclassembly_rep /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/nuclassembly_rep_cycle /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/nuclassembly_rep -v 3

Time for merging to nuclassembly_rep_h: 0h 0m 0s 6ms
Time for processing: 0h 0m 0s 15ms
convert2fasta /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/nuclassembly_rep /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/nuclassembly_rep.fasta -v 3

Start writing file to /mnt/c/SeqAnalysis/20240812_FS10002637_24_BTR99511-3318/deNovo_penguin/tmp/4908128141019153203/nuclassembly_rep.fasta
Time for processing: 0h 0m 0s 14ms

Is there anything that I did wrong?