failing to perform DESeq2 on the provided example

[YiJessePi]

Hi!
Thank you for developing bactseq!
I'm having error while trying to run deseq2 on the test_data.
The command:
nextflow run /tools/BactSeq/BactSeq --data_dir /tools/BactSeq/BactSeq/test_data/ --ref_genome /tools/BactSeq/BactSeq/test_data/Mabs.fasta --ref_ann /tools/BactSeq/BactSeq/test_data/Mabs.gff3 --sample_file /tools/BactSeq/BactSeq/test_data/sample_sheet_1.tsv -profile singularity --outdir ./test_singularity4 --cont_tabl /tools/BactSeq/BactSeq/test_data/contratst.txt

The contrasts file is attached.
contratst.txt

error log:
executor > local (13)
[64/bd83ac] process > MAKE_META_FILE (sample_sheet_1.tsv) [100%] 1 of 1 ✔
[6d/de3a9d] process > TRIMGALORE (3C3) [100%] 4 of 4 ✔
[1f/6294e1] process > MAKE_BWA_INDEX (Mabs.fasta) [100%] 1 of 1 ✔
[ca/258ef2] process > BWA_ALIGN (3D3) [100%] 4 of 4 ✔
[12/77d6fc] process > COUNT_READS (Mabs.gff3) [100%] 1 of 1 ✔
[03/53307a] process > NORMALISE_COUNTS (gene_counts_pc.tsv) [ 0%] 0 of 1
[- ] process > PCA_SAMPLES -
[b0/02a06a] process > DIFF_EXPRESSION (gene_counts_pc.tsv) [ 0%] 0 of 1
ERROR ~ Error executing process > 'DIFF_EXPRESSION (gene_counts_pc.tsv)'

Caused by:
Process DIFF_EXPRESSION (gene_counts_pc.tsv) terminated with an error exit status (1)

Command executed:

[ ! -f contrast_table.tsv ] && ln -s contratst.txt contrast_table.tsv
diffexpr.R -p 0.05 -l 1 -o ./

Command exit status:
1

Command output:
(empty)

Thank you for any kind of help!

[adamd3]

Hi there!

It looks like your contrast table is space-delimited instead of tab-delimited. Can you try again inserting a tab between the columns in contrasts.txt?

Also, if this still throws an error, could you take a look at the working directory when the command exits and share the contents? It should give the working directory after the exit message.