adamd3 / bactseq Goto Github PK

I am wondering if i can use the pipeline to detect bacterial infections in human illumina paired ended fastq files.
I assume i would use already host removed files and use these against ncbi bacterial genomes?

Thanks

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!

Dear Adam

I'm hoping you can perhaps help with the following error. I ran the pipeline without setting a contrast file previously. Worked perfectly. Now I'm trying to repeat with the contrast file. It's a simple two condition experiment. I have attached the command.err file for the step as well as the sample sheet, contrasts file and my stdout file

Running on a HPC with Ubuntu 20 installed.
The command I ran was within a slurm launcher. I've had to pull the github repository in a rather unusual way. The command after exporting singularity temp paths is:

nextflow run https://github.com/adamd3/BactSeq -latest -r main --paired --data_dir /scratch/sysuser/jonathan/ops/MRC/DE_RNA --sample_file /scratch/sysuser/jonathan/ops/MRC/DE_RNA/samplesheet.txt --ref_genome /scratch/sysuser/jonathan/ops/MRC/DE_RNA/GCF_000195955.2_ASM19595v2_genomic.fna --ref_ann /scratch/sysuser/jonathan/ops/MRC/DE_RNA/genomic.gff --cont_tabl contrasts.tsv -profile singularity

I recognize the group_INF_vs_EFF as a DESEQ2 parameter but I don't know what causes the error or what mistake I may have made.

Kind regards,
Jonathan
stdout.txt
command.txt
samplesheet.txt
contrasts.txt