adamd3
commented
8 months ago 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.
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.txtThe 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!