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feature counts invalid parameter

Hi, my script for feature counts is:

featureCounts -a ncbi_dataset/data/GCA_002738505.1/genomic.gff \
-o Feature_counts.txt \
-p -s 2 -T 10 \
*_sorted.bam

This worked before on another set of data. However, I am now getting: ERROR: invalid parameter: '*_sorted.bam'

Can someone please help me? My files are like: JRM1_RNAseq_MS_2_TTATAACC_Arabidopsis_I1187_L1_sorted.bam

invalid feature counts parameter
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updated by Ram Ram • written by smithkthedale • smithkthedale

Could you run the following just to ensure that featureCounts is finding the bam file at the right location? Let us know how it goes.

featureCounts -a ncbi_dataset/data/GCA_002738505.1/genomic.gff \
-o Feature_counts.txt \
-p -s 2 -T 10 \
 JRM1_RNAseq_MS_2_TTATAACC_Arabidopsis_I1187_L1_sorted.bam
• 0 views • link
written by mark.ziemann mark.ziemann

I have the same error, is this a software installation issue?

docker run -v /input/:/input -v  6.amazonaws.com/bioinfo-notebooks /root/miniconda/condabin/conda run -n bioinfo-notebook featureCounts -s 0 -p -O -T 6 -a /iutput/Reference.gtf -o /input/output.txt /input/sortedByCoord.out.bam
ERROR: invalid parameter: '/input/sortedByCoord.out.bam'
ERROR conda.cli.main_run:execute(49): `conda run featureCounts -s 0 -p -O -T 6 -a /output/Reference.gtf -o /input/output.txt /input/sortedByCoord.out.bam` failed. (See above for error)
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updated by Ram Ram • written by Ermin • Ermin

Do not add answers unless you're answering the top level question. Use Add Comment or Add Reply instead. I'm moving your post to a comment this time, but please be more careful next time.

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written by Ram Ram

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