search

ConesaLab / SQANTI3

Tool for the Quality Control of Long-Read Defined Transcriptomes
GNU General Public License v3.0
198 stars 49 forks source link

sqanti3_qc.py command not found #268

Closed Upendra19993 closed 7 months ago

Upendra19993 commented 8 months ago

Is there an existing issue for this?

Have you loaded the SQANTI3.env conda environment?

Problem description

I tried to run the sqanti3 quality control step. (sqanti3 installation was done using conda). But when I put the command and tried to run, I got an error saying sqanti3_qc.py command not found.

Kindly request your help to resolve this issue.

Many thanks, Upendra.

Code sample

sqanti3_qc.py --fasta clustering_clustered_hq_lq_279057_CD-Hit0.99.fasta Neelam_transcript-mRNA_gtfinfo_NIPB01022023QU_AGAT_FromBioBamMarta.gtf Neelam-Genome_Inv-corrected_Chr_QL_NIPB260822.fasta -o Neelum_HPC4 -d Neelum_HPC4 --short_reads RNA_seq_Neelum.fofn --cpus 24 --report pdf --force_id_ignore

Error

(SQANTI3.env) [uqwwijes@bun016 SQANTI3-5.2]$ sqanti3_qc.py --fasta clustering_clustered_hq_lq_279057_CD-Hit0.99.fasta Neelam_transcript-mRNA_gtfinfo_NIPB01022023QU_AGAT_FromBioBamMarta.gtf Neelam-Genome_Inv-corrected_Chr_QL_NIPB260822.fasta -o Neelum_HPC4 -d Neelum_HPC4 --short_reads RNA_seq_Neelum.fofn --cpus 24 --report pdf --force_id_ignore bash: sqanti3_qc.py: command not found

Anything else?

No response

carolinamonzo commented 7 months ago

Hi @Upendra19993 This is not a SQANTI issue. You didn't call for the interpreter before putting the name of the script. Please look at the errors you receive and try to solve them yourself or call a supervisor and ask them for help before reporting a bug.