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TrinityCTAT / CTAT-SPLICING

detection of cancer splicing aberrations
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stat: path should be string, bytes, os.PathLike or integer, not NoneType #9

Open Dhwani-2410 opened 3 months ago

Dhwani-2410 commented 3 months ago

/DATA1/Softwares/CTAT-SPLICING.v0.0.3.FULL/CTAT-SPLICING.v0.0.3/STAR_to_cancer_introns.py --SJ_tab_file ./0710-0496_10_R1_RNA/0710-0496_10_R1_RNA_star_SJ.out.tab --chimJ_file ./0710-0496_10_R1_RNA/0710-0496_10_R1_RNA_star_Chimeric.out.junction --vis --bam_file ./0710-0496_10_R1_RNA/0710-0496_10_R1_RNA_star_Aligned.sortedByCoord.out.bam --output_prefix ./0710-0496_10_R1_RNA/0710-0496_10_R1_RNA --sample_name 0710-0496_10_R1_RNA

Traceback (most recent call last): File "/DATA1/Softwares/CTAT-SPLICING.v0.0.3.FULL/CTAT-SPLICING.v0.0.3/STAR_to_cancer_introns.py", line 418, in main() File "/DATA1/Softwares/CTAT-SPLICING.v0.0.3.FULL/CTAT-SPLICING.v0.0.3/STAR_to_cancer_introns.py", line 103, in main if not os.path.exists(ctat_genome_lib): File "/home/dhwani/miniconda3/lib/python3.9/genericpath.py", line 19, in exists os.stat(path) TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType

brianjohnhaas commented 3 months ago

Hi,

The ctat genome lib needs to be set up for ctat splicing and the CTAT_GENOME_LIB env var needs to be set or the path to it needs to be given as a parameter.

hope this helps

On Mon, Jun 3, 2024 at 6:29 AM Dhwani-2410 @.***> wrote:

/DATA1/Softwares/CTAT-SPLICING.v0.0.3.FULL/CTAT-SPLICING.v0.0.3/STAR_to_cancer_introns.py --SJ_tab_file ./0710-0496_10_R1_RNA/0710-0496_10_R1_RNA_star_SJ.out.tab --chimJ_file ./0710-0496_10_R1_RNA/0710-0496_10_R1_RNA_star_Chimeric.out.junction --vis --bam_file ./0710-0496_10_R1_RNA/0710-0496_10_R1_RNA_star_Aligned.sortedByCoord.out.bam --output_prefix ./0710-0496_10_R1_RNA/0710-0496_10_R1_RNA --sample_name 0710-0496_10_R1_RNA

Traceback (most recent call last): File "/DATA1/Softwares/CTAT-SPLICING.v0.0.3.FULL/CTAT-SPLICING.v0.0.3/STAR_to_cancer_introns.py", line 418, in main() File "/DATA1/Softwares/CTAT-SPLICING.v0.0.3.FULL/CTAT-SPLICING.v0.0.3/STAR_to_cancer_introns.py", line 103, in main if not os.path.exists(ctat_genome_lib): File "/home/dhwani/miniconda3/lib/python3.9/genericpath.py", line 19, in exists os.stat(path) TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas