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singleron-RD / CeleScope

Single Cell Analysis Pipelines
https://www.singleron.bio/
MIT License
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Splitting VDJ fails #274

Closed MarcElvld closed 7 months ago

MarcElvld commented 7 months ago

Describe the bug Splitting the VDJ of a multiplexed sample fails.

celescope tag split_tag --outdir .//LMI_S001_HTO_v2/05.split_tag --sample LMI_S001_HTO_v2 --thread 4 --split_vdj --vdj_dir /mnt/home/marce/Analyses/LMI_S001_TCR_v2 --split_matrix --match_dir /mnt/home2/marce/Analyses/LMI_S001_cDNA_v2 --umi_tag_file .//LMI_S001_HTO_v2/03.count_tag/LMI_S001_HTO_v2_umi_tag.tsv

Splitting the expression matrix works fine (when --split_vdj --vdj_dir /mnt/home/marce/Analyses/LMI_S001_TCR_v2 is removed from the line)

Splitting VDJ gives an error: Traceback (most recent call last): File "/home/marce/anaconda3/envs/celescope/bin/celescope", line 8, in sys.exit(main()) File "/home/marce/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/celescope.py", line 54, in main args.func(args) File "/home/marce/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/tag/split_tag.py", line 246, in split_tag with Split_tag(args) as runner: File "/home/marce/anaconda3/envs/celescope/lib/python3.9/site-packages/celescope/tag/split_tag.py", line 98, in init self.cell_confident_vdj = glob.glob(f'{args.vdj_dir}/count_vdj/cell_confident.tsv*')[0] IndexError: list index out of range

Celescope version 2.0.6

Chenjunjie1996 commented 7 months ago

Can you check if the cell confident vdj file exists?

/mnt/home/marce/Analyses/LMI_S001_TCR_v2/*count_vdj/*cell_confident.tsv
MarcElvld commented 7 months ago

The file exists. I added it to the mail.

From: Chenjunjie1996 @.> Date: Wednesday, 28 February 2024 at 11:18 To: singleron-RD/CeleScope @.> Cc: Eleveld, Marc @.>, Author @.> Subject: Re: [singleron-RD/CeleScope] Splitting VDJ fails (Issue #274) U ontvangt niet vaak e-mail van @.*** Meer informatie over waarom dit belangrijk ishttps://aka.ms/LearnAboutSenderIdentification

Can you check if the cell confident vdj file exists?

/mnt/home/marce/Analyses/LMI_S001_TCR_v2/count_vdj/cell_confident.tsv

— Reply to this email directly, view it on GitHubhttps://github.com/singleron-RD/CeleScope/issues/274#issuecomment-1968663368, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AZ2DE4XYYSAE6QE7N634JT3YV376HAVCNFSM6AAAAABD5WTGGGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNRYGY3DGMZWHA. You are receiving this because you authored the thread.Message ID: @.***>

MarcElvld commented 7 months ago

Ok, retried by making new shell files and now it works again. Looks like the was a mistake in a folder reference. It works again. Thank you for your help.